1
|
Zhang K, Liu J, Jiang Y, Sun S, Wang R, Sun J, Ma C, Chen Y, Wang W, Hou X, Zhu T, Zhang G, Che Q, Keyzers RA, Liu M, Li D. Sorbremnoids A and B: NLRP3 Inflammasome Inhibitors Discovered from Spatially Restricted Crosstalk of Biosynthetic Pathways. J Am Chem Soc 2024. [PMID: 38888159 DOI: 10.1021/jacs.4c06538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Crosstalk-oriented chemical evolution of natural products (NPs) is an efficacious strategy for generating novel skeletons through coupling reactions between NP fragments. In this study, two NOD-like receptor protein 3 (NLRP3) inflammasome inhibitors, sorbremnoids A and B (1 and 2), with unprecedented chemical architectures were identified from a fungus Penicillium citrinum. Compounds 1 and 2 exemplify rare instances of hybrid NPs formed via a major facilitator superfamily (MFS)-like enzyme by coupling reactive intermediates from two separate biosynthetic gene clusters (BGCs), pcisor and pci56. Both sorbremnoids A and B are NLRP3 inflammasome inhibitors. Sorbremnoid A demonstrated strong inhibition of IL-1β by directly binding to the NLRP3 protein, inhibiting the assembly and activation of the NLRP3 inflammasome in vitro, with potential application in diabetic refractory wound healing through the suppression of excessive inflammatory responses. This research will inspire the development of anti-NLRP3 inflammasome agents as lead treatments and enhance knowledge pertaining to NPs derived from biosynthetic crosstalk.
Collapse
Affiliation(s)
- Kaijin Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Junyu Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuqi Jiang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Simin Sun
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Rongrong Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Jingxian Sun
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yinghan Chen
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Wenxue Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Xuewen Hou
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Robert A Keyzers
- School of Chemical and Physical Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Ming Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| |
Collapse
|
2
|
Pahl A, Liu J, Patil S, Rezaei Adariani S, Schölermann B, Warmers J, Bonowski J, Koska S, Akbulut Y, Seitz C, Sievers S, Ziegler S, Waldmann H. Illuminating Dark Chemical Matter Using the Cell Painting Assay. J Med Chem 2024; 67:8862-8876. [PMID: 38687818 PMCID: PMC11181314 DOI: 10.1021/acs.jmedchem.4c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Screening for small-molecule modulators of disease-relevant targets and phenotypes is the first step on the way to new drugs. Large compound libraries have been synthesized by academia and, particularly, pharmaceutical companies to meet the need for novel chemical entities that are as diverse as possible. Screening of these compound libraries revealed a portion of small molecules that is inactive in more than 100 different assays and was therefore termed "dark chemical matter" (DCM). Deorphanization of DCM promises to yield very selective compounds as they are expected to have less off-target effects. We employed morphological profiling using the Cell Painting assay to detect bioactive DCM. Within the DCM collection, we identified bioactive compounds and confirmed several modulators of microtubules, DNA synthesis, and pyrimidine biosynthesis. Profiling approaches are, therefore, powerful tools to probe compound collections for bioactivity in an unbiased manner and are particularly suitable for deorphanization of DCM.
Collapse
Affiliation(s)
- Axel Pahl
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jie Liu
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sohan Patil
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Soheila Rezaei Adariani
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Beate Schölermann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jens Warmers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Jana Bonowski
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sandra Koska
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Yasemin Akbulut
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Carina Seitz
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Slava Ziegler
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| |
Collapse
|
3
|
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] [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.
Collapse
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.
| |
Collapse
|
4
|
Bag S, Liu J, Patil S, Bonowski J, Koska S, Schölermann B, Zhang R, Wang L, Pahl A, Sievers S, Brieger L, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. A divergent intermediate strategy yields biologically diverse pseudo-natural products. Nat Chem 2024; 16:945-958. [PMID: 38365941 PMCID: PMC11164679 DOI: 10.1038/s41557-024-01458-4] [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: 11/22/2022] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The efficient exploration of biologically relevant chemical space is essential for the discovery of bioactive compounds. A molecular design principle that possesses both biological relevance and structural diversity may more efficiently lead to compound collections that are enriched in diverse bioactivities. Here the diverse pseudo-natural product (PNP) strategy, which combines the biological relevance of the PNP concept with synthetic diversification strategies from diversity-oriented synthesis, is reported. A diverse PNP collection was synthesized from a common divergent intermediate through developed indole dearomatization methodologies to afford three-dimensional molecular frameworks that could be further diversified via intramolecular coupling and/or carbon monoxide insertion. In total, 154 PNPs were synthesized representing eight different classes. Cheminformatic analyses showed that the PNPs are structurally diverse between classes. Biological investigations revealed the extent of diverse bioactivity enrichment of the collection in which four inhibitors of Hedgehog signalling, DNA synthesis, de novo pyrimidine biosynthesis and tubulin polymerization were identified from four different PNP classes.
Collapse
Affiliation(s)
- Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sohan Patil
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jana Bonowski
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Lukas Brieger
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
| |
Collapse
|
5
|
Wang L, Yilmaz F, Yildirim O, Schölermann B, Bag S, Greiner L, Pahl A, Sievers S, Scheel R, Strohmann C, Squire C, Foley DJ, Ziegler S, Grigalunas M, Waldmann H. Discovery of a Novel Pseudo-Natural Product Aurora Kinase Inhibitor Chemotype through Morphological Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309202. [PMID: 38569218 DOI: 10.1002/advs.202309202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Indexed: 04/05/2024]
Abstract
The pseudo-natural product (pseudo-NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments are combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three-dimensional pseudo-NPs. Target hypothesis generation by morphological profiling via the cell painting assay guides the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly 3D structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicate that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.
Collapse
Affiliation(s)
- Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Furkan Yilmaz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
| | - Okan Yildirim
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Luca Greiner
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), 44227, Dortmund, Germany
| | - Rebecca Scheel
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Inorganic Chemistry, TU Dortmund University, 44227, Dortmund, Germany
| | - Christopher Squire
- School of Biological Sciences, University of Auckland, 1142, Auckland, New Zealand
| | - Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury, 8041, Christchurch, New Zealand
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227, Dortmund, Germany
| |
Collapse
|
6
|
Cheng S, Dong C, Ma Y, Xu X, Zhao Y. Skeletal Transformations of Terpenoid Forskolin Employing an Oxidative Rearrangement Strategy. J Org Chem 2024; 89:5741-5745. [PMID: 38568052 DOI: 10.1021/acs.joc.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The skeletal transformations of diterpenoid forskolin were achieved by employing an oxidative rearrangement strategy. A library of 36 forskolin analogues with structural diversity was effectively generated. Computational analysis shows that 12 CTD compounds with unique scaffolds and ring systems were produced during the course of this work.
Collapse
Affiliation(s)
- Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Chenhu Dong
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yujie Ma
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Xiaoyu Xu
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China
| |
Collapse
|
7
|
Das AP, Agarwal SM. Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches. Mol Divers 2024; 28:901-925. [PMID: 36670282 PMCID: PMC9859751 DOI: 10.1007/s11030-022-10590-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Phytocompounds are a well-established source of drug discovery due to their unique chemical and functional diversities. In the area of cancer therapeutics, several phytocompounds have been used till date to design and develop new drugs. One of the desired interests of pharmaceutical companies and researchers globally is that new anti-cancer leads are discovered, for which phytocompounds can be considered a valuable source. Simultaneously, in recent years, the growth of computational approaches like virtual screening (VS), molecular dynamics (MD), pharmacophore modelling, Quantitative structure-activity relationship (QSAR), Absorption Distribution Metabolism Excretion and Toxicity (ADMET), network biology, and machine learning (ML) has gained importance due to their efficiency, reduced time-consuming nature, and cost-effectiveness. Therefore, the present review amalgamates the information on plant-based molecules identified for cancer lead discovery from in silico approaches. The mandate of this review is to discuss studies published in the last 5-6 years that aim to identify the phytomolecules as leads against cancer with the help of traditional computational approaches as well as newer techniques like network pharmacology and ML. This review also lists the databases and webservers available in the public domain for phytocompounds related information that can be harnessed for drug discovery. It is expected that the present review would be useful to pharmacologists, medicinal chemists, molecular biologists, and other researchers involved in the development of natural products (NPs) into clinically effective lead molecules.
Collapse
Affiliation(s)
- Agneesh Pratim Das
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India
| | - Subhash Mohan Agarwal
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India.
| |
Collapse
|
8
|
Shenvi RA. Natural Product Synthesis in the 21st Century: Beyond the Mountain Top. ACS CENTRAL SCIENCE 2024; 10:519-528. [PMID: 38559299 PMCID: PMC10979479 DOI: 10.1021/acscentsci.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
Research into natural products emerged from humanity's curiosity about the nature of matter and its role in the materia medica of diverse civilizations. Plants and fungi, in particular, supplied materials that altered behavior, perception, and well-being profoundly. Many active principles remain well-known today: strychnine, morphine, psilocybin, ephedrine. The potential to circumvent the constraints of natural supply and explore the properties of these materials led to the field of natural product synthesis. This research delivered new molecules with new properties, but also led to fundamental insights into the chemistry of the nonmetal elements H, C, N, O, P, S, Se, and their combinations, i.e., organic chemistry. It also led to a potent culture focused on bigger molecules and races to the finish line, perhaps at the expense of actionable next steps. About 20 years ago, the field began to contract in the United States. Research that focused solely on chemical reaction development, especially catalysis, filled the void. After all, new reactions and mechanistic insight could be immediately implemented by the chemistry community, so it became hard to justify the lengthy procurement of a complex molecule that sat in the freezer unused. This shift coincided with a divestment of natural product portfolios by pharmaceutical companies and an emphasis in academic organic chemistry on applications-driven research, perhaps at the expense of more fundamental science. However, as bioassays and the tools of chemical biology become widespread, synthesis finds a new and powerful ally that allows us to better deliver on the premise of the field. And the hard-won insights of complex synthesis can be better encoded digitally, mined by data science, and applied to new challenges, as chemists perturb and even surpass the properties of complex natural products. The 21st century promises powerful developments, both in fundamental organic chemistry and at the interface of synthesis and biology, if the community of scientists fosters its growth. This essay tries to contextualize natural product synthesis for a broad audience, looks ahead to its transformation in the coming years, and expects the future to be bright.
Collapse
Affiliation(s)
- Ryan A. Shenvi
- Department
of Chemistry, Scripps Research, La Jolla, California 92037, United States
- Graduate
School of Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| |
Collapse
|
9
|
Pahl I, Pahl A, Hauk A, Budde D, Sievers S, Fruth L, Menzel R. Assessing biologic/toxicologic effects of extractables from plastic contact materials for advanced therapy manufacturing using cell painting assay and cytotoxicity screening. Sci Rep 2024; 14:5933. [PMID: 38467674 PMCID: PMC10928227 DOI: 10.1038/s41598-024-55952-3] [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: 10/11/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Plastic components are essential in the pharmaceutical industry, encompassing container closure systems, laboratory handling equipment, and single-use systems. As part of their material qualification process, studies on interactions between plastic contact materials and process solutions or drug products are conducted. The assessment of single-use systems includes their potential impact on patient safety, product quality, and process performance. This is particularly crucial in cell and gene therapy applications since interactions with the plastic contact material may result in an adverse effect on the isolated therapeutic human cells. We utilized the cell painting assay (CPA), a non-targeted method, for profiling the morphological characteristics of U2OS human osteosarcoma cells in contact with chemicals related to plastic contact materials. Specifically, we conducted a comprehensive analysis of 45 common plastic extractables, and two extracts from single-use systems. Results of the CPA are compared with a standard cytotoxicity assay, an osteogenesis differentiation assay, and in silico toxicity predictions. The findings of this feasibility study demonstrate that the device extracts and most of the tested compounds do not evoke any measurable biological changes on the cells (induction ≤ 5%) among the 579 cell features measured at concentrations ≤ 50 µM. CPA can serve as an important assay to reveal unique information not accessible through quantitative structure-activity relationship analysis and vice versa. The results highlight the need for a combination of in vitro and in silico methods in a comprehensive assessment of single-use equipment utilized in advanced therapy medicinal products manufacturing.
Collapse
Affiliation(s)
- Ina Pahl
- Sartorius Stedim Biotech GmbH, August-Spindler-Str. 11, 37079, Göttingen, Germany.
| | - Axel Pahl
- Compound Management and Screening Center, MPI of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Armin Hauk
- Sartorius Stedim Biotech GmbH, August-Spindler-Str. 11, 37079, Göttingen, Germany
| | - Dana Budde
- Sartorius Stedim Biotech GmbH, August-Spindler-Str. 11, 37079, Göttingen, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, MPI of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Lothar Fruth
- Tox Expert GmbH, An der Feldscheide 1, 37083, Göttingen, Germany
| | - Roberto Menzel
- Sartorius Stedim Biotech GmbH, August-Spindler-Str. 11, 37079, Göttingen, Germany
| |
Collapse
|
10
|
Achimba F, Faezov B, Cohen B, Dunbrack R, Holford M. Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides. Mol Cancer Ther 2024; 23:139-147. [PMID: 38015557 PMCID: PMC10831335 DOI: 10.1158/1535-7163.mct-23-0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/04/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
The regulation of cellular processes by ion channels has become central to the study of cancer mechanisms. Designing molecules that can modify ion channels specific to tumor cells is a promising area of targeted drug delivery and therapy. Despite their potential in drug discovery, venom peptides-a group of natural products-have largely remained understudied and under-characterized. In general, venom peptides display high specificity and selectivity for their target ion channels. Therefore, they may represent an effective strategy for selectively targeting the dysregulation of ion channels in tumor cells. This review examines existing venom peptide therapies for different cancer types and focuses on the application of snail venom peptides in hepatocellular carcinoma (HCC), the most common form of primary liver cancer worldwide. We provide insights into the mode of action of venom peptides that have been shown to target tumors. We also explore the benefit of using new computational methods like de novo protein structure prediction to screen venom peptides and identify potential druggable candidates. Finally, we summarize the role of cell culture, animal, and organoid models in developing effective therapies against HCC and highlight the need for creating models that represent the most disproportionately affected ethnicities in HCC.
Collapse
Affiliation(s)
- Favour Achimba
- The PhD Program in Biochemistry, Graduate Center, City University of New York, New York, New York
- Hunter College, City University of New York, New York, New York
| | - Bulat Faezov
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russian Federation
| | - Brandon Cohen
- Hunter College, City University of New York, New York, New York
| | - Roland Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mandë Holford
- The PhD Program in Biochemistry, Graduate Center, City University of New York, New York, New York
- Hunter College, City University of New York, New York, New York
- The PhD Program in Chemistry, Graduate Center of the City University of New York, New York, New York
- The PhD Program in Biology, Graduate Center of the City University of New York, New York, New York
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, New York
- Department of Biochemistry, Weill Cornell Medicine, New York, New York
| |
Collapse
|
11
|
Hou BL, Wu K, Liu R, Liu J, Wang J, Wang C, Liang Y, Wang Z. Natural products fragment-based design and synthesis of a novel pentacyclic ring system as potential MAPK inhibitor. Bioorg Med Chem Lett 2024; 99:129598. [PMID: 38169246 DOI: 10.1016/j.bmcl.2023.129598] [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: 11/08/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
The synthesis of compounds based on fragments derived from natural products (NPs) serves as a source of inspiration for the design of pseudo-natural products (PNPs), to identify bioactive molecules that exhibit similar characteristics to NPs. These novel molecular scaffolds exhibit previously unexplored biological activities as well. This study reports the development and synthesis of a novel pentacyclic ring system, the indole-pyrimidine-quinoline (IPQ) scaffold. The design of this scaffold was based on the structural characteristics of four natural products, namely tryptanthrin, luotonin A, rutaecarpine, and camptothecin. Several successive steps accomplished the effective synthesis of the IPQ scaffold. The constituent components of the pentacycle, containing the indole, quinazolinone, pyrimidone, and quinoline units, possess significant biological significance. Compound 1a demonstrated noteworthy anti-tumor activity efficacy against A549 cell lines among the tested compounds. The compound 1a was observed to elicit cell cycle arrest in both the G2/M and S phases, as well as trigger apoptosis in A549 cells. These effects were attributed to its ability to modulate the activation of mitochondrial-related mitogen-activated protein kinase (MAPK) signaling pathways.
Collapse
Affiliation(s)
- Bao-Long Hou
- Collaborative Innovation Center of Chinese Medicine Resources Industrialization, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, China
| | - Kenan Wu
- Collaborative Innovation Center of Chinese Medicine Resources Industrialization, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, China
| | - Rongrong Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China
| | - Jianli Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China; Xi'an Peihua University, Xi'an 710125, China
| | - Jinrui Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China
| | - Cuiling Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.
| | - Yanni Liang
- Collaborative Innovation Center of Chinese Medicine Resources Industrialization, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, China.
| | - Zheng Wang
- Collaborative Innovation Center of Chinese Medicine Resources Industrialization, State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Shaanxi Innovative Drug Research Center, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi 712046, China.
| |
Collapse
|
12
|
Aoyama H, Davies C, Liu J, Pahl A, Kirchhoff JL, Scheel R, Sievers S, Strohmann C, Grigalunas M, Waldmann H. Collective Synthesis of Sarpagine and Macroline Alkaloid-Inspired Compounds. Chemistry 2024; 30:e202303027. [PMID: 37755456 DOI: 10.1002/chem.202303027] [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: 09/17/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023]
Abstract
Design strategies that can access natural-product-like chemical space in an efficient manner may facilitate the discovery of biologically relevant compounds. We have employed a divergent intermediate strategy to construct an indole alkaloid-inspired compound collection derived from two different molecular design principles, i.e. biology-oriented synthesis and pseudo-natural products. The divergent intermediate was subjected to acid-catalyzed or newly discovered Sn-mediated conditions to selectively promote intramolecular C- or N-acylation, respectively. After further derivatization, a collection totalling 84 compounds representing four classes was obtained. Morphological profiling via the cell painting assay coupled with a subprofile analysis showed that compounds derived from different design principles have different bioactivity profiles. The subprofile analysis suggested that a pseudo-natural product class is enriched in modulators of tubulin, and subsequent assays led to the identification of compounds that suppress in vitro tubulin polymerization and mitotic progression.
Collapse
Affiliation(s)
- Hikaru Aoyama
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Caitlin Davies
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Jan-Lukas Kirchhoff
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry, Chemical Biology, 44227, Dortmund, Germany
| |
Collapse
|
13
|
Cai J, Qiao Y, Chen L, Lu Y, Zheng D. Regulation of the Notch signaling pathway by natural products for cancer therapy. J Nutr Biochem 2024; 123:109483. [PMID: 37848105 DOI: 10.1016/j.jnutbio.2023.109483] [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: 03/16/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023]
Abstract
The Notch signaling pathway is an evolutionarily conserved pathway that modulates normal biological processes involved in cellular differentiation, apoptosis, and stem cell self-renewal in a context-dependent fashion. Attributed to its pleiotropic physiological roles, both overexpression and silencing of the pathway are associated with the emergence, progression, and poorer prognosis in various types of cancer. To decrease disease incidence and promote survival, targeting Notch may have chemopreventive and anti-cancer effects. Natural products with profound historical origins have distinguished themselves from other therapies due to their easy access, high biological compatibility, low toxicity, and reliable effects at specific physiological sites in vivo. This review describes the Notch signaling pathway, particularly its normal activation process, and some main illnesses related to Notch signaling pathway dysregulation. Emphasis is placed on the effects and mechanisms of natural products targeting the Notch signaling pathway in diverse cancer types, including curcumin, ellagic acid (EA), resveratrol, genistein, epigallocatechin-3-gallate (EGCG), quercetin, and xanthohumol and so on. Existing evidence indicates that natural products are feasible solution to fight against cancer by targeting Notch signaling, either alone or in combination with current therapeutic agents.
Collapse
Affiliation(s)
- Jiayi Cai
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Yajie Qiao
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Lingbin Chen
- School of Stomatology, Fujian Medical University, Fuzhou 350122, China
| | - Youguang Lu
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350004, China; Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou 350001, China
| | - Dali Zheng
- Fujian Key Laboratory of Oral Diseases, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, 350004, China.
| |
Collapse
|
14
|
Corkery D, Ursu A, Lucas B, Grigalunas M, Kriegler S, Oliva R, Dec R, Koska S, Pahl A, Sievers S, Ziegler S, Winter R, Wu YW, Waldmann H. Inducin Triggers LC3-Lipidation and ESCRT-Mediated Lysosomal Membrane Repair. Chembiochem 2023; 24:e202300579. [PMID: 37869939 DOI: 10.1002/cbic.202300579] [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: 08/17/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 10/24/2023]
Abstract
Lipidation of the LC3 protein has frequently been employed as a marker of autophagy. However, LC3-lipidation is also triggered by stimuli not related to canonical autophagy. Therefore, characterization of the driving parameters for LC3 lipidation is crucial to understanding the biological roles of LC3. We identified a pseudo-natural product, termed Inducin, that increases LC3 lipidation independently of canonical autophagy, impairs lysosomal function and rapidly recruits Galectin 3 to lysosomes. Inducin treatment promotes Endosomal Sorting Complex Required for Transport (ESCRT)-dependent membrane repair and transcription factor EB (TFEB)-dependent lysosome biogenesis ultimately leading to cell death.
Collapse
Affiliation(s)
- Dale Corkery
- Department of Chemistry, Umeå University, Umeå Centre for Microbial Research, Umeå, SE-90187, Sweden
| | - Andrei Ursu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Belén Lucas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Simon Kriegler
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Rosario Oliva
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
- Present address: Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, Naples, 80126, Italy
| | - Robert Dec
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Yao-Wen Wu
- Department of Chemistry, Umeå University, Umeå Centre for Microbial Research, Umeå, SE-90187, Sweden
| | - 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, Dortmund, 44227, Germany
| |
Collapse
|
15
|
Hassan AH, Bayoumi WA, El-Sayed SM, Phan TN, Oh T, Ham G, Mahmoud K, No JH, Lee YS. Design, Synthesis, and Repurposing of Rosmarinic Acid-β-Amino-α-Ketoamide Hybrids as Antileishmanial Agents. Pharmaceuticals (Basel) 2023; 16:1594. [PMID: 38004459 PMCID: PMC10675174 DOI: 10.3390/ph16111594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
A series of rosmarinic acid-β-amino-α-ketoamide hybrids were synthesized and rationally repurposed towards the identification of new antileishmanial hit compounds. Two hybrids, 2g and 2h, showed promising activity (IC50 values of 9.5 and 8.8 μM against Leishmania donovani promastigotes, respectively). Their activities were comparable to erufosine. In addition, cytotoxicity evaluation employing human THP-1 cells revealed that the two hybrids 2g and 2h possess no cytotoxic effects up to 100 µM, while erufosine possessed cytotoxicity with CC50 value of 19.4 µM. In silico docking provided insights into structure-activity relationship emphasizing the importance of the aliphatic chain at the α-carbon of the cinnamoyl carbonyl group establishing favorable binding interactions with LdCALP and LARG in both hybrids 2g and 2h. In light of these findings, hybrids 2g and 2h are suggested as potential safe antileishmanial hit compounds for further development of anti-leishmanial agents.
Collapse
Affiliation(s)
- Ahmed H.E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Waleed A. Bayoumi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M. El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Trong-Nhat Phan
- Institute of Applied Science and Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam
| | - Taegeun Oh
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Gyeongpyo Ham
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kazem Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Egypt
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yong Sup Lee
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| |
Collapse
|
16
|
Li S, Wang X. Design and synthesis of antiviral pseudo-natural products through effective one-step acylmethylation macrocyclization. Chin J Nat Med 2023; 21:721-722. [PMID: 37879790 DOI: 10.1016/s1875-5364(23)60440-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Indexed: 10/27/2023]
Affiliation(s)
- Shang Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaobing Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
17
|
Bunyat-Zada AR, Ross AC. Highlights of bioinformatic tools and methods for validating bioinformatics derived hypotheses for microbial natural products research. Curr Opin Chem Biol 2023; 76:102367. [PMID: 37453164 DOI: 10.1016/j.cbpa.2023.102367] [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: 12/20/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Historically, bacterial natural products have served as an excellent source of drug leads, however, in recent decades the rate of discovery has slowed due to multiple challenges. Rapid advances in genome sequencing science in recent years have revealed the vast untapped encoded potential of bacteria to make natural products. To access these molecules, researchers can employ the ever-growing array of bioinformatic tools at their disposal and leverage newly developed experimental approaches to validate these bioinformatic-driven hypotheses. When used together effectively, bioinformatic and experimental tools enable researchers to deeply examine the full diversity of bacterial natural products. This review briefly outlines recent bioinformatic tools that can facilitate natural product research in bacteria including the use of CRISPR, co-occurrence network analysis, and combinatorial generation of microbial natural products to test bioinformatic hypotheses in the lab.
Collapse
Affiliation(s)
- Amir R Bunyat-Zada
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada.
| |
Collapse
|
18
|
Krzyzanowski A, Pahl A, Grigalunas M, Waldmann H. Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity. J Med Chem 2023; 66:12739-12750. [PMID: 37651653 PMCID: PMC10544027 DOI: 10.1021/acs.jmedchem.3c00689] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Indexed: 09/02/2023]
Abstract
The fraction of sp3-hybridized carbons (Fsp3) and the fraction of stereogenic carbons (FCstereo) are two widely employed scores of molecular complexity with strong links to biologically relevant features. However, they do not comprehensively express molecular topology, and they often do not match the chemical intuition of complexity. We propose the spacial score (SPS) as an empirical scoring system that builds upon the principle underlying Fsp3 and FCstereo and expresses the spacial complexity of a compound in a uniform manner on a highly granular scale. The size-normalized SPS (nSPS) can differentiate distributions of natural products and synthetic compounds and is applicable in the analysis of biological activity data. Analysis of the ChEMBL database revealed general trends of increasing selectivity and potency with increasing nSPS. SPS can also be used advantageously in planning and analysis of synthesis programs for direct comparison of chemical transformations and intermediates in reaction sequences.
Collapse
Affiliation(s)
- Adrian Krzyzanowski
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry, Chemical Biology Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| | - Axel Pahl
- Compound
Management and Screening Center, Max Planck
Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Michael Grigalunas
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 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, Chemical Biology Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| |
Collapse
|
19
|
Abstract
Molecular complexity (MC) lacks a universal definition, but various studies address it in contexts ranging from ligand-receptor interactions to DNA sequencing, with the overarching emphasis being its significance in synthetic organic chemistry and pharmaceutical research. Efforts to quantify MC in drug discovery have been numerous, but a unified approach remains challenging. Strategies based on graph theory, information theory, and substructural feature counts employed to gauge MC are often correlated to molecular weight (MW). Herbert Waldmann and his team introduced a new MC metric called the spacial score (SPS), which is based on factors like atom hybridization and stereoisomeric considerations. While SPS and its normalized version, nSPS, correlate with the natural product likeness score, they do not align with traditional chemical properties. We examined nSPS trends for approved drugs and found no significant changes in MC over eight decades, nor did nSPS capture drug innovation during that period. Furthermore, our analysis indicates that while the majority of approved drugs have an nSPS value between 10 and 20, this metric does not correlate with key drug properties like target bioactivity and oral bioavailability. Mirroring a chemist's intuitive sense of chemical complexity, nSPS addresses the need for a precise empirical tool while a universal definition of MC remains elusive.
Collapse
Affiliation(s)
- Tudor I. Oprea
- Expert
Systems Inc, 12760 High
Bluff Dr #370, San Diego, California 92130, United States
- Department
of Internal Medicine, University of New
Mexico, MSC09-5025, Albuquerque, New Mexico 87131, United States
| | - Cristian Bologa
- Department
of Internal Medicine, University of New
Mexico, MSC09-5025, Albuquerque, New Mexico 87131, United States
| |
Collapse
|
20
|
Qin LQ, Sun JY, Chen NY, Li XW, Gao DF, Wang W, Mo DL, Su JC, Su GF, Pan CX. Design and synthesis of pseudo-rutaecarpines as potent anti-inflammatory agents via regulating MAPK/NF-κB pathways to relieve inflammation-induced acute liver injury in mice. Bioorg Chem 2023; 138:106611. [PMID: 37236073 DOI: 10.1016/j.bioorg.2023.106611] [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: 02/22/2023] [Revised: 04/11/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
Pseudo-natural products (PNPs) design strategy provides a great valuable entrance to effectively identify of novel bioactive scaffolds. In this report, novel pseudo-rutaecarpines were designed via the combination of several privileged structure units and 46 target compounds were synthesized. Most of them display moderate to potent inhibitory effect on LPS-induced NO production and low cytotoxicity in RAW264.7 macrophage. The results of the anti-inflammatory efficacy and action mechanism of compounds 7l and 8c indicated that they significantly reduced the release of IL-6, IL-1β and TNF-α. Further studies revealed that they can strongly inhibit the activation of NF-κB and MAPK signal pathways. The LPS-induced acute liver injury mice model studies not only confirmed their anti-inflammatory efficacy in vivo but also could effectively relieve the liver injury in mice. The results suggest that compounds 7l and 8c might serve as lead compounds to develop therapeutic drugs for treatment of inflammation.
Collapse
Affiliation(s)
- Li-Qing Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China; Department of Chemistry and Pharmaceutical Science, Guilin Normal College, 9 Feihu Road, Gulin 541199, China
| | - Jia-Yi Sun
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Nan-Ying Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Xin-Wei Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - De-Feng Gao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Wang Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Dong-Liang Mo
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China
| | - Jun-Cheng Su
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Gui-Fa Su
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| | - Cheng-Xue Pan
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, 15 Yu Cai Road, Guilin 541004, China.
| |
Collapse
|
21
|
Yao R, Jensen AA, Bryce-Rogers HP, Schultz-Knudsen K, Zhou L, Hovendal NP, Pedersen H, Kubus M, Ulven T, Laraia L. Identification of 5-HT2 Serotonin Receptor Modulators through the Synthesis of a Diverse, Tropane- and Quinuclidine-alkaloid-Inspired Compound Library. J Med Chem 2023; 66:11536-11554. [PMID: 37566000 DOI: 10.1021/acs.jmedchem.3c01059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The recombination of natural product (NP) fragments in unprecedented ways has emerged as an important strategy for bioactive compound discovery. In this context, we propose that privileged primary fragments predicted to be enriched in activity against a specific target class can be coupled to diverse secondary fragments to engineer selectivity among closely related targets. Here, we report the synthesis of an alkaloid-inspired compound library enriched in spirocyclic ring fusions, comprising 58 compounds from 12 tropane- or quinuclidine-containing scaffolds, all of which can be considered pseudo-NPs. The library displays excellent predicted drug-like properties including high Fsp3 content and Lipinski's rule-of-five compliance. Targeted screening against selected members of the serotonin and dopamine G protein-coupled receptor family led to the identification of several hits that displayed significant agonist or antagonist activity against 5-HT2A and/or 5-HT2C, and subsequent optimization of one of these delivered a lead dual 5-HT2B/C antagonist with a highly promising selectivity profile.
Collapse
Affiliation(s)
- Ruwei Yao
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Hogan P Bryce-Rogers
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Katrine Schultz-Knudsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Libin Zhou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nicklas P Hovendal
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Henrik Pedersen
- Medicinal Chemistry, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Mariusz Kubus
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Trond Ulven
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| |
Collapse
|
22
|
Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan DJ, Concannon JB, Lardeau CH, Mouchet E, Singh S, Shafqat Abbasi H, Aspesi P, Boyd JD, Gilbert T, Gnutt D, Hariharan S, Hernandez D, Hormel G, Juhani K, Melanson M, Mervin LH, Monteverde T, Pilling JE, Skepner A, Swalley SE, Vrcic A, Weisbart E, Williams G, Yu S, Zapiec B, Carpenter AE. Optimizing the Cell Painting assay for image-based profiling. Nat Protoc 2023; 18:1981-2013. [PMID: 37344608 PMCID: PMC10536784 DOI: 10.1038/s41596-023-00840-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/28/2023] [Indexed: 06/23/2023]
Abstract
In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years' experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay's ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1-2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1-2 weeks.This protocol is an update to Nat. Protoc. 11, 1757-1774 (2016): https://doi.org/10.1038/nprot.2016.105.
Collapse
Affiliation(s)
- Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Maria Kost-Alimova
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa Miller
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Briana Fritchman
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Byrne
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David J Logan
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - John B Concannon
- Chemical Biology & Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Peter Aspesi
- Chemical Biology & Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Justin D Boyd
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Tamara Gilbert
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - David Gnutt
- Bayer AG, Research & Development, Pharmaceuticals, Wuppertal, Germany
| | | | - Desiree Hernandez
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Michelle Melanson
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Adam Skepner
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Anita Vrcic
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guy Williams
- AstraZeneca BioPharmaceuticals R&D, Cambridge, UK
| | - Shan Yu
- Takeda Development Center Americas, Inc., San Diego, CA, USA
| | | | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
23
|
Pahl A, Schölermann B, Lampe P, Rusch M, Dow M, Hedberg C, Nelson A, Sievers S, Waldmann H, Ziegler S. Morphological subprofile analysis for bioactivity annotation of small molecules. Cell Chem Biol 2023:S2451-9456(23)00159-9. [PMID: 37385259 DOI: 10.1016/j.chembiol.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]
Abstract
Fast prediction of the mode of action (MoA) for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. Morphological profiling, e.g., using the Cell Painting assay, offers a fast, unbiased assessment of compound activity on various targets in one experiment. However, due to incomplete bioactivity annotation and unknown activities of reference compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the MoA for both, reference and unexplored compounds. We defined MoA clusters and extracted cluster subprofiles that contain only a subset of morphological features. Subprofile analysis allows for the assignment of compounds to, currently, twelve targets or MoA. This approach enables rapid bioactivity annotation of compounds and will be extended to further clusters in the future.
Collapse
Affiliation(s)
- Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Beate Schölermann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Philipp Lampe
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Marion Rusch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Mark Dow
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Hedberg
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 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 and Chemical Biology, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| |
Collapse
|
24
|
Liu J, Mallick S, Xie Y, Grassin C, Lucas B, Schölermann B, Pahl A, Scheel R, Strohmann C, Protzel C, Berg T, Merten C, Ziegler S, Waldmann H. Morphological Profiling Identifies the Motor Protein Eg5 as Cellular Target of Spirooxindoles. Angew Chem Int Ed Engl 2023; 62:e202301955. [PMID: 36929571 DOI: 10.1002/anie.202301955] [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: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/18/2023]
Abstract
Oxindoles and iso-oxindoles are natural product-derived scaffolds that provide inspiration for the design and synthesis of novel biologically relevant compound classes. Notably, the spirocyclic connection of oxindoles with iso-oxindoles has not been explored by nature but promises to provide structurally related compounds endowed with novel bioactivity. Therefore, methods for their efficient synthesis and the conclusive discovery of their cellular targets are highly desirable. We describe a selective RhIII -catalyzed scaffold-divergent synthesis of spirooxindole-isooxindoles and spirooxindole-oxindoles from differently protected diazooxindoles and N-pivaloyloxy aryl amides which includes a functional group-controlled Lossen rearrangement as key step. Unbiased morphological profiling of a corresponding compound collection in the Cell Painting assay efficiently identified the mitotic kinesin Eg5 as the cellular target of the spirooxindoles, defining a unique Eg5 inhibitor chemotype.
Collapse
Affiliation(s)
- Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Shubhadip Mallick
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Yusheng Xie
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Corentin Grassin
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, University-Street 150, 44801, Bochum, Germany
| | - Belén Lucas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
- Compound Management and Screening Center, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Street 6, 44221, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Street 6, 44221, Dortmund, Germany
| | - Christoph Protzel
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Thorsten Berg
- Leipzig University, Institute of Organic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Christian Merten
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Organic Chemistry II, University-Street 150, 44801, Bochum, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Street 6, 44221, Dortmund, Germany
| |
Collapse
|
25
|
Li J, Ye J, Zhou R, Gui K, Li J, Feng J, Ma Z, Lei P, Gao Y. Systematic Study on Turpentine-Derived Amides from Natural Plant Monoterpenes as Potential Antifungal Candidates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5507-5515. [PMID: 36988236 DOI: 10.1021/acs.jafc.3c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
To overcome the high volatility, low aqueous solubility, and few definite action sites of monoterpenoid pesticides and improve their properties and effectiveness in the control of crop pathogenic fungi, herein, a series of natural turpentine-based amide derivatives exhibiting satisfactory antifungal activity were designed and synthesized. A systematic study was conducted on antifungal activity and the physiological and biochemical response of compounds 5o (EC50 = 1.139 μg/mL) and 5j (EC50 = 1.762 μg/mL) against Rhizoctonia solani. The effect of the target compound on the potential target-site succinate dehydrogenase was evaluated. The soluble concentrates of compounds 5o and 5j possessing good performance and control effects were prepared for practical application. To conduct a comprehensive analysis of the relationship between structural descriptors and activity, four representative title compounds were selected for theoretical calculation: 5o, 5j, 5k, and 5j. The binding mode of compound 5o and boscalid with succinate dehydrogenase was analyzed via molecular docking. This study provides a reference for the development of monoterpene pesticides with high efficiency, elucidated target sites, and the appropriate formula.
Collapse
Affiliation(s)
- Jiening Li
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Jiuhui Ye
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Rui Zhou
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Kuo Gui
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Jian Li
- Jiangsu Province Key Laboratory of Biomass Energy and Materials, College of Forestry, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Juntao Feng
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Zhiqing Ma
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Peng Lei
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| | - Yanqing Gao
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang, Shaanxi 712100, People's Republic of China
| |
Collapse
|
26
|
Tangara S, Faïon L, Piveteau C, Capet F, Godelier R, Michel M, Flipo M, Deprez B, Willand N, Villemagne B. Rapid and Efficient Access to Novel Bio-Inspired 3-Dimensional Tricyclic SpiroLactams as Privileged Structures via Meyers’ Lactamization. Pharmaceuticals (Basel) 2023; 16:ph16030413. [PMID: 36986512 PMCID: PMC10054226 DOI: 10.3390/ph16030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
The concept of privileged structure has been used as a fruitful approach for the discovery of novel biologically active molecules. A privileged structure is defined as a semi-rigid scaffold able to display substituents in multiple spatial directions and capable of providing potent and selective ligands for different biological targets through the modification of those substituents. On average, these backbones tend to exhibit improved drug-like properties and therefore represent attractive starting points for hit-to-lead optimization programs. This article promotes the rapid, reliable, and efficient synthesis of novel, highly 3-dimensional, and easily functionalized bio-inspired tricyclic spirolactams, as well as an analysis of their drug-like properties.
Collapse
Affiliation(s)
- Salia Tangara
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Frédéric Capet
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181—UCCS—Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Romain Godelier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Michel
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
- Correspondence:
| |
Collapse
|
27
|
Whitmarsh-Everiss T, Wang Z, Hauberg Hansen C, Depta L, Sassetti E, Rafn Dan O, Pahl A, Sievers S, Laraia L. Identification of Biologically Diverse Tetrahydronaphthalen-2-ols through the Synthesis and Phenotypic Profiling of Chemically Diverse, Estradiol-Inspired Compounds. Chembiochem 2023; 24:e202200555. [PMID: 36594441 DOI: 10.1002/cbic.202200555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/02/2023] [Accepted: 01/02/2023] [Indexed: 01/04/2023]
Abstract
Combining natural product fragments to design new scaffolds with unprecedented bioactivity is a powerful strategy for the discovery of tool compounds and potential therapeutics. However, the choice of fragments to couple and the biological screens to employ remain open questions in the field. By choosing a primary fragment containing the A/B ring system of estradiol and fusing it to nine different secondary fragments, we were able to identify compounds that modulated four different phenotypes: inhibition of autophagy and osteoblast differentiation, as well as potassium channel and tubulin modulation. The latter two were uncovered by using unbiased morphological profiling with a cell-painting assay. The number of hits and variety in bioactivity discovered validates the use of recombining natural product fragments coupled to phenotypic screening for the rapid identification of biologically diverse compounds.
Collapse
Affiliation(s)
- Thomas Whitmarsh-Everiss
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Zhou Wang
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Cecilie Hauberg Hansen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Elisa Sassetti
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Oliver Rafn Dan
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs Lyngby, Denmark
| |
Collapse
|
28
|
Wang ZZ, Shi XX, Huang GY, Hao GF, Yang GF. Fragment-based drug discovery supports drugging 'undruggable' protein-protein interactions. Trends Biochem Sci 2023; 48:539-552. [PMID: 36841635 DOI: 10.1016/j.tibs.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Protein-protein interactions (PPIs) have important roles in various cellular processes, but are commonly described as 'undruggable' therapeutic targets due to their large, flat, featureless interfaces. Fragment-based drug discovery (FBDD) has achieved great success in modulating PPIs, with more than ten compounds in clinical trials. Here, we highlight the progress of FBDD in modulating PPIs for therapeutic development. Targeting hot spots that have essential roles in both fragment binding and PPIs provides a shortcut for the development of PPI modulators via FBDD. We highlight successful cases of cracking the 'undruggable' problems of PPIs using fragment-based approaches. We also introduce new technologies and future trends. Thus, we hope that this review will provide useful guidance for drug discovery targeting PPIs.
Collapse
Affiliation(s)
- Zhi-Zheng Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Xing-Xing Shi
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Guang-Yi Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China.
| |
Collapse
|
29
|
Ogawa K, Sakamoto D, Hosoki R. Computer Science Technology in Natural Products Research: A Review of Its Applications and Implications. Chem Pharm Bull (Tokyo) 2023; 71:486-494. [PMID: 37394596 DOI: 10.1248/cpb.c23-00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Computational approaches to drug development are rapidly growing in popularity and have been used to produce significant results. Recent developments in information science have expanded databases and chemical informatics knowledge relating to natural products. Natural products have long been well-studied, and a large number of unique structures and remarkable active substances have been reported. Analyzing accumulated natural product knowledge using emerging computational science techniques is expected to yield more new discoveries. In this article, we discuss the current state of natural product research using machine learning. The basic concepts and frameworks of machine learning are summarized. Natural product research that utilizes machine learning is described in terms of the exploration of active compounds, automatic compound design, and application to spectral data. In addition, efforts to develop drugs for intractable diseases will be addressed. Lastly, we discuss key considerations for applying machine learning in this field. This paper aims to promote progress in natural product research by presenting the current state of computational science and chemoinformatics approaches in terms of its applications, strengths, limitations, and implications for the field.
Collapse
Affiliation(s)
- Keiko Ogawa
- Laboratory of Regulatory Science, College of Pharmaceutical Sciences, Ritsumeikan University
| | - Daiki Sakamoto
- Laboratory of Regulatory Science, College of Pharmaceutical Sciences, Ritsumeikan University
| | - Rumiko Hosoki
- Laboratory of Regulatory Science, College of Pharmaceutical Sciences, Ritsumeikan University
| |
Collapse
|
30
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
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
| |
Collapse
|
31
|
Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
Collapse
Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - 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 of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| |
Collapse
|
32
|
Schölermann B, Bonowski J, Grigalunas M, Burhop A, Xie Y, Hoock JGF, Liu J, Dow M, Nelson A, Nowak C, Pahl A, Sievers S, Ziegler S. Identification of Dihydroorotate Dehydrogenase Inhibitors Using the Cell Painting Assay. Chembiochem 2022; 23:e202200475. [PMID: 36134475 PMCID: PMC9828254 DOI: 10.1002/cbic.202200475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/21/2022] [Indexed: 02/03/2023]
Abstract
Profiling approaches have been increasingly employed for the characterization of disease-relevant phenotypes or compound perturbation as they provide a broad, unbiased view on impaired cellular states. We report that morphological profiling using the cell painting assay (CPA) can detect modulators of de novo pyrimidine biosynthesis and of dihydroorotate dehydrogenase (DHODH) in particular. The CPA can differentiate between impairment of pyrimidine and folate metabolism, which both affect cellular nucleotide pools. The identified morphological signature is shared by inhibitors of DHODH and the functionally tightly coupled complex III of the mitochondrial respiratory chain as well as by UMP synthase, which is downstream of DHODH. The CPA appears to be particularly suited for the detection of DHODH inhibitors at the site of their action in cells. As DHODH is a validated therapeutic target, the CPA will enable unbiased identification of DHODH inhibitors and inhibitors of de novo pyrimidine biosynthesis for biological research and drug discovery.
Collapse
Affiliation(s)
- Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jana Bonowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Annina Burhop
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Yusheng Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Joseph G. F. Hoock
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Jie Liu
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Mark Dow
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Adam Nelson
- School of Chemistry andAstbury Centre for Structural Molecular BiologyUniversity of LeedsLS2 9JTLeedsUK
| | - Christine Nowak
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany,Compound Management and Screening Center44227DortmundGermany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical Biology44227DortmundGermany
| |
Collapse
|
33
|
Schaub J, Zander J, Zielesny A, Steinbeck C. Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). J Cheminform 2022; 14:79. [PMID: 36357931 PMCID: PMC9650898 DOI: 10.1186/s13321-022-00656-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022] Open
Abstract
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.
Collapse
Affiliation(s)
- Jonas Schaub
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
| | - Julian Zander
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Achim Zielesny
- grid.454254.60000 0004 0647 4362Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Christoph Steinbeck
- grid.9613.d0000 0001 1939 2794Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743 Jena, Germany
| |
Collapse
|
34
|
Wesseler F, Lohmann S, Riege D, Halver J, Roth A, Pichlo C, Weber S, Takamiya M, Müller E, Ketzel J, Flegel J, Gihring A, Rastegar S, Bertrand J, Baumann U, Knippschild U, Peifer C, Sievers S, Waldmann H, Schade D. Phenotypic Discovery of Triazolo[1,5- c]quinazolines as a First-In-Class Bone Morphogenetic Protein Amplifier Chemotype. J Med Chem 2022; 65:15263-15281. [DOI: 10.1021/acs.jmedchem.2c01199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fabian Wesseler
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Compound Management and Screening Center COMAS, Max Planck Institute of Molecular Physiology (MPI), 44227 Dortmund, Germany
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Stefan Lohmann
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Daniel Riege
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Jonas Halver
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Aileen Roth
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Christian Pichlo
- Department of Chemistry, University of Cologne, Greinstraße 6, 50939 Cologne, Germany
| | - Sabrina Weber
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Eva Müller
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Jana Ketzel
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Jana Flegel
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Adrian Gihring
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing at Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Jessica Bertrand
- Department of Orthopedic Surgery, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ulrich Baumann
- Department of Chemistry, University of Cologne, Greinstraße 6, 50939 Cologne, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Sonja Sievers
- Compound Management and Screening Center COMAS, Max Planck Institute of Molecular Physiology (MPI), 44227 Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227Dortmund, Germany
| | - Herbert Waldmann
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227Dortmund, Germany
| | - Dennis Schade
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
- Partner Site Kiel, DZHK, German Center for Cardiovascular Research, 24105 Kiel, Germany
| |
Collapse
|
35
|
Davies C, Dötsch L, Ciulla MG, Hennes E, Yoshida K, Gasper R, Scheel R, Sievers S, Strohmann C, Kumar K, Ziegler S, Waldmann H. Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype. Angew Chem Int Ed Engl 2022; 61:e202209374. [PMID: 35959923 DOI: 10.1002/anie.202209374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Natural product (NP)-inspired design principles provide invaluable guidance for bioactive compound discovery. Pseudo-natural products (PNPs) are de novo combinations of NP fragments to target biologically relevant chemical space not covered by NPs. We describe the design and synthesis of apoxidoles, a novel pseudo-NP class, whereby indole- and tetrahydropyridine fragments are linked in monopodal connectivity not found in nature. Apoxidoles are efficiently accessible by an enantioselective [4+2] annulation reaction. Biological evaluation revealed that apoxidoles define a new potent type IV inhibitor chemotype of indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme considered a target for the treatment of neurodegeneration, autoimmunity and cancer. Apoxidoles target apo-IDO1, prevent heme binding and induce unique amino acid positioning as revealed by crystal structure analysis. Novel type IV apo-IDO1 inhibitors are in high demand, and apoxidoles may provide new opportunities for chemical biology and medicinal chemistry research.
Collapse
Affiliation(s)
- Caitlin Davies
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lara Dötsch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Maria Gessica Ciulla
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Current address: Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, Italy.,Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy
| | - Elisabeth Hennes
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kei Yoshida
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University of Dortmund, Department of Inorganic Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS), Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technical University of Dortmund, Department of Inorganic Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kamal Kumar
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Current address: AiCuris Anti-infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University of Dortmund, Department of Chemical Biology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| |
Collapse
|
36
|
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.
Collapse
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.
| |
Collapse
|
37
|
Davies C, Dötsch L, Ciulla MG, Hennes E, Yoshida K, Gasper R, Scheel R, Sievers S, Strohmann C, Kumar K, Ziegler S, Waldmann H. Identification of a Novel Pseudo‐Natural Product Type IV IDO1 Inhibitor Chemotype. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Caitlin Davies
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Lara Dötsch
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Maria Gessica Ciulla
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Elisabeth Hennes
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Kei Yoshida
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Raphael Gasper
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Crystallography and Biophysics Facility GERMANY
| | - Rebecca Scheel
- Technische Universität Dortmund: Technische Universitat Dortmund Inorganic Chemistry GERMANY
| | - Sonja Sievers
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Compound Management and Screening Center GERMANY
| | - Carsten Strohmann
- Technische Universität Dortmund: Technische Universitat Dortmund Inorganic Chemistry GERMANY
| | - Kamal Kumar
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie: Max-Planck-Institut fur molekulare Physiologie Chemical Biology GERMANY
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology: Max-Planck-Institut fur molekulare Physiologie Chemical Biology Otto-Hahn-Str. 11 44227 Dortmund GERMANY
| |
Collapse
|
38
|
Wu G, Qian X, Huang Y, Liu Y, Zhou L, Wang W, Li J, Zhu T, Gu Q, Li D. Nonenzymatic Self-Assembly Access to Diverse ortho-Quinone Methide-Based Pseudonatural Products. Org Lett 2022; 24:5235-5239. [DOI: 10.1021/acs.orglett.2c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guangwei Wu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
| | - Xuan Qian
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
| | - Yeqiang Huang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
| | - Yujia Liu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
| | - Luning Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, People’s Republic of China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, People’s Republic of China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, Shandong 26003, People’s Republic of China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, People’s Republic of China
| |
Collapse
|
39
|
Jia W, Di C, Zhang R, Shi L. Application of liquid chromatography mass spectrometry-based lipidomics to dairy products research: An emerging modulator of gut microbiota and human metabolic disease risk. Food Res Int 2022; 157:111206. [DOI: 10.1016/j.foodres.2022.111206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/19/2022]
|
40
|
Sánchez P, Salas CO, Gallardo-Fuentes S, Villegas A, Veloso N, Honores J, Inman M, Isaacs M, Contreras R, Moody CJ, Cisterna J, Brito I, Tapia RA. Phenoxy- and Phenylamino-Heterocyclic Quinones: Synthesis and Preliminary Anti-Pancreatic Cancer Activity. Chem Biodivers 2022; 19:e202101036. [PMID: 35581163 DOI: 10.1002/cbdv.202101036] [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: 12/29/2021] [Accepted: 04/22/2022] [Indexed: 11/06/2022]
Abstract
The successful application of fragment-based drug discovery strategy for the efficient synthesis of phenoxy- or phenylamino-2-phenyl-benzofuran, -benzoxazole and -benzothiazole quinones is described. Interestingly, in the final step of the synthesis of the target compounds, unusual results were observed on the regiochemistry of the reaction of bromoquinones with phenol and aniline. A theoretical study was carried out for better understanding the factors that control the regiochemistry of these reactions. The substituted heterocyclic quinones were evaluated in vitro to determine their cytotoxicity by the MTT method in three pancreatic cancer cell lines (MIA-PaCa-2, BxPC-3, and AsPC-1). Phenoxy benzothiazole quinone 26a showed potent cytotoxic activity against BxPC-3 cell lines, while phenylamino benzoxazole quinone 20 was the most potent on MIA-PaCa-2 cells. Finally, electrochemical properties of these quinones were determined to correlate with a potential mechanism of action. All these results, indicate that the phenoxy quinone fragment led to compounds with increased activity against pancreatic cancer cells.
Collapse
Affiliation(s)
- Patricio Sánchez
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Cristian O Salas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Sebastián Gallardo-Fuentes
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, 7750000, Santiago, Chile
| | - Alondra Villegas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Nicolás Veloso
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Jessica Honores
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Martyn Inman
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Mauricio Isaacs
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| | - Renato Contreras
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, 7750000, Santiago, Chile
| | - Christopher J Moody
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jonathan Cisterna
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, 02800, Antofagasta, Chile
| | - Iván Brito
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, 02800, Antofagasta, Chile
| | - Ricardo A Tapia
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 6094411, Santiago, Chile
| |
Collapse
|
41
|
Foley DJ, Waldmann H. Ketones as strategic building blocks for the synthesis of natural product-inspired compounds. Chem Soc Rev 2022; 51:4094-4120. [PMID: 35506561 DOI: 10.1039/d2cs00101b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Natural product-inspired compound collections serve as excellent sources for the identification of new bioactive compounds to treat disease. However, such compounds must necessarily be more structurally-enriched than traditional screening compounds, therefore inventive synthetic strategies and reliable methods are needed to prepare them. Amongst the various possible starting materials that could be considered for the synthesis of natural product-inspired compounds, ketones can be especially valuable due to the vast variety of complexity-building synthetic transformations that they can take part in, their high prevalence as commercial building blocks, and relative ease of synthesis. With a view towards developing a unified synthetic strategy for the preparation of next generation bioactive compound collections, this review considers whether ketones could serve as general precursors in this regard, and summarises the opulence of synthetic transformations available for the annulation of natural product ring-systems to ketone starting materials.
Collapse
Affiliation(s)
- Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand. .,Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Abstract
![]()
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.
Collapse
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
| |
Collapse
|
44
|
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
| |
Collapse
|
45
|
Zhang XJ, Wang Z, Zhang H, Gao JJ, Yang KR, Fan WY, Wu RX, Feng ML, Zhu W, Zhu YP. Iodine-Mediated Domino Cyclization for One-Pot Synthesis of Indolizine-Fused Chromones via Metal-Free sp 3 C-H Functionalization. J Org Chem 2021; 87:835-845. [PMID: 34962788 DOI: 10.1021/acs.joc.1c02508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An efficient method for the synthesis of new indolizine-fused chromones has been accomplished from ethyl (E)-3-(2-acetylphenoxy)acrylates and pyridines in a "one-pot" manner. Facile operation in open-air, metal-free, and mild conditions renders this protocol particularly practical and attractive. Moreover, this method can simultaneously construct two molecular fragments of chromone and indolizine. Scale-up experiment and the construction of natural products further prove the practicability of this strategy.
Collapse
Affiliation(s)
- Xiang-Jin Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Zhuo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Han Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Jing-Jing Gao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Kai-Rui Yang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Wei-Yu Fan
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Rui-Xue Wu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Meng-Lin Feng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Wei Zhu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| | - Yan-Ping Zhu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, PR China
| |
Collapse
|
46
|
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: 16] [Impact Index Per Article: 5.3] [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.
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Liu J, Flegel J, Otte F, Pahl A, Sievers S, Strohmann C, Waldmann H. Combination of Pseudo‐Natural Product Design and Formal Natural Product Ring Distortion Yields Stereochemically and Biologically Diverse Pseudo‐Sesquiterpenoid Alkaloids. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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
| | - Jana Flegel
- 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
| | - 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
| |
Collapse
|
49
|
Liu J, Flegel J, Otte F, Pahl A, Sievers S, Strohmann C, Waldmann H. Combination of Pseudo-Natural Product Design and Formal Natural Product Ring Distortion Yields Stereochemically and Biologically Diverse Pseudo-Sesquiterpenoid Alkaloids. Angew Chem Int Ed Engl 2021; 60:21384-21395. [PMID: 34297473 PMCID: PMC8518946 DOI: 10.1002/anie.202106654] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 12/28/2022]
Abstract
We describe the synthesis and biological evaluation of a new natural product‐inspired compound class obtained by combining the conceptually complementary pseudo‐natural product (pseudo‐NP) design strategy and a formal adaptation of the complexity‐to‐diversity ring distortion approach. Fragment‐sized α‐methylene‐sesquiterpene lactones, whose scaffolds can formally be viewed as related to each other or are obtained by ring distortion, were combined with alkaloid‐derived pyrrolidine fragments by means of highly selective stereocomplementary 1,3‐dipolar cycloaddition reactions. The resulting pseudo‐sesquiterpenoid alkaloids were found to be both chemically and biologically diverse, and their biological performance distinctly depends on both the structure of the sesquiterpene lactone‐derived scaffolds and the stereochemistry of the pyrrolidine fragment. Biological investigation of the compound collection led to the discovery of a novel chemotype inhibiting Hedgehog‐dependent osteoblast differentiation
Collapse
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
| | - Jana Flegel
- 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
| | - 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
| |
Collapse
|
50
|
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: 30] [Impact Index Per Article: 10.0] [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.
Collapse
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
| |
Collapse
|