1
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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.
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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
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2
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Porte V, van Veen BC, Zhang H, Piacentini P, Matheu SA, Woolford S, Sokol KR, Shaaban S, Weinstabl H, Maulide N. Synthesis of Complex Tetracyclic Fused Scaffolds Enabled by (3 + 2) Cycloaddition. Org Lett 2024; 26:4873-4876. [PMID: 38820198 PMCID: PMC11187634 DOI: 10.1021/acs.orglett.4c01269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
We describe the single-step formation of complex tetracyclic fused scaffolds enabled by (3 + 2) cycloaddition of azomethine ylides. Various indoles, N-protecting groups, and amino acids are well tolerated. The products are obtained in a catalyst-free manner with moderate to excellent yield and high diastereoselectivity. Representing a new scaffold that is not yet found in nature, the construction of pyrrolidine-fused cyclohepta-, azepino-, or oxepinoindoles could be found valuable in the synthesis of new pseudo-natural products.
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Affiliation(s)
- Vincent Porte
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Branca C. van Veen
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Haoqi Zhang
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Paolo Piacentini
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Sergio Armentia Matheu
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Sophie Woolford
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Kevin R. Sokol
- Boehringer
Ingelheim RCV GmbH&CoKG, 1120 Vienna, Austria
| | - Saad Shaaban
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | | | - Nuno Maulide
- Christian
Doppler Laboratory for Entropy-Oriented Drug Design, Institute of
Organic Chemistry, University of Vienna, 1090 Vienna, Austria
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3
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Yadav M, Roy N, Mandal K, Nagpure M, Santra MK, Guchhait SK. Rutaecarpine-inspired scaffold-hopping strategy and Ullmann cross-coupling based synthetic approach: Identification of pyridopyrimidinone-indole based novel anticancer chemotypes. Bioorg Med Chem 2024; 109:117799. [PMID: 38897138 DOI: 10.1016/j.bmc.2024.117799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Natural products as starting templates have shown historically major contribution to development of drugs. Inspired by the structure-function of an anticancer natural alkaloid Rutaecarpine, the Scaffold-hopped Acyclic Analogues of Rutaecarpine (SAAR) with 'N'-atom switch (1°-hop) and ring-opening (2°-hop) were investigated. A new synthetic route was developed for an effective access to the analogues, i.e. 2-indolyl-pyrido[1,2-a]pyrimidinones, which involved preparation of N-Boc-N'-phthaloyltryptamine/mexamine-bromides and pyridopyrmidinon-2-yl triflate, a nickel/palladium-catalysed Ullmann cross-coupling of these bromides and triflate, deprotection of phthalimide followed by N-aroylation, and Boc-deprotection. Fourteen novel SAAR-compounds were prepared, and they showed characteristic antiproliferative activity against various cancer cells. Three most active compounds (11a, 11b, and 11c) exhibited good antiproliferative activity, IC50 7.7-15.8 µM against human breast adenocarcinoma cells (MCF-7), lung cancer cells (A549), and colon cancer cells (HCT-116). The antiproliferative property was also observed in the colony formation assay. The SAAR compound 11b was found to have superior potency than original natural product Rutaecarpine and an anticancer drug 5-FU in antiproliferative activities with relatively lower cytotoxicity towards normal breast epithelial cells (MCF10A) and significantly higher inhibitory effect on cancer cells' migration. The compound 11b was found to possess favourable in silico physicochemical characteristics (lipophilicity-MLOGP, TPSA, and water solubility-ESOL, and others), bioavailability score, and pharmacokinetic properties (GI absorption, BBB non-permeant, P-gp, and CYP2D6). Interestingly, the compound 11b did not show any medicinal chemistry structural alert of PAINS and Brenk filter. The study represents for the first time the successful discovery of new potent anticancer chemotypes using Rutaecarpine natural alkaloid as starting template and reaffirms the significance of natural product-inspired scaffold-hopping technique in drug discovery research.
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Affiliation(s)
- Mukul Yadav
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Nibedita Roy
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Kartik Mandal
- National Centre for Cell Science, NCCS Complex, Pune University Campus Ganeshkhind, Pune, Maharastra 411007, India
| | - Mithilesh Nagpure
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Manas K Santra
- National Centre for Cell Science, NCCS Complex, Pune University Campus Ganeshkhind, Pune, Maharastra 411007, India
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India.
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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.
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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.
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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.
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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
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6
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Qiu Z, Huang R, Wu Y, Li X, Sun C, Ma Y. Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation. Microb Drug Resist 2024. [PMID: 38648550 DOI: 10.1089/mdr.2023.0232] [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: 04/25/2024] Open
Abstract
The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.
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Affiliation(s)
- Ziying Qiu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Rongkun Huang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yuxuan Wu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xinghao Li
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Chunyu Sun
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yunqi Ma
- School of Pharmacy, Binzhou Medical University, Yantai, China
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Tang J, Su L, He X, Liu D, Zhao C, Zhang S, Li Q, Li R, Li H. Biotransformation of Patchouli Alcohol by Cladosporium cladosporioides and the Anti-Influenza Virus Activities of Biotransformation Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7991-8005. [PMID: 38544458 DOI: 10.1021/acs.jafc.3c09753] [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: 04/11/2024]
Abstract
The biotransformation of patchouli alcohol by Cladosporium cladosporioides afforded 31 products, including 21 new ones (1-3, 5, 6, 8-14, and 17-25). Their structures were determined by extensive spectroscopic data analysis (1H and 13C NMR, HSQC, HMBC, 1H-1H COSY, ROESY, and HRESIMS), and the absolute configuration of compounds 1, 2, 8, 9, and 17 was determined by single-crystal X-ray diffraction using Cu Kα radiation. Structurally, compounds 21-24 were patchoulol-type norsesquiterpenoids without Me-12. Among them, a Δ3(4) double bond existed in compounds 21 and 22; a three-membered ring was formed between C-4, C-5, and C-6 in compound 23; an epoxy moiety appeared between C-3 and C-4 in compound 24. Furthermore, the biotransformation products 9, 10, 12, and 25 showed potent anti-influenza virus activity with EC50 values of 2.11, 7.94, 20.87, and 3.45 μM, respectively.
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Affiliation(s)
- Jianxian Tang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Lu Su
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Xiu He
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Dan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Chunyan Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Shixian Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Qin Li
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming 650500, P.R. China
| | - Rongtao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Hongmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
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8
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Lee H, Kim J, Koh M. Medium-Sized Ring Expansion Strategies: Enhancing Small-Molecule Library Development. Molecules 2024; 29:1562. [PMID: 38611841 PMCID: PMC11013129 DOI: 10.3390/molecules29071562] [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: 03/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The construction of a small molecule library that includes compounds with medium-sized rings is increasingly essential in drug discovery. These compounds are essential for identifying novel therapeutic agents capable of targeting "undruggable" targets through high-throughput and high-content screening, given their structural complexity and diversity. However, synthesizing medium-sized rings presents notable challenges, particularly with direct cyclization methods, due to issues such as transannular strain and reduced degrees of freedom. This review presents an overview of current strategies in synthesizing medium-sized rings, emphasizing innovative approaches like ring-expansion reactions. It highlights the challenges of synthesis and the potential of these compounds to diversify the chemical space for drug discovery, underscoring the importance of medium-sized rings in developing new bioactive compounds.
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Affiliation(s)
- Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Republic of Korea;
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
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9
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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.
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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
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10
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Zhang Y, Lin L, Qiao S, Zhao X, Li T, Liang Q. Screening and evaluation of the hit compound from a DNA-encoded library derived from natural products based on immobilized endothelin receptor A. Int J Biol Macromol 2024; 256:128206. [PMID: 37981276 DOI: 10.1016/j.ijbiomac.2023.128206] [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: 07/06/2023] [Revised: 10/29/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
The enormous growing demand for drug candidates binding to endothelin receptor A (ETA) has made it necessary to continuously pursue new strategies for ligand screening and early evaluation. This work achieved the one-step immobilization of ETA based on the bioorthogonal chemistry between the epidermal growth factor receptor tag (EGFR-tag) and ibrutinib. Comprehensive characterizations including Western blot analysis are performed to realize the morphology, antibody/ligand recognition activity, and specificity of the immobilized ETA. Taking macitentan, ambrisentan, and bosentan as an example, we utilized the immobilized ETA to construct a thermodynamic model for the evaluation of the specific ligands binding to ETA. Using this model, we screened the potential compound NP845 from a DNA-encoded library with 10,686 members derived from natural products and calculated the association constant as (2.24 ± 0.15) × 105 M-1 at 37 °C, thereby demonstrating the good pharmacological activity of NP845. The entropy change (∆Sθ), enthalpy change (∆Hθ), and Gibbs free energy (∆Gθ) were 1.75 J/mol·K, -31.1 kJ/mol, and -31.6 kJ/mol at 37 °C, whereby we recognized the electrostatic force was the driving force of the interaction between NP845 and ETA. In vitro cell tests proved that NP845 can downregulate the expression level of PKA, B-Raf, MEK, and ERK1 in VSMC. Our results indicated that NP845 was a potential lead compound for fighting the ailments mediated by ETA.
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Affiliation(s)
- Yajun Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Li Lin
- Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Sai Qiao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Ting Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Qi Liang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China; Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China.
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11
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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.
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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
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12
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Plotniece A, Sobolev A, Supuran CT, Carta F, Björkling F, Franzyk H, Yli-Kauhaluoma J, Augustyns K, Cos P, De Vooght L, Govaerts M, Aizawa J, Tammela P, Žalubovskis R. Selected strategies to fight pathogenic bacteria. J Enzyme Inhib Med Chem 2023; 38:2155816. [PMID: 36629427 PMCID: PMC9848314 DOI: 10.1080/14756366.2022.2155816] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised in vitro and in vivo models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems.
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Affiliation(s)
- Aiva Plotniece
- Latvian Institute of Organic Synthesis, Riga, Latvia,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Riga Stradiņš University, Riga, Latvia,CONTACT Aiva Plotniece Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Carta
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Koen Augustyns
- Infla-Med, Centre of Excellence, University of Antwerp, Antwerp, Belgium,Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Juliana Aizawa
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia,Faculty of Materials Science and Applied Chemistry, Institute of Technology of Organic Chemistry, Riga Technical University, Riga, Latvia
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13
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Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
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Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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14
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Xie J, Pahl A, Krzyzanowski A, Krupp A, Liu J, Koska S, Schölermann B, Zhang R, Bonowski J, Sievers S, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. Synthetic Matching of Complex Monoterpene Indole Alkaloid Chemical Space. Angew Chem Int Ed Engl 2023; 62:e202310222. [PMID: 37818743 DOI: 10.1002/anie.202310222] [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: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are endowed with high structural and spatial complexity and characterized by diverse biological activities. Given this complexity-activity combination in MIAs, rapid and efficient access to chemical matter related to and with complexity similar to these alkaloids would be highly desirable, since such compound classes might display novel bioactivity. We describe the design and synthesis of a pseudo-natural product (pseudo-NP) collection obtained by the unprecedented combination of MIA fragments through complexity-generating transformations, resulting in arrangements not currently accessible by biosynthetic pathways. Cheminformatic analyses revealed that both the pseudo-NPs and the MIAs reside in a unique and common area of chemical space with high spatial complexity-density that is only sparsely populated by other natural products and drugs. Investigation of bioactivity guided by morphological profiling identified pseudo-NPs that inhibit DNA synthesis and modulate tubulin. These results demonstrate that the pseudo-NP collection occupies similar biologically relevant chemical space that Nature has endowed MIAs with.
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Affiliation(s)
- Jianing Xie
- 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
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology, 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 6, 44227, Dortmund, Germany
| | - Anna Krupp
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Jana Bonowski
- 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
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Slava Ziegler
- 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
| | - 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, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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15
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Fernandes RA. Deciphering the quest in the divergent total synthesis of natural products. Chem Commun (Camb) 2023; 59:12205-12230. [PMID: 37746673 DOI: 10.1039/d3cc03564f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The divergent synthesis of natural products is rapidly developing towards achieving the goal of efficiency and economy in total synthesis. However, presently, the sustainable development of the synthesis of natural products does not permit the linear synthesis of a single target. In this case, divergent total synthesis is based on the identification of an advanced intermediate with structural features that can be mapped in more than two molecules. However, the identification of this intermediate and its scalable synthesis in enantiopure form are challenging. Herein, we present the details of the ingenious efforts by researchers in the last six years toward the divergent synthesis of two to as many as eight natural products initially via a single route, and then diverging from a common intermediate and further branching out toward several natural products. The planning and strategies adopted can serve as guidelines for the future development of efficient divergent routes aimed at achieving higher efficiency toward multiple targets, causing divergent synthesis to become an accepted common practice.
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Affiliation(s)
- Rodney A Fernandes
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, Maharashtra, India.
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16
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Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel) 2023; 16:1388. [PMID: 37895859 PMCID: PMC10609821 DOI: 10.3390/ph16101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Daniel A. Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
| | - William J. Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José 1174-1200, Costa Rica
| | - Haruna L. Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Miguel Á. Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Vanderlan da S. Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara 14800-900, SP, Brazil;
| | - Dionisio A. Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Pablo N. Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Marvin J. Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador 01101, El Salvador;
| | - Johny R. Rodríguez Pérez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, Colombia
| | - Hoover A. Valencia Sánchez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - Héctor F. Cortés Hernández
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
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17
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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.
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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.
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18
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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.
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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
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19
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Liu J, Zhang R, Mallick S, Patil S, Wientjens C, Flegel J, Krupp A, Strohmann C, Grassin C, Merten C, Pahl A, Grigalunas M, Waldmann H. A highly enantioselective intramolecular 1,3-dipolar cycloaddition yields novel pseudo-natural product inhibitors of the Hedgehog signalling pathway. Chem Sci 2023; 14:7936-7943. [PMID: 37502335 PMCID: PMC10370549 DOI: 10.1039/d3sc01240a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/18/2023] [Indexed: 07/29/2023] Open
Abstract
De novo combination of natural product (NP) fragments by means of efficient, complexity- and stereogenic character-generating transformations to yield pseudo-natural products (PNPs) may explore novel biologically relevant chemical space. Pyrrolidine- and tetrahydroquinoline fragments rarely occur in combination in nature, such that PNPs that embody both fragments might represent novel NP-inspired chemical matter endowed with bioactivity. We describe the synthesis of pyrrolo[3,2-c]quinolines by means of a highly enantioselective intramolecular exo-1,3-dipolar cycloaddition catalysed by the AgOAc/(S)-DMBiphep complex. The cycloadditions proceeded in excellent yields (up to 98%) and with very high enantioselectivity (up to 99% ee). Investigation of the resulting PNP collection in cell-based assays monitoring different biological programmes led to the discovery of a structurally novel and potent inhibitor of the Hedgehog signalling pathway that targets the Smoothened protein.
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Affiliation(s)
- Jie Liu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Shubhadip Mallick
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Sohan Patil
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Chantal Wientjens
- Faculty of Chemistry, Chemical Biology, Technical University Dortmund Otto-Hahn-Street 6 44221 Dortmund Germany
| | - Jana Flegel
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Anna Krupp
- Faculty of Chemistry, Inorganic Chemistry, Technical University Dortmund Otto-Hahn-Street 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Faculty of Chemistry, Inorganic Chemistry, Technical University Dortmund Otto-Hahn-Street 6 44221 Dortmund Germany
| | - Corentin Grassin
- Faculty of Chemistry and Biochemistry, Organic Chemistry II, Ruhr University Bochum University-Street 150 44801 Bochum Germany
| | - Christian Merten
- Faculty of Chemistry and Biochemistry, Organic Chemistry II, Ruhr University Bochum University-Street 150 44801 Bochum Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
- Compound Management and Screening Center Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology Otto-Hahn-Street 11 44227 Dortmund Germany
- Faculty of Chemistry, Chemical Biology, Technical University Dortmund Otto-Hahn-Street 6 44221 Dortmund Germany
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20
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [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: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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21
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Sanchez A, Gurajapu A, Guo W, Kong WY, Laconsay CJ, Settineri NS, Tantillo DJ, Maimone TJ. A Shapeshifting Roadmap for Polycyclic Skeletal Evolution. J Am Chem Soc 2023. [PMID: 37279177 DOI: 10.1021/jacs.3c03960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Polycyclic ring systems are ubiquitous three-dimensional (3D) structural motifs central to the function of many biologically active small molecules and organic materials. Indeed, subtle changes to the overall molecular shape and connectivity of atoms in a polycyclic framework (i.e., isomerism) can drastically alter its function and properties. Unfortunately, direct evaluation of these structure-function relationships typically requires the development of distinct synthetic strategies toward a specific isomer. Dynamic, "shapeshifting" carbon cages present a promising approach for sampling isomeric chemical space but are often difficult to control and are largely limited to thermodynamic mixtures of positional isomers about a single core scaffold. Here, we describe the development of a new shapeshifting C9-chemotype and a chemical blueprint for its evolution into structurally and energetically diverse isomeric ring systems. By leveraging the unique molecular topology of π-orbitals interacting through-space (homoconjugation), a common skeletal ancestor evolved into a complex network of valence isomers. This unusual system represents an exceedingly rare small molecule capable of undergoing controllable and continuous isomerization processes through the iterative use of just two chemical steps (light and organic base). Computational and photophysical studies of the isomer network provide fundamental insight into the reactivity, mechanism, and role of homoconjugative interactions. Importantly, these insights may inform the rational design and synthesis of new dynamic, shapeshifting systems. We anticipate this process could be a powerful tool for the synthesis of structurally diverse, isomeric polycycles central to many bioactive small molecules and functional organic materials.
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Affiliation(s)
- Andre Sanchez
- Department of Chemistry, University of California-Berkeley, 826 Latimer Hall, Berkeley, California 94720, United States
| | - Anjali Gurajapu
- Department of Chemistry, University of California-Berkeley, 826 Latimer Hall, Berkeley, California 94720, United States
| | - Wentao Guo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Croix J Laconsay
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Nicholas S Settineri
- Department of Chemistry, University of California-Berkeley, 826 Latimer Hall, Berkeley, California 94720, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
| | - Thomas J Maimone
- Department of Chemistry, University of California-Berkeley, 826 Latimer Hall, Berkeley, California 94720, United States
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22
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Sakai T, Furuhata T, Hosoe K, Umemura K, Mori Y. Synthesis of Fused Tricyclic Amines Bearing Tetrasubstituted Carbons Using an Alkylation-Cyclization-Isomerization-3-aza-Cope Cascade Reaction. Org Lett 2023; 25:2986-2990. [PMID: 37093615 DOI: 10.1021/acs.orglett.3c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
A new cascade reaction sequence that involves alkylation, cyclization, isomerization, and 3-aza-Cope rearrangement was discovered. The stereogenic centers of the starting piperidines were transferred to the bicyclic enamine products, and a range of electron-withdrawing groups on the alkyne moieties, from ketones to amides, were tolerated under the reaction conditions. The bicyclic enamines underwent trifluoroacetic acid (TFA)-mediated cyclization to form tricyclic amines bearing tetrasubstituted carbons.
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Affiliation(s)
- Takeo Sakai
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Tomoki Furuhata
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Kota Hosoe
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Kaho Umemura
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Yuji Mori
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
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23
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Lv S, Li Q, Sang JW, Zhang Y, Wang J, Zhang WD. Uranyl nitrate as a recyclable homogeneous photocatalyst for selective cross-coupling of N-substituted amines and indoles. RSC Adv 2023; 13:11929-11937. [PMID: 37077263 PMCID: PMC10108382 DOI: 10.1039/d3ra01037f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
A homogeneous photocatalytic recyclable system for the selective radical-radical cross-coupling of N-substituted amines and indoles has been established. This system could conduct in water or acetonitrile, featuring the reuse of uranyl nitrate as the recyclable photocatalyst via a simple extraction. With this mild strategy in hand, good to excellent yields of cross-coupling products could be achieved even under the irradiation of sunlight, including 26 natural product derivatives and 16 natural product inspired re-engineered compounds. A radical-radical cross-coupling mechanism was newly proposed based on experimental evidence and reported literature. This strategy has been also applied to a gram scale synthesis to demonstrate its practical utility.
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Affiliation(s)
- Shuaipeng Lv
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine No. 1200, Cailun Road Shanghai 201203 China
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Qiannan Li
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine No. 1200, Cailun Road Shanghai 201203 China
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Ji-Wei Sang
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Yu Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine No. 1200, Cailun Road Shanghai 201203 China
| | - Jinxin Wang
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
| | - Wei-Dong Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine No. 1200, Cailun Road Shanghai 201203 China
- School of Pharmacy, Second Military Medical University Shanghai 200433 China
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24
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Srikanth G, Ravi A, Sebastian A, Joseph J, Khanfar MA, El‐Gamal MI, Al‐Qawasmeh RA, Shehadi IA, McN. Sieburth S, Abu‐Yousef IA, Majdalawieh AF, Al‐Tel TH. Diastereoselective Synthesis of Camptothecin‐like Scaffolds: Construction of a New Class of Pseudo‐natural Products. European J Org Chem 2023. [DOI: 10.1002/ejoc.202300080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Gourishetty Srikanth
- Department of Biology Chemistry and Environmental Sciences American University of Sharjah 26666 Sharjah United Arab Emirates
| | - Anil Ravi
- Sharjah Institute for Medical research University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical research University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Jobi Joseph
- Sharjah Institute for Medical research University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Monther A. Khanfar
- College of Science Department of Chemistry University of Sharjah 27272 Sharjah United Arab Emirates
| | - Mohammed I. El‐Gamal
- Sharjah Institute for Medical research University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- College of Pharmacy University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
| | - Raed A. Al‐Qawasmeh
- College of Science Department of Chemistry University of Sharjah 27272 Sharjah United Arab Emirates
| | - Ihsan A. Shehadi
- College of Science Department of Chemistry University of Sharjah 27272 Sharjah United Arab Emirates
| | - Scott McN. Sieburth
- Department of Chemistry Temple University 201 Beury Hall 19122 Philadelphia PA USA
| | - Imad A. Abu‐Yousef
- Department of Biology Chemistry and Environmental Sciences American University of Sharjah 26666 Sharjah United Arab Emirates
| | - Amin F. Majdalawieh
- Department of Biology Chemistry and Environmental Sciences American University of Sharjah 26666 Sharjah United Arab Emirates
| | - Taleb H. Al‐Tel
- Sharjah Institute for Medical research University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
- College of Pharmacy University of Sharjah P.O. Box 27272 Sharjah United Arab Emirates
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25
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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.
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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
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26
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Liu B, Yu X, Liu L, Wang L, Wang J, Huang Q, Xu Z, Luo C, Lou L, Huang W, Yang W. Modular Biomimetic Strategy Enabled Discovery of Simplified Pseudo-Natural Macrocyclic P-Glycoprotein Inhibitors Capable of Overcoming Multidrug Resistance. J Med Chem 2023; 66:2550-2565. [PMID: 36728755 DOI: 10.1021/acs.jmedchem.2c01424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Natural macrocycles have shown impressive activity to overcome P-glycoprotein (P-gp)-mediated multidrug resistance (MDR). However, the total synthesis and structural modification of natural macrocycles are challenging, which would hamper the deeper investigations of their structure-activity relationship (SAR) and drug likeness. Herein, we describe a modular biomimetic strategy to expeditiously achieve a new class of macrocycles featuring polysubstituted 1,3-diene, which efficiently inhibited P-gp and reversed MDR in cancer cells. The SAR analysis revealed that the size and linker of the macrocycles are important structural characteristics to restore activity. Particularly, 32 containing a naphthyl group and (d)-Phe moiety has higher potency with an excellent reversal fold than verapamil at a concentration of 5 μM, which induces conformational change of P-gp and inhibits its function instead of altering P-gp expression. Furthermore, 23 and 32 were identified to be attractive leads, which possess a good pharmacokinetic profile and antitumor activity in a KBV200 xenograft mouse model.
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Affiliation(s)
- Bo Liu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xueni Yu
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Liu
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Qianqian Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zhongliang Xu
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liguang Lou
- State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibo Yang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,State key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Li J, Sheng H, Wang Y, Lai Z, Wang Y, Cui S. Scaffold Hybrid of the Natural Product Tanshinone I with Piperidine for the Discovery of a Potent NLRP3 Inflammasome Inhibitor. J Med Chem 2023; 66:2946-2963. [PMID: 36786612 DOI: 10.1021/acs.jmedchem.2c01967] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Natural products provide inspiration and have proven to be the most valuable source for drug discovery. Herein, we report a scaffold hybrid strategy of Tanshinone I for the discovery of NLRP3 inflammasome inhibitors. 36 compounds were designed and synthesized, and the cheminformatic analyses showed that these compounds occupy a unique chemical space. The biological evaluation identified compounds 5j, 12a, and 12d as NLRP3 inflammasome inhibitors with significant potency, selectivity, and drug-likeness. Mechanistic studies revealed that these Tanshinone I derivatives could inhibit the degradation of the protein NLRP3 and block the oligomerization of NLRP3-induced apoptosis-associated speck-like proteins, thus inhibiting NLRP3 inflammasome activation. In addition, the water solubility, in vitro metabolic stability, and oral bioavailability of these compounds were also greatly improved compared to Tanshinone I. Therefore, this protocol provides a new structural evolution of Tanshinone I and a new class of potent NLRP3 inflammasome inhibitors.
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Affiliation(s)
- Jiaming Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongda Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchao Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhencheng Lai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunliang Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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28
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Computational Approaches to Enzyme Inhibition by Marine Natural Products in the Search for New Drugs. Mar Drugs 2023; 21:md21020100. [PMID: 36827141 PMCID: PMC9961086 DOI: 10.3390/md21020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
The exploration of biologically relevant chemical space for the discovery of small bioactive molecules present in marine organisms has led not only to important advances in certain therapeutic areas, but also to a better understanding of many life processes. The still largely untapped reservoir of countless metabolites that play biological roles in marine invertebrates and microorganisms opens new avenues and poses new challenges for research. Computational technologies provide the means to (i) organize chemical and biological information in easily searchable and hyperlinked databases and knowledgebases; (ii) carry out cheminformatic analyses on natural products; (iii) mine microbial genomes for known and cryptic biosynthetic pathways; (iv) explore global networks that connect active compounds to their targets (often including enzymes); (v) solve structures of ligands, targets, and their respective complexes using X-ray crystallography and NMR techniques, thus enabling virtual screening and structure-based drug design; and (vi) build molecular models to simulate ligand binding and understand mechanisms of action in atomic detail. Marine natural products are viewed today not only as potential drugs, but also as an invaluable source of chemical inspiration for the development of novel chemotypes to be used in chemical biology and medicinal chemistry research.
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29
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Berestetskiy A. Modern Approaches for the Development of New Herbicides Based on Natural Compounds. PLANTS (BASEL, SWITZERLAND) 2023; 12:234. [PMID: 36678947 PMCID: PMC9864389 DOI: 10.3390/plants12020234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/24/2022] [Indexed: 05/12/2023]
Abstract
Weeds are a permanent component of anthropogenic ecosystems. They require strict control to avoid the accumulation of their long-lasting seeds in the soil. With high crop infestation, many elements of crop production technologies (fertilization, productive varieties, growth stimulators, etc.) turn out to be practically meaningless due to high yield losses. Intensive use of chemical herbicides (CHs) has led to undesirable consequences: contamination of soil and wastewater, accumulation of their residues in the crop, and the emergence of CH-resistant populations of weeds. In this regard, the development of environmentally friendly CHs with new mechanisms of action is relevant. The natural phytotoxins of plant or microbial origin may be explored directly in herbicidal formulations (biorational CHs) or indirectly as scaffolds for nature-derived CHs. This review considers (1) the main current trends in the development of CHs that may be important for the enhancement of biorational herbicides; (2) the advances in the development and practical application of natural compounds for weed control; (3) the use of phytotoxins as prototypes of synthetic herbicides. Some modern approaches, such as computational methods of virtual screening and design of herbicidal molecules, development of modern formulations, and determination of molecular targets, are stressed as crucial to make the exploration of natural compounds more effective.
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Affiliation(s)
- Alexander Berestetskiy
- Laboratory of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, Pushkin, 196608 Saint-Petersburg, Russia
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30
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Iusupov IR, Lukyanenko ER, Altieri A, Kurkin AV. Design and Synthesis of Fsp3-Enriched Spirocyclic-Based Biological Screening Compound Arrays via DOS Strategies and Their NNMT Inhibition Profiling. ChemMedChem 2022; 17:e202200394. [PMID: 36193863 DOI: 10.1002/cmdc.202200394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/26/2022] [Indexed: 01/14/2023]
Abstract
Medicinal chemists are keen to explore tridimensional compounds, especially when it comes to small molecules. It has already been stressed that the majority of known drugs tend to be flat, whereas natural products tend to be more tridimensional and represent a good source of active compounds. 3D metrics have been implemented and computational descriptors are available to evaluate and prioritize compounds based on their 3D geometry. This is usually done by comparing the saturated carbon atoms in a molecule with the total number of its non-hydrogen atoms (the Fsp3 value). While this aspect is clear, still there are not enough synthetic tools that support the realization of novel chemotypes that conform to these criteria. Herein we describe a diversity oriented synthesis (DOS) synthetic cascade technology that starts from two simple reagents, and generates highly enriched Fsp3 novel and diverse spiro-scaffolds with pragmatic synthetic handles (points of diversity). The spiro nature of these scaffolds not only ensures high Fsp3 values but renders the compounds more rigid and therefore more effective in forming precise stereo-interactions with their potential biological targets. These compounds were also profiled for their drug-like properties and as potential modulators of the NNMT enzyme.
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Affiliation(s)
- Ildar R Iusupov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninsky Gory, Moscow, 119991, Russia
| | - Evgeny R Lukyanenko
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninsky Gory, Moscow, 119991, Russia
| | - Andrea Altieri
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninsky Gory, Moscow, 119991, Russia.,EDASA Scientific Srls, Via Stingi, 3, 66050, San Salvo, Italy
| | - Alexander V Kurkin
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninsky Gory, Moscow, 119991, Russia
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31
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Grigalunas M, Patil S, Krzyzanowski A, Pahl A, Flegel J, Schölermann B, Xie J, Sievers S, Ziegler S, Waldmann H. Unprecedented Combination of Polyketide Natural Product Fragments Identifies the New Hedgehog Signaling Pathway Inhibitor Grismonone. Chemistry 2022; 28:e202202164. [PMID: 36083197 PMCID: PMC10091983 DOI: 10.1002/chem.202202164] [Citation(s) in RCA: 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.
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Affiliation(s)
- Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sohan Patil
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Adrian Krzyzanowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Jana Flegel
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Jianing Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
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32
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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.
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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
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33
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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.
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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
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34
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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.
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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
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35
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Li Y, Cheng S, Tian Y, Zhang Y, Zhao Y. Recent ring distortion reactions for diversifying complex natural products. Nat Prod Rep 2022; 39:1970-1992. [PMID: 35972343 DOI: 10.1039/d2np00027j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2013-2022.Chemical diversification of natural products is an efficient way to generate natural product-like compounds for modern drug discovery programs. Utilizing ring-distortion reactions for diversifying natural products would directly alter the core ring systems of small molecules and lead to the production of structurally complex and diverse compounds for high-throughput screening. We review the ring distortion reactions recently used in complexity-to-diversity (CtD) and pseudo natural products (pseudo-NPs) strategies for diversifying complex natural products. The core ring structures of natural products are altered via ring expansion, ring cleavage, ring edge-fusion, ring spiro-fusion, ring rearrangement, and ring contraction. These reactions can rapidly provide natural product-like collections with properties suitable for a wide variety of biological and medicinal applications. The challenges and limitations of current ring distortion reactions are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We also provide a toolbox for chemists for the application of ring distortion reactions to access natural product-like molecules.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yun Tian
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yanan Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China.
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36
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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
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37
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Combining visible-light induction and copper catalysis for chemo-selective nitrene transfer for late-stage amination of natural products. Commun Chem 2022; 5:79. [PMID: 36697627 PMCID: PMC9814389 DOI: 10.1038/s42004-022-00692-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/22/2022] [Indexed: 01/28/2023] Open
Abstract
Nitrene transfer chemistry is an effective strategy for introducing C-N bonds, which are ubiquitous in pharmaceuticals, agrochemicals and diverse bioactive natural products. The development of chemical methodology that can functionalize unique sites within natural products through nitrene transfer remains a challenge in the field. Herein, we developed copper catalyzed chemoselective allylic C-H amination and catalyst-free visible-light induced aziridination of alkenes through nitrene transfer. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Furthermore, combination of these two methods enable the intermolecular chemo-selective late-stage amination of biologically active natural products, leading to C-H amination or C=C aziridination products in a tunable way. A series of control experiments indicate two-step radical processes were involved in both reaction systems.
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38
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Peraka S, Gorachand B, Hussain A, Sravanthi R, Ramachary DB. Organocatalytic One‐pot Synthesis of Pseudo‐Terpenoids. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Swamy Peraka
- University of Hyderabad School of Chemistry INDIA
| | | | | | | | - Dhevalapally B. Ramachary
- University of Hyderabad School of Chemistry Prof. C.R.Rao RoadCentral University PostGachi BowliHyderabad 500 046 Hyderabad INDIA
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39
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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.
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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
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40
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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.
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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
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Akbarzadeh M, Flegel J, Patil S, Shang E, Narayan R, Buchholzer M, Kazemein Jasemi NS, Grigalunas M, Krzyzanowski A, Abegg D, Shuster A, Potowski M, Karatas H, Karageorgis G, Mosaddeghzadeh N, Zischinsky M, Merten C, Golz C, Brieger L, Strohmann C, Antonchick AP, Janning P, Adibekian A, Goody RS, Ahmadian MR, Ziegler S, Waldmann H. The Pseudo‐Natural Product Rhonin Targets RHOGDI. Angew Chem Int Ed Engl 2022; 61:e202115193. [PMID: 35170181 PMCID: PMC9313812 DOI: 10.1002/anie.202115193] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 11/18/2022]
Abstract
For the discovery of novel chemical matter generally endowed with bioactivity, strategies may be particularly efficient that combine previous insight about biological relevance, e.g., natural product (NP) structure, with methods that enable efficient coverage of chemical space, such as fragment‐based design. We describe the de novo combination of different 5‐membered NP‐derived N‐heteroatom fragments to structurally unprecedented “pseudo‐natural products” in an efficient complexity‐generating and enantioselective one‐pot synthesis sequence. The pseudo‐NPs inherit characteristic elements of NP structure but occupy areas of chemical space not covered by NP‐derived chemotypes, and may have novel biological targets. Investigation of the pseudo‐NPs in unbiased phenotypic assays and target identification led to the discovery of the first small‐molecule ligand of the RHO GDP‐dissociation inhibitor 1 (RHOGDI1), termed Rhonin. Rhonin inhibits the binding of the RHOGDI1 chaperone to GDP‐bound RHO GTPases and alters the subcellular localization of RHO GTPases.
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Affiliation(s)
- Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Jana Flegel
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Sumersing Patil
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Erchang Shang
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Rishikesh Narayan
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- School of Chemical and Materials Sciences IIT Goa, Farmagudi Ponda Goa-403401 India
| | - Marcel Buchholzer
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Michael Grigalunas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Marco Potowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Hacer Karatas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - George Karageorgis
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | | | - Christian Merten
- Faculty of Chemistry and Biochemistry Organic Chemistry II Ruhr-University Bochum Universitätsstrasse 150 44780 Bochum Germany
| | - Christopher Golz
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Lucas Brieger
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Roger S. Goody
- Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Slava Ziegler
- 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 and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
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42
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022; 61:e202114328. [PMID: 34978373 PMCID: PMC9303634 DOI: 10.1002/anie.202114328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 01/02/2023]
Abstract
Design and synthesis of pseudo‐natural products (PNPs) through recombination of natural product (NP) fragments in unprecedented arrangements enables the discovery of novel biologically relevant chemical matter. With a view to wider coverage of NP‐inspired chemical and biological space, we describe the combination of this principle with macrocycle formation. PNP‐macrocycles were synthesized efficiently in a stereoselective one‐pot procedure including the 1,3‐dipolar cycloadditions of different dipolarophiles with dimeric cinchona alkaloid‐derived azomethine ylides formed in situ. The 20‐membered bis‐cycloadducts embody 18 stereocenters and an additional fragment‐sized NP‐structure. After further functionalization, a collection of 163 macrocyclic PNPs was obtained. Biological investigation revealed potent inducers of the lipidation of the microtubule associated protein 1 light chain 3 (LC3) protein, which plays a prominent role in various autophagy‐related processes.
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Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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43
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Akbarzadeh M, Flegel J, Patil S, Shang E, Narayan R, Buchholzer M, Kazemein Jasemi NS, Grigalunas M, Krzyzanowski A, Abegg D, Shuster A, Potowski M, Karatas H, Karageorgis G, Mosaddeghzadeh N, Zischinsky M, Merten C, Golz C, Brieger L, Strohmann C, Antonchick AP, Janning P, Adibekian A, Goody RS, Ahmadian MR, Ziegler S, Waldmann H. The Pseudo‐Natural Product Rhonin Targets RHOGDI. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mohammad Akbarzadeh
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Jana Flegel
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Sumersing Patil
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Erchang Shang
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Rishikesh Narayan
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- School of Chemical and Materials Sciences IIT Goa, Farmagudi Ponda Goa-403401 India
| | - Marcel Buchholzer
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Michael Grigalunas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Marco Potowski
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Hacer Karatas
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - George Karageorgis
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | | | - Christian Merten
- Faculty of Chemistry and Biochemistry Organic Chemistry II Ruhr-University Bochum Universitätsstrasse 150 44780 Bochum Germany
| | - Christopher Golz
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Lucas Brieger
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Roger S. Goody
- Max Planck Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II Medical Faculty and University Hospital Düsseldorf Heinrich Heine University Düsseldorf Universitätsstrasse 1, Building 22.03.05 40225 Düsseldorf Germany
| | - Slava Ziegler
- 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 and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44221 Dortmund Germany
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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.
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Affiliation(s)
- Michael Grigalunas
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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45
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Davies C, Shaaban S, Waldmann H. Asymmetric catalysis with chiral cyclopentadienyl complexes to access privileged scaffolds. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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46
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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47
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Liu H, Panjikar S, Sheng X, Futamura Y, Zhang C, Shao N, Osada H, Zou H. β-Methyltryptamine Provoking the Crucial Role of Strictosidine Synthase Tyr151-OH for Its Stereoselective Pictet-Spengler Reactions to Tryptoline-type Alkaloids. ACS Chem Biol 2022; 17:187-197. [PMID: 34994203 DOI: 10.1021/acschembio.1c00844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strictosidine synthase (STR), the gate enzyme for monoterpenoid indole alkaloid biosynthesis, catalyzes the Pictet-Spengler reaction (PSR) of various tryptamine derivatives with secologanin assisted by "indole sandwich" stabilization. Continuous exploration with β-methyltryptamine (IPA) stereoselectively delivered the C6-methylstrictosidines and C6-methylvincosides by enzymatic and nonenzymatic PSR, respectively. Unexpectedly, the first "nonindole sandwich" binding mode was witnessed by the X-ray structures of STR1-ligand complexes. Site-directed mutagenesis revealed the critical cryptic role of the hydroxyl group of Tyr151 in IPA biotransformation. Further computational calculations demonstrated the adjustable IPA position in STR1 upon the binding of secologanin, and Tyr151-OH facilitates the productive PSR binding mode via an advantageous hydrogen-bond network. Further chemo-enzymatic manipulation of C6-methylvincosides successfully resulted in the discovered antimalarial framework (IC50 = 0.92 μM).
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Affiliation(s)
- Haicheng Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Santosh Panjikar
- Australia & Department of Molecular Biology and Biochemistry, Monash University, ANSTO, Australian Synchrotron, 800 Blackburn Road, Victoria 3168, Australia
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, & National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chenghua Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, & National Technology Innovation Center for Synthetic Biology, Tianjin 300308, China
- School of Basic Medical Sciences, North Sichuan Medical College, No. 55 Dongshun Road, Gaoping District, Nanchong 637000, China
| | - Nana Shao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hongbin Zou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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48
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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.
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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
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49
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Whitmarsh-Everiss T, Olsen AH, Laraia L. Identification of Inhibitors of Cholesterol Transport Proteins Through the Synthesis of a Diverse, Sterol-Inspired Compound Collection. Angew Chem Int Ed Engl 2021; 60:26755-26761. [PMID: 34626154 DOI: 10.1002/anie.202111639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/26/2022]
Abstract
Cholesterol transport proteins regulate a vast array of cellular processes including lipid metabolism, vesicular and non-vesicular trafficking, organelle contact sites, and autophagy. Despite their undoubted importance, the identification of selective modulators of this class of proteins has been challenging due to the structural similarities in the cholesterol-binding site. Herein we report a general strategy for the identification of selective inhibitors of cholesterol transport proteins via the synthesis of a diverse sterol-inspired compound collection. Fusion of a primary sterol fragment to an array of secondary privileged scaffolds led to the identification of potent and selective inhibitors of the cholesterol transport protein Aster-C, which displayed a surprising preference for the unnatural-sterol AB-ring stereochemistry and new inhibitors of Aster-A. We propose that this strategy can and should be applied to any therapeutically relevant sterol-binding protein.
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Affiliation(s)
- Thomas Whitmarsh-Everiss
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
| | - Asger Hegelund Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
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50
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Whitmarsh‐Everiss T, Olsen AH, Laraia L. Identification of Inhibitors of Cholesterol Transport Proteins Through the Synthesis of a Diverse, Sterol‐Inspired Compound Collection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111639] [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)
- Thomas Whitmarsh‐Everiss
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Asger Hegelund Olsen
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Luca Laraia
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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