1
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Wright BA, Sarpong R. Molecular complexity as a driving force for the advancement of organic synthesis. Nat Rev Chem 2024; 8:776-792. [PMID: 39251714 DOI: 10.1038/s41570-024-00645-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2024] [Indexed: 09/11/2024]
Abstract
The generation of molecular complexity is a primary goal in the field of synthetic chemistry. In the context of retrosynthetic analysis, the concept of molecular complexity is central to identifying productive disconnections and the development of efficient total syntheses. However, this field-defining concept is frequently invoked on an intuitive basis without precise definition or appreciation of its subtleties. Methods for quantifying molecular complexity could prove useful for characterizing the state of synthesis in a more rigorous, reliable and reproducible fashion. As a first step to evaluating the importance of these methods to the state of the field, here we present our perspective on the development of molecular complexity quantification and its implications for chemical synthesis. The extension and application of these methods beyond computer-aided synthesis planning and medicinal chemistry to the traditional practice of 'complex molecule' synthesis could have the potential to unearth new opportunities and more efficient approaches for synthesis.
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Affiliation(s)
- Brandon A Wright
- Department of Chemistry, University of California, Berkeley, USA
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, USA.
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2
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Jaiswal MK, Tiwari VK. Growing Impact of Intramolecular Click Chemistry in Organic Synthesis. CHEM REC 2023; 23:e202300167. [PMID: 37522634 DOI: 10.1002/tcr.202300167] [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: 05/06/2023] [Revised: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Click Chemistry, a modular, rapid, and one of the most reliable tool for the regioselective 1,2,3-triazole forming [3+2] reaction of organic azide and terimal alkyne is widely explored in various emerging domains of research ranging from chemical biology to catalysis and medicinal chemistry to material science. This regioselective reaction from a diverse range of azido-alkyne scaffolds has been well performed in both intermolecular as well as intramolecular fashions. In comparison to the intermolecular metal (Cu/Ru/Ni) variant of 'Click Chemistry', the intramolecular click tool is little addressed. The intramolecular click chemistry is exemplified as a mordern tool of cyclization which involves metal-catalyzed (CuAAC/RuAAC) cyclization, organo-catalyzed cyclization, and thermal-induced topochemical reaction. Thus, we report herein the recent approaches on intramolecular azide-alkyne cycloaddition 'Click Chemistry' with their wide-spread emerging applications in the developement of a diverse range of molecules including fused-heterocycles, well-defined peptidomemics, and macrocyclic architectures of various notable features.
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Affiliation(s)
- Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
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3
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:4930. [PMID: 37582753 PMCID: PMC10427684 DOI: 10.1038/s41467-023-40575-5] [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: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
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Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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4
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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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5
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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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6
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Multicomponent coupling and macrocyclization enabled by Rh(III)-catalyzed dual C–H activation: Macrocyclic oxime inhibitor of influenza H1N1. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Uguen M, Davison G, Sprenger LJ, Hunter JH, Martin MP, Turberville S, Watt JE, Golding BT, Noble MEM, Stewart HL, Waring MJ. Build-Couple-Transform: A Paradigm for Lead-like Library Synthesis with Scaffold Diversity. J Med Chem 2022; 65:11322-11339. [PMID: 35943172 PMCID: PMC9421646 DOI: 10.1021/acs.jmedchem.2c00897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-throughput screening provides one of the most common ways of finding hit compounds. Lead-like libraries, in particular, provide hits with compatible functional groups and vectors for structural elaboration and physical properties suitable for optimization. Library synthesis approaches can lead to a lack of chemical diversity because they employ parallel derivatization of common building blocks using single reaction types. We address this problem through a "build-couple-transform" paradigm for the generation of lead-like libraries with scaffold diversity. Nineteen transformations of a 4-oxo-2-butenamide scaffold template were optimized, including 1,4-cyclizations, 3,4-cyclizations, reductions, and 1,4-additions. A pool-transformation approach efficiently explored the scope of these transformations for nine different building blocks and synthesized a >170-member library with enhanced chemical space coverage and favorable drug-like properties. Screening revealed hits against CDK2. This work establishes the build-couple-transform concept for the synthesis of lead-like libraries and provides a differentiated approach to libraries with significantly enhanced scaffold diversity.
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Affiliation(s)
- Mélanie Uguen
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Gemma Davison
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Lukas J Sprenger
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Mathew P Martin
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Shannon Turberville
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Jessica E Watt
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Bernard T Golding
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Martin E M Noble
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Hannah L Stewart
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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8
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Lenci E, Trabocchi A. Diversity‐Oriented Synthesis and Chemoinformatics: A Fruitful Synergy towards Better Chemical Libraries. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200575] [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)
- Elena Lenci
- Universita degli Studi di Firenze Department of Chemistry Via della Lastruccia 1350019Italia 50019 Sesto Fiorentino ITALY
| | - Andrea Trabocchi
- University of Florence: Universita degli Studi di Firenze Department of Chemistry "Ugo Schiff" ITALY
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9
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Charitou V, van Keulen SC, Bonvin AMJJ. Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4. J Chem Theory Comput 2022; 18:4027-4040. [PMID: 35652781 PMCID: PMC9202357 DOI: 10.1021/acs.jctc.2c00075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclization and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to the critical assessment of prediction of interaction criteria for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top 10) both in the bound and unbound docking scenarios. Moreover, its performance in both bound and fully unbound docking is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclization and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.
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Affiliation(s)
- Vicky Charitou
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Siri C van Keulen
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science─Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
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10
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Recent Advances in Divergent Synthetic Strategies for Indole-Based Natural Product Libraries. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072171. [PMID: 35408569 PMCID: PMC9000743 DOI: 10.3390/molecules27072171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/26/2023]
Abstract
Considering the potential bioactivities of natural product and natural product-like compounds with highly complex and diverse structures, the screening of collections and small-molecule libraries for high-throughput screening (HTS) and high-content screening (HCS) has emerged as a powerful tool in the development of novel therapeutic agents. Herein, we review the recent advances in divergent synthetic approaches such as complexity-to-diversity (Ctd) and biomimetic strategies for the generation of structurally complex and diverse indole-based natural product and natural product-like small-molecule libraries.
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11
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Comprehensive exploration of chemical space using trisubstituted carboranes. Sci Rep 2021; 11:24101. [PMID: 34916538 PMCID: PMC8677773 DOI: 10.1038/s41598-021-03459-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
A total of 42 trisubstituted carboranes categorised into five scaffolds were systematically designed and synthesized by exploiting the different reactivities of the twelve vertices of o-, m-, and p-carboranes to cover all directions in chemical space. Significant inhibitors of hypoxia inducible factor transcriptional activitay were mainly observed among scaffold V compounds (e.g., Vi–m, and Vo), whereas anti-rabies virus activity was observed among scaffold V (Va–h), scaffold II (IIb–g), and scaffold IV (IVb) compounds. The pharmacophore model predicted from compounds with scaffold V, which exhibited significant anti-rabies virus activity, agreed well with compounds IIb–g with scaffold II and compound IVb with scaffold IV. Normalized principal moment of inertia analysis indicated that carboranes with scaffolds I–V cover all regions in the chemical space. Furthermore, the first compounds shown to stimulate the proliferation of the rabies virus were found among scaffold V carboranes.
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12
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Fumagalli G, Carbajo RJ, Nissink JWM, Tart J, Dou R, Thomas AP, Spring DR. Targeting a Novel KRAS Binding Site: Application of One-Component Stapling of Small (5-6-mer) Peptides. J Med Chem 2021; 64:17287-17303. [PMID: 34787423 DOI: 10.1021/acs.jmedchem.1c01334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RAS proteins are central in the proliferation of many types of cancer, but a general approach toward the identification of pan-mutant RAS inhibitors has remained unresolved. In this work, we describe the application of a binding pharmacophore identified from analysis of known RAS binding peptides to the design of novel peptides. Using a chemically divergent approach, we generated a library of small stapled peptides from which we identified compounds with weak binding activity. Exploration of structure-activity relationships (SARs) and optimization of these early compounds led to low-micromolar binders of KRAS that block nucleotide exchange.
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Affiliation(s)
- Gabriele Fumagalli
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K.,Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Jonathan Tart
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Rongxuan Dou
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Andrew P Thomas
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - David R Spring
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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13
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Xu W, Brown LE, Porco JA. Divergent, C-C Bond Forming Macrocyclizations Using Modular Sulfonylhydrazone and Derived Substrates. J Org Chem 2021; 86:16485-16510. [PMID: 34730970 PMCID: PMC8783553 DOI: 10.1021/acs.joc.1c01848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A divergent approach to C-C bond forming macrocycle construction is described. Modular sulfonylhydrazone and derived pyridotriazole substrates with three key building blocks have been constructed and cyclized to afford diverse macrocyclic frameworks. Broad substrate scope and functional group tolerance have been demonstrated. In addition, site-selective postfunctionalization allowed for further diversification of macrocyclic cores.
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Affiliation(s)
- Wenqing Xu
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - Lauren E. Brown
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
| | - John A. Porco
- Department of Chemistry, Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States
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14
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Bhuyan S, Das D, Chakraborty A, Mandal S, Dhanabal K, Roy BG. A Carbohydrate-based Synthetic Approach to Diverse Structurally and Stereochemically Complex Chiral Polyheterocycles. Chem Asian J 2021; 16:4108-4121. [PMID: 34706155 DOI: 10.1002/asia.202101123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 10/22/2021] [Indexed: 12/27/2022]
Abstract
Chiral polyheterocycles are one of the most frequently encountered scaffolds in natural products and in current drugs repertoire. A carbohydrate-based diversity oriented synthetic (DOS) approach has been employed for gaining access to many structurally diverse and stereochemically complex rigid polyheterocyclic molecules with multiple chiral hydroxyl groups to enhance aqueous solubility. Inexpensive chiral pool of D-Glucose has been judiciously exploited to get access of complex chiral polyheterocyclic structures using inexpensive, common achiral reagents and domino-Knoevenagel hetero-Diels-Alder (DKHDA) reaction as one of the key synthetic tools. Stereochemistry of newly generated stereocenters of polycyclic structures are unambiguously determined through NMR and X-ray crystallographic study. A chemoinformatic comparison (PCA and PMI) with 40 branded blockbuster drugs showed that newly generated polyheterocycles have good three-dimensional scaffold diversity and most of these pass the Lipinski filter of drug-likeness.
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Affiliation(s)
- Samuzal Bhuyan
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Dharmendra Das
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Amit Chakraborty
- Department of Mathematics, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Susanta Mandal
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | | | - Biswajit Gopal Roy
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
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15
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Shang FF, Wang MY, Ai JP, Shen QK, Guo HY, Jin CM, Chen FE, Quan ZS, Jin L, Zhang C. Synthesis and evaluation of mycophenolic acid derivatives as potential anti-Toxoplasma gondii agents. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02803-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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16
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products-Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021; 60:15705-15723. [PMID: 33644925 PMCID: PMC8360037 DOI: 10.1002/anie.202016575] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Indexed: 01/05/2023]
Abstract
Pseudo-natural products (PNPs) combine natural product (NP) fragments in novel arrangements not accessible by current biosynthesis pathways. As such they can be regarded as non-biogenic fusions of NP-derived fragments. They inherit key biological characteristics of the guiding natural product, such as chemical and physiological properties, yet define small molecule chemotypes with unprecedented or unexpected bioactivity. We iterate the design principles underpinning PNP scaffolds and highlight their syntheses and biological investigations. We provide a cheminformatic analysis of PNP collections assessing their molecular properties and shape diversity. We propose and discuss how the iterative analysis of NP structure, design, synthesis, and biological evaluation of PNPs can be regarded as a human-driven branch of the evolution of natural products, that is, a chemical evolution of natural product structure.
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Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyPrivate Bag 4800Christchurch8140New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of Denmark, kemitorvet 2072800 Kgs.LyngbyDenmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
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17
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Kharchenko SH, Iampolska AD, Radchenko DS, Vashchenko BV, Voitenko ZV, Grygorenko OO. A Diversity‐Oriented Approach to Large Libraries of Artificial Macrocycles. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Anna D. Iampolska
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Zoia V. Voitenko
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd. Chervonotkatska Street 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
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18
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products—Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016575] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: School of Physical and Chemical Sciences University of Canterbury Private Bag 4800 Christchurch 8140 New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: Department of Chemistry Technical University of Denmark, kemitorvet 207 2800 Kgs. Lyngby Denmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
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19
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Marine furanocembranoids-inspired macrocycles enabled by Pd-catalyzed unactivated C(sp 3)-H olefination mediated by donor/donor carbenes. Nat Commun 2021; 12:1304. [PMID: 33637703 PMCID: PMC7910576 DOI: 10.1038/s41467-021-21484-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/26/2021] [Indexed: 02/08/2023] Open
Abstract
Biomimetic modularization and function-oriented synthesis of structurally diversified natural product-like macrocycles in a step-economical fashion is highly desirable. Inspired by marine furanocembranoids, herein, we synthesize diverse alkenes substituted furan-embedded macrolactams via a modular biomimetic assembly strategy. The success of this assembly is the development of crucial Pd-catalyzed carbene coupling between ene-yne-ketones as donor/donor carbene precursors and unactivated Csp3‒H bonds which represents a great challenge in organic synthesis. Notably, this method not only obviates the use of unstable, explosive, and toxic diazo compounds, but also can be amenable to allenyl ketones carbene precursors. DFT calculations demonstrate that a formal 1,4-Pd shift could be involved in the mechanism. Moreover, the collected furanocembranoids-like macrolactams show significant anti-inflammatory activities against TNF-α, IL-6, and IL-1β and the cytotoxicity is comparable to Dexamethasone. Furanocembranoid-like natural products with the alkene-substituted furan scaffold display a range of biological activities, but are difficult to access. Here, the authors report a modular biomimetic strategy to synthesise diverse alkene-substituted furan-containing macrolactams via palladium-catalysed unactivated Csp3-H olefination.
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20
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Sun T, He S, Xu Z, Zuo J, Yu Y, Yang W. Rh-Catalyzed C-H alkylation enabling modular synthesis of CF 3-substituted benzannulated macrocyclic inhibitors of B cell responses. Org Biomol Chem 2021; 19:3589-3594. [PMID: 33908550 DOI: 10.1039/d1ob00296a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inspired by aspirin and chalcone, herein, we describe a modular biomimetic strategy to achieve a new class of CF3-bearing benzannulated macrolactams. The key to the success of macrolactams was the utilization of a highly chemoselective Rh(iii)-catalyzed native carboxylic acid-directed C-H alkylation. Moreover, the unique CF3-containing benzannulated macrocycles showed decent immunosuppressive effects on B cells in vitro, including proliferation, activation, and antibody production upon specific stimulation implicating TLR and BCR signaling.
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Affiliation(s)
- Tao Sun
- Center for Supramolecular Chemistry and Catalysis and Department of Chemistry, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| | - Shijun He
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongliang Xu
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China.
| | - Jianping Zuo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Center for Supramolecular Chemistry and Catalysis and Department of Chemistry, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| | - Weibo Yang
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China. and University of Chinese Academy of Sciences, Beijing 100049, China and School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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21
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Jayarajan R, Kottha T, Subbaramanian S, Vasuki G. Base Promoted Cascade Reaction: A Convenient Route to Hybrid S and N Polyheterocycles. ChemistrySelect 2020. [DOI: 10.1002/slct.202003412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ramasamy Jayarajan
- Department of Chemistry Pondicherry University Puducherry 605014 India
- Presently at Department of Organic Chemistry Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Sweden
| | | | - Sabarinathan Subbaramanian
- Department of Chemistry Pondicherry University Puducherry 605014 India
- Department of Chemistry Faculty of Engineering and Technology SRM Institute of Science and Technology, Vadapalani Campus, No. 1 Jawaharlal Nehru Road, Vadapalani TN India
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22
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Utaka Y, Kashiwazaki G, Tsuchida N, Fukushima M, Takahashi I, Kawai Y, Kitayama T. Remarkable Potential of Zerumbone to Generate a Library with Six Natural Product-like Skeletons by Natural Material-Related Diversity-Oriented Synthesis. J Org Chem 2020; 85:8371-8386. [PMID: 32524816 DOI: 10.1021/acs.joc.0c00689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diversity-oriented synthesis (DOS) is an effective strategy for the quick creation of diverse and high three-dimensional compounds from simple starting materials. The selection of a starting material is the key to constructing useful, chemically diverse compound libraries for the development of new drugs. Here, we report a novel, general, and facile strategy for the creation of diverse compounds with high structural diversity from readily available natural products, such as zerumbone, as the synthetic starting material. Zerumbone is the major component of the essential oil from wild ginger, Zingiber zerumbet Smith. It is noteworthy that zerumbone has a powerful latent reactivity, partly because of its three double bonds, two conjugated and one isolated, and a double conjugated carbonyl group in an 11-membered ring structure. In fact, zerumbone has been shown to be a successful example of natural material-related DOS (NMRDOS). We will report that zerumbone can be converted in one chemical step from four zerumbone derivatives into rare and markedly different scaffolds by transannulation.
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Affiliation(s)
- Yoshimi Utaka
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Gengo Kashiwazaki
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Noriko Tsuchida
- Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Miyuki Fukushima
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Issei Takahashi
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Yasushi Kawai
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Takashi Kitayama
- Major in Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
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23
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Yao Z, Cai Z, Zhen L, Jiang L. Cobalt-Catalyzed Switchable Intramolecular Thioenolization/C-H Thiolation and C(sp 2)-H/C(sp 3)-H Dehydrogenative Coupling. Org Lett 2020; 22:4505-4510. [PMID: 32459500 DOI: 10.1021/acs.orglett.0c01514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mild cobalt-catalyzed switchable regioselective and chemoselective thioenolization/C-H thiolation and C(sp2)-H/C(sp3)-H dehydrogenative couplings of N-aryl-N-alkyl-thioamides are developed, providing 2-methylene-2,3-dihydrobenzo[d]thiazoles and thio-oxindoles in moderate to excellent yields from the same precursors, respectively. Details mechanistic studies suggest that the thioenolization/C-H thiolation process involves a radical mechanism, whereas the C(sp2)-H/C(sp3)-H dehydrogenative coupling might proceed through an electrophilic cobaltation(III) pathway. Thus, the selectivity for either product is achieved by accessing unique catalytic cycles involving different valence states for cobalt.
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Affiliation(s)
- Zhi Yao
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhongliang Cai
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Long Zhen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Liqin Jiang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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24
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Gagnon C, Godin É, Minozzi C, Sosoe J, Pochet C, Collins SK. Biocatalytic synthesis of planar chiral macrocycles. Science 2020; 367:917-921. [DOI: 10.1126/science.aaz7381] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/21/2020] [Indexed: 12/25/2022]
Abstract
Macrocycles can restrict the rotation of substituents through steric repulsions, locking in conformations that provide or enhance the activities of pharmaceuticals, agrochemicals, aroma chemicals, and materials. In many cases, the arrangement of substituents in the macrocycle imparts an element of planar chirality. The difficulty in predicting when planar chirality will arise, as well as the limited number of synthetic methods to impart selectivity, have led to planar chirality being regarded as an irritant. We report a strategy for enantio- and atroposelective biocatalytic synthesis of planar chiral macrocycles. The macrocycles can be formed with high enantioselectivity from simple building blocks and are decorated with functionality that allows one to further modify the macrocycles with diverse structural features.
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Affiliation(s)
- Christina Gagnon
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Éric Godin
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Clémentine Minozzi
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Johann Sosoe
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Corentin Pochet
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
| | - Shawn K. Collins
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, CP 6128 Station Downtown, Montréal, Québec H3C 3J7, Canada
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25
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Conformational analysis of macrocycles: comparing general and specialized methods. J Comput Aided Mol Des 2020; 34:231-252. [PMID: 31965404 PMCID: PMC7036058 DOI: 10.1007/s10822-020-00277-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/03/2020] [Indexed: 11/24/2022]
Abstract
Abstract Macrocycles represent an important class of medicinally relevant small molecules due to their interesting biological properties. Therefore, a firm understanding of their conformational preferences is important for drug design. Given the importance of macrocycle-protein modelling in drug discovery, we envisaged that a systematic study of both classical and recent specialized methods would provide guidance for other practitioners within the field. In this study we compare the performance of the general, well established conformational analysis methods Monte Carlo Multiple Minimum (MCMM) and Mixed Torsional/Low-Mode sampling (MTLMOD) with two more recent and specialized macrocycle sampling techniques: MacroModel macrocycle Baseline Search (MD/LLMOD) and Prime macrocycle conformational sampling (PRIME-MCS). Using macrocycles extracted from 44 macrocycle-protein X-ray crystallography complexes, we evaluated each method based on their ability to (i) generate unique conformers, (ii) generate unique macrocycle ring conformations, (iii) identify the global energy minimum, (iv) identify conformers similar to the X-ray ligand conformation after Protein Preparation Wizard treatment (X-rayppw), and (v) to the X-rayppw ring conformation. Computational speed was also considered. In addition, conformational coverage, as defined by the number of conformations identified, was studied. In order to study the relative energies of the bioactive conformations, the energy differences between the global energy minima and the energy minimized X-rayppw structures and, the global energy minima and the MCMM-Exhaustive (1,000,000 search steps) generated conformers closest to the X-rayppw structure, were calculated and analysed. All searches were performed using relatively short run times (10,000 steps for MCMM, MTLMOD and MD/LLMOD). To assess the performance of the methods, they were compared to an exhaustive MCMM search using 1,000,000 search steps for each of the 44 macrocycles (requiring ca 200 times more CPU time). Prior to our analysis, we also investigated if the general search methods MCMM and MTLMOD could also be optimized for macrocycle conformational sampling. Taken together, our work concludes that the more general methods can be optimized for macrocycle modelling by slightly adjusting the settings around the ring closure bond. In most cases, MCMM and MTLMOD with either standard or enhanced settings performed well in comparison to the more specialized macrocycle sampling methods MD/LLMOD and PRIME-MCS. When using enhanced settings for MCMM and MTLMOD, the X-rayppw conformation was regenerated with the greatest accuracy. The, MD/LLMOD emerged as the most efficient method for generating the global energy minima. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10822-020-00277-2) contains supplementary material, which is available to authorized users.
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26
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Song R, Yu H, Huang H, Chen Y. Controlled One‐Pot Synthesis of Multiple Heterocyclic Scaffolds Based on an Amphiphilic Claisen‐Schmidt Reaction Intermediate. ChemistrySelect 2019. [DOI: 10.1002/slct.201904110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rong Song
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan University, Changsha Hunan 410082 China
| | - Hui Yu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan University, Changsha Hunan 410082 China
| | - Haowen Huang
- Key Laboratory of Theoretical Organic Chemistry and Function MoleculeMinistry of Education, School of Chemistry and Chemical EngineeringHunan University of Science and Technology Xiangtan 411201 China
| | - Yun Chen
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Chemistry and Chemical EngineeringHunan University, Changsha Hunan 410082 China
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27
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Potowski M, Losch F, Wünnemann E, Dahmen JK, Chines S, Brunschweiger A. Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions. Chem Sci 2019; 10:10481-10492. [PMID: 32055372 PMCID: PMC7003951 DOI: 10.1039/c9sc04708e] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022] Open
Abstract
DNA-encoded compound libraries are widely used in drug discovery. Screening of catalysts for compatibility with solid phase-coupled DNA sequences guided the selection of encoded reactions, exemplified by a Zn(II)-mediated aza-Diels–Alder reaction.
DNA-encoded compound libraries are a widely used technology for target-based small molecule screening. Generally, these libraries are synthesized by solution phase combinatorial chemistry requiring aqueous solvent mixtures and reactions that are orthogonal to DNA reactivity. Initiating library synthesis with readily available controlled pore glass-coupled DNA barcodes benefits from enhanced DNA stability due to nucleobase protection and choice of dry organic solvents for encoded compound synthesis. We screened the compatibility of solid-phase coupled DNA sequences with 53 metal salts and organic reagents. This screening experiment suggests design of encoded library synthesis. Here, we show the reaction optimization and scope of three sp3-bond containing heterocyclic scaffolds synthesized on controlled pore glass-connected DNA sequences. A ZnCl2-promoted aza-Diels–Alder reaction with Danishefsky's diene furnished diverse substituted DNA-tagged pyridones, and a phosphoric acid organocatalyst allowed for synthesis of tetrahydroquinolines by the Povarov reaction and pyrimidinones by the Biginelli reaction, respectively. These three reactions caused low levels of DNA depurination and cover broad and only partially overlapping chemical space though using one set of DNA-coupled starting materials.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Elena Wünnemann
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Janina K Dahmen
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Silvia Chines
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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28
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Grygorenko OO, Volochnyuk DM, Ryabukhin SV, Judd DB. The Symbiotic Relationship Between Drug Discovery and Organic Chemistry. Chemistry 2019; 26:1196-1237. [PMID: 31429510 DOI: 10.1002/chem.201903232] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Indexed: 12/20/2022]
Abstract
All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.
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Affiliation(s)
- Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kiev, 02660, Ukraine
| | - Sergey V Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Duncan B Judd
- Awridian Ltd., Stevenage Bioscience Catalyst, Gunnelswood Road, Stevenage, Herts, SG1 2FX, UK
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29
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A general strategy for diversifying complex natural products to polycyclic scaffolds with medium-sized rings. Nat Commun 2019; 10:4015. [PMID: 31488839 PMCID: PMC6728360 DOI: 10.1038/s41467-019-11976-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/15/2019] [Indexed: 01/12/2023] Open
Abstract
The interrogation of complex biological pathways demands diverse small molecule tool compounds, which can often lead to important therapeutics for the treatment of human diseases. Since natural products are the most valuable source for the discovery of therapeutics, the derivatization of natural products has been extensively investigated to generate molecules for biological screenings. However, most previous approaches only modified a limited number of functional groups, which resulted in a limited number of skeleta. Here we show a general strategy for the preparation of a library of complex small molecules by combining state-of-the-art chemistry – the site-selective oxidation of C-H bonds - with reactions that expand rigid, small rings in polycyclic steroids to medium-sized rings. This library occupies a unique chemical space compared to selected diverse reference compounds. The diversification strategy developed herein for steroids can also be expanded to other types of natural products. Derivatization of natural products is a powerful approach to generate new molecules for biological screenings. Here, the authors employ C-H oxidation and ring expansion methods for the preparation of a library of medium-sized ring skeleta, which occupy a unique chemical space based on chemoinformatic analysis.
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30
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Gaiser BI, Danielsen M, Marcher-Rørsted E, Røpke Jørgensen K, Wróbel TM, Frykman M, Johansson H, Bräuner-Osborne H, Gloriam DE, Mathiesen JM, Sejer Pedersen D. Probing the Existence of a Metastable Binding Site at the β 2-Adrenergic Receptor with Homobivalent Bitopic Ligands. J Med Chem 2019; 62:7806-7839. [PMID: 31298548 DOI: 10.1021/acs.jmedchem.9b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Herein, we report the development of bitopic ligands aimed at targeting the orthosteric binding site (OBS) and a metastable binding site (MBS) within the same receptor unit. Previous molecular dynamics studies on ligand binding to the β2-adrenergic receptor (β2AR) suggested that ligands pause at transient, less-conserved MBSs. We envisioned that MBSs can be regarded as allosteric binding sites and targeted by homobivalent bitopic ligands linking two identical pharmacophores. Such ligands were designed based on docking of the antagonist (S)-alprenolol into the OBS and an MBS and synthesized. Pharmacological characterization revealed ligands with similar potency and affinity, slightly increased β2/β1AR-selectivity, and/or substantially slower β2AR off-rates compared to (S)-alprenolol. Truncated bitopic ligands suggested the major contribution of the metastable pharmacophore to be a hydrophobic interaction with the β2AR, while the linkers alone decreased the potency of the orthosteric fragment. Altogether, the study underlines the potential of targeting MBSs for improving the pharmacological profiles of ligands.
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Affiliation(s)
- Birgit I Gaiser
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Emil Marcher-Rørsted
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Kira Røpke Jørgensen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Tomasz M Wróbel
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark.,Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy , Medical University of Lublin , 4A Chodźki 20093 Lublin , Poland
| | - Mikael Frykman
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Henrik Johansson
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
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31
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Li Y, Huang JH, Wang JL, Song GT, Tang DY, Yao F, Lin HK, Yan W, Li HY, Xu ZG, Chen ZZ. Diversity-Oriented Synthesis of Imidazo-Dipyridines with Anticancer Activity via the Groebke–Blackburn–Bienaymé and TBAB-Mediated Cascade Reaction in One Pot. J Org Chem 2019; 84:12632-12638. [DOI: 10.1021/acs.joc.9b01385] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yong Li
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Jiu-Hong Huang
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Juan-Li Wang
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Gui-Ting Song
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Dian-Yong Tang
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Fang Yao
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Hui-kuan Lin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Hong-yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Zhi-Gang Xu
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
| | - Zhong-Zhu Chen
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, 319 Honghe Avenue, Yongchuan, Chongqing 402160, China
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32
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Shen QK, Deng H, Wang SB, Tian YS, Quan ZS. Synthesis, and evaluation of in vitro and in vivo anticancer activity of 14-substituted oridonin analogs: A novel and potent cell cycle arrest and apoptosis inducer through the p53-MDM2 pathway. Eur J Med Chem 2019; 173:15-31. [DOI: 10.1016/j.ejmech.2019.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
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33
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Mortensen KT, Osberger TJ, King TA, Sore HF, Spring DR. Strategies for the Diversity-Oriented Synthesis of Macrocycles. Chem Rev 2019; 119:10288-10317. [DOI: 10.1021/acs.chemrev.9b00084] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kim T. Mortensen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas J. Osberger
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Thomas A. King
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Hannah F. Sore
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - David R. Spring
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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34
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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35
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Li B, Li X, Han B, Chen Z, Zhang X, He G, Chen G. Construction of Natural-Product-Like Cyclophane-Braced Peptide Macrocycles via sp3 C–H Arylation. J Am Chem Soc 2019; 141:9401-9407. [DOI: 10.1021/jacs.9b04221] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xinghua Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Boyang Han
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhijie Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuekai Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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36
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Lee H, Sylvester K, Derbyshire ER, Hong J. Synthesis and Analysis of Natural-Product-Like Macrocycles by Tandem Oxidation/Oxa-Conjugate Addition Reactions. Chemistry 2019; 25:6500-6504. [PMID: 30912197 DOI: 10.1002/chem.201900620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/18/2019] [Indexed: 11/06/2022]
Abstract
As traditional small-molecule drug discovery programs focus on a relatively narrow range of chemical space, most human proteins are viewed as unreachable targets. Consequently, there is a strong interest in expanding the chemical space in drug discovery beyond traditional small molecules. Here, a strategy for the preparation of a broad natural-product-like macrocyclic library by using the tandem allylic oxidation/oxa-conjugate addition and macrocyclization reactions is reported. Cheminformatic analyses demonstrate that this tetrahydropyran-containing macrocyclic library shows a significant overlap with natural products in the chemical space. This approach can be used for designing libraries that may probe more deeply into natural-product-like space.
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Affiliation(s)
- Hyunji Lee
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Kayla Sylvester
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
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37
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Leonardi M, Estévez V, Villacampa M, Menéndez JC. Diversity‐Oriented Synthesis of Complex Pyrrole‐Based Architectures from Very Simple Starting Materials. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Leonardi
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas. Facultad de FarmaciaUniversidad Complutense 28040 Madrid Spain
| | - Verónica Estévez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas. Facultad de FarmaciaUniversidad Complutense 28040 Madrid Spain
| | - Mercedes Villacampa
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas. Facultad de FarmaciaUniversidad Complutense 28040 Madrid Spain
| | - J. Carlos Menéndez
- Unidad de Química Orgánica y Farmacéutica, Departamento de Química en Ciencias Farmacéuticas. Facultad de FarmaciaUniversidad Complutense 28040 Madrid Spain
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38
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Gomes RFA, Coelho JAS, Afonso CAM. Direct Conversion of Activated 5-Hydroxymethylfurfural into δ-Lactone-Fused Cyclopentenones. CHEMSUSCHEM 2019; 12:420-425. [PMID: 30512226 DOI: 10.1002/cssc.201802537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Valorization of biomass derived feedstock (e.g., 5-hydroxymethylfurfural platform) is a very active field of chemical research. In this study, 5-hydroxymethylfurfural is converted into cyclopenten-2-ones by virtue of furfural's activation and Meldrum's acid's tendency to undergo decomposition/esterification. Experimental and computational studies suggest a domino rearrangement-lactonization reaction involving BINOL-catalyzed lactonization as the rate-determining step. The novel lactone-fused cyclopenten-2-ones, which bear a quaternary carbon and resemble a didemnenone natural product structure, are converted into several derivatives with potential interest for the fields of synthetic and medicinal chemistry.
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Affiliation(s)
- Rafael F A Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Jaime A S Coelho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Carlos A M Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
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39
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Yi S, Varun BV, Choi Y, Park SB. A Brief Overview of Two Major Strategies in Diversity-Oriented Synthesis: Build/Couple/Pair and Ring-Distortion. Front Chem 2018; 6:507. [PMID: 30406085 PMCID: PMC6204370 DOI: 10.3389/fchem.2018.00507] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
In the interdisciplinary research field of chemical biology and drug discovery, diversity-oriented synthesis (DOS) has become indispensable in the construction of novel small-molecule libraries rich in skeletal and stereochemical diversity. DOS aims to populate the unexplored chemical space with new potential bioactive molecules via forward synthetic analysis. Since the introduction of this concept by Schreiber, DOS has evolved along with many significant breakthroughs. It is therefore important to understand the key DOS strategies to build molecular diversity with maximized biological relevancy. Due to the length limitations of this mini review, we briefly discuss the recent DOS plans using build/couple/pair (B/C/P) and ring-distortion strategies for the synthesis of major biologically relevant target molecules like natural products and their related compounds, macrocycles, and privileged structures.
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Affiliation(s)
- Sihyeong Yi
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Begur Vasanthkumar Varun
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Yoona Choi
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Seung Bum Park
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
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40
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Kidd SL, Osberger TJ, Mateu N, Sore HF, Spring DR. Recent Applications of Diversity-Oriented Synthesis Toward Novel, 3-Dimensional Fragment Collections. Front Chem 2018; 6:460. [PMID: 30386766 PMCID: PMC6198038 DOI: 10.3389/fchem.2018.00460] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established approach for the discovery of novel medicines, illustrated by the approval of two FBBD-derived drugs. This methodology is based on the utilization of small "fragment" molecules (<300 Da) as starting points for drug discovery and optimization. Organic synthesis has been identified as a significant obstacle in FBDD, however, in particular owing to the lack of novel 3-dimensional (3D) fragment collections that feature useful synthetic vectors for modification of hit compounds. Diversity-oriented synthesis (DOS) is a synthetic strategy that aims to efficiently produce compound collections with high levels of structural diversity and three-dimensionality and is therefore well-suited for the construction of novel fragment collections. This Mini-Review highlights recent studies at the intersection of DOS and FBDD aiming to produce novel libraries of diverse, polycyclic, fragment-like compounds, and their application in fragment-based screening projects.
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Affiliation(s)
| | | | | | | | - David R. Spring
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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41
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Jackson P, Lapinsky DJ. Appendage and Scaffold Diverse Fully Functionalized Small-Molecule Probes via a Minimalist Terminal Alkyne-Aliphatic Diazirine Isocyanide. J Org Chem 2018; 83:11245-11253. [DOI: 10.1021/acs.joc.8b01831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Jackson
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - David J. Lapinsky
- Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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42
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43
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David R. Spring. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201800487] [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]
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44
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Silica-bonded DABCO hydrogen sulfate ((SB-DABCO)HSO4): a new dual-interphase catalyst for the diversity-oriented pseudo-five-component synthesis of bis(pyrazolyl)methanes and novel 4-[bis(pyrazolyl)methane]phenylmethylene-bis(indole)s. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2018. [DOI: 10.1007/s13738-018-1424-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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45
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A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C−H arylation. Nat Chem 2018; 10:540-548. [DOI: 10.1038/s41557-018-0006-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 12/06/2017] [Indexed: 11/08/2022]
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46
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Curtin BH, Manoni F, Park J, Sisto LJ, Lam YH, Gravel M, Roulston A, Harran PG. Assembly of Complex Macrocycles by Incrementally Amalgamating Unprotected Peptides with a Designed Four-Armed Insert. J Org Chem 2018; 83:3090-3108. [DOI: 10.1021/acs.joc.7b02958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brice H. Curtin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Francesco Manoni
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Jiyong Park
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Luke J. Sisto
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yu-hong Lam
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michel Gravel
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Anne Roulston
- Laboratory for Therapeutic Development, Rosalind and Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Patrick G. Harran
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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47
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Vonnegut CL, Shonkwiler AM, Zakharov LN, Haley MM, Johnson DW. Harnessing solid-state packing for selective detection of chloride in a macrocyclic anionophore. Chem Commun (Camb) 2018; 52:9506-9. [PMID: 27375117 DOI: 10.1039/c6cc03795j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the synthesis of an inherently fluorescent macrocyclic receptor for chloride. The use of a disulphide tether provides for an excellent yield in the macrocyclization step. This compound binds chloride in the solution and solid state, and while unstable over time in aqueous solution, shows a selective response toward chloride over other anions in the solid state due to intermolecular interactions between fluorophore backbones. Surprisingly, the optoelectronic response to anions differs in solution and the films, with a distinct colorimetric response observed only in the film.
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Affiliation(s)
- Chris L Vonnegut
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA.
| | - Airlia M Shonkwiler
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA.
| | - Lev N Zakharov
- CAMCOR, University of Oregon, 1443 East 13th Ave., Eugene, Oregon 97403, USA
| | - Michael M Haley
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA.
| | - Darren W Johnson
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA.
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48
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Lauder K, Toscani A, Scalacci N, Castagnolo D. Synthesis and Reactivity of Propargylamines in Organic Chemistry. Chem Rev 2017; 117:14091-14200. [PMID: 29166000 DOI: 10.1021/acs.chemrev.7b00343] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Propargylamines are a versatile class of compounds which find broad application in many fields of chemistry. This review aims to describe the different strategies developed so far for the synthesis of propargylamines and their derivatives as well as to highlight their reactivity and use as building blocks in the synthesis of chemically relevant organic compounds. In the first part of the review, the different synthetic approaches to synthesize propargylamines, such as A3 couplings and C-H functionalization of alkynes, have been described and organized on the basis of the catalysts employed in the syntheses. Both racemic and enantioselective approaches have been reported. In the second part, an overview of the transformations of propargylamines into heterocyclic compounds such as pyrroles, pyridines, thiazoles, and oxazoles, as well as other relevant organic derivatives, is presented.
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Affiliation(s)
- Kate Lauder
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Anita Toscani
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Nicolò Scalacci
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical Sciences, King's College London , Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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49
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Visini R, Arús-Pous J, Awale M, Reymond JL. Virtual Exploration of the Ring Systems Chemical Universe. J Chem Inf Model 2017; 57:2707-2718. [PMID: 29019686 DOI: 10.1021/acs.jcim.7b00457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.
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Affiliation(s)
- Ricardo Visini
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Josep Arús-Pous
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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Li G, Lou HX. Strategies to diversify natural products for drug discovery. Med Res Rev 2017; 38:1255-1294. [PMID: 29064108 DOI: 10.1002/med.21474] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/18/2017] [Accepted: 09/28/2017] [Indexed: 12/11/2022]
Abstract
Natural product libraries contain specialized metabolites derived from plants, animals, and microorganisms that play a pivotal role in drug discovery due to their immense structural diversity and wide variety of biological activities. The strategies to greatly extend natural product scaffolds through available biological and chemical approaches offer unique opportunities to access a new series of natural product analogues, enabling the construction of diverse natural product-like libraries. The affordability of these structurally diverse molecules has been a crucial step in accelerating drug discovery. This review provides an overview of various approaches to exploit the diversity of compounds for natural product-based drug development, drawing upon a series of examples to illustrate each strategy.
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Affiliation(s)
- Gang Li
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China
| | - Hong-Xiang Lou
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China.,Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
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