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Tian J, Li W, Deng X, Lakshminarayanan R, Srinivasan R. Chemoselective N-Acylation of Amines with Acylsilanes under Aqueous Acidic Conditions. Org Lett 2023; 25:5740-5744. [PMID: 37515781 DOI: 10.1021/acs.orglett.3c01911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2023]
Abstract
We report a facile method for forming amide bonds between acylsilanes and a wide range of amines in the presence of a mild chlorinating agent under aqueous acidic conditions. The reaction is highly chemoselective, as exemplified by the late-stage modification of a panel of approved drugs and natural products containing reactive functionalities.
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Affiliation(s)
- Jing Tian
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai Minzu University, Xining 810007, P. R. China
| | - Wei Li
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, Tianjin 300072, P.R. China
| | - Xingwang Deng
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, Tianjin 300072, P.R. China
| | | | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, Tianjin 300072, P.R. China
- Singapore Eye Research Institute (SERI), The Academia, 20 College Road, Singapore 169856, Singapore
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2
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Francis D, Farooque S, Meager A, Derks D, Leggott A, Warriner S, O'Neill AJ, Nelson A. Algorithm-driven activity-directed expansion of a series of antibacterial quinazolinones. Org Biomol Chem 2022; 20:9672-9678. [PMID: 36448404 DOI: 10.1039/d2ob01404a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Activity-directed synthesis (ADS) is a structure-blind, function driven approach that can drive the discovery of bioactive small molecules. In ADS, arrays of reactions are designed and executed, and the crude product mixtures are then directly screened to identify reactions that yield bioactive products. The design of subsequent reaction arrays is then informed by the hit reactions that are discovered. In this study, algorithms for reaction array design were developed in which the reactions to be executed were selected from a large set of virtual reactions; the reactions were selected on the basis of similarity to reactions known to yield bioactive products. The algorithms were harnessed to design arrays of photoredox-catalysed alkylation reactions whose crude products were then screened for inhibition of growth of S. aureus ATCC29213. It was demonstrated that the approach enabled expansion of a series of antibacterial quinazolinones. It is envisaged that such algorithms could ultimately enable fully autonomous activity-directed molecular discovery.
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Affiliation(s)
- Daniel Francis
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sannia Farooque
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Archie Meager
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Didi Derks
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.
| | - Abbie Leggott
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stuart Warriner
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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3
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Sohtome Y, Sodeoka M. Theoretical Insights into the Substrate-Dependent Diastereodivergence in (3 + 2) Cycloaddition of α-Keto Ester Enolates with Nitrones. Chem Pharm Bull (Tokyo) 2022; 70:616-623. [DOI: 10.1248/cpb.c22-00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research
| | - Mikiko Sodeoka
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science
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4
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Deng X, Zhou G, Tian J, Srinivasan R. Chemoselective Amide-Forming Ligation Between Acylsilanes and Hydroxylamines Under Aqueous Conditions. Angew Chem Int Ed Engl 2021; 60:7024-7029. [PMID: 33135292 DOI: 10.1002/anie.202012459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/19/2020] [Indexed: 12/20/2022]
Abstract
We report the facile amide-forming ligation of acylsilanes with hydroxylamines (ASHA ligation) under aqueous conditions. The ligation is fast, chemoselective, mild, high-yielding and displays excellent functional-group tolerance. Late-stage modifications of an array of marketed drugs, peptides, natural products, and biologically active compounds showcase the robustness and functional-group tolerance of the reaction. The key to the success of the reaction could be the possible formation of the strong Si-O bond via a Brook-type rearrangement. Given its simplicity and efficiency, this ligation has the potential to unfold new applications in the areas of medicinal chemistry and chemical biology.
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Affiliation(s)
- Xingwang Deng
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, 92 Weijin Road, Building 24, Nankai District, Tianjin, 300072, P. R. China
| | - Guan Zhou
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, 92 Weijin Road, Building 24, Nankai District, Tianjin, 300072, P. R. China
| | - Jing Tian
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, 92 Weijin Road, Building 24, Nankai District, Tianjin, 300072, P. R. China
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology (SPST), Tianjin University, 92 Weijin Road, Building 24, Nankai District, Tianjin, 300072, P. R. China
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5
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Luo Z, Yu S, Zeng W, Zhou J. Comparative analysis of the chemical and biochemical synthesis of keto acids. Biotechnol Adv 2021; 47:107706. [PMID: 33548455 DOI: 10.1016/j.biotechadv.2021.107706] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022]
Abstract
Keto acids are essential organic acids that are widely applied in pharmaceuticals, cosmetics, food, beverages, and feed additives as well as chemical synthesis. Currently, most keto acids on the market are prepared via chemical synthesis. The biochemical synthesis of keto acids has been discovered with the development of metabolic engineering and applied toward the production of specific keto acids from renewable carbohydrates using different metabolic engineering strategies in microbes. In this review, we provide a systematic summary of the types and applications of keto acids, and then summarize and compare the chemical and biochemical synthesis routes used for the production of typical keto acids, including pyruvic acid, oxaloacetic acid, α-oxobutanoic acid, acetoacetic acid, ketoglutaric acid, levulinic acid, 5-aminolevulinic acid, α-ketoisovaleric acid, α-keto-γ-methylthiobutyric acid, α-ketoisocaproic acid, 2-keto-L-gulonic acid, 2-keto-D-gluconic acid, 5-keto-D-gluconic acid, and phenylpyruvic acid. We also describe the current challenges for the industrial-scale production of keto acids and further strategies used to accelerate the green production of keto acids via biochemical routes.
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Affiliation(s)
- Zhengshan Luo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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6
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Deng X, Zhou G, Tian J, Srinivasan R. Chemoselective Amide‐Forming Ligation Between Acylsilanes and Hydroxylamines Under Aqueous Conditions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xingwang Deng
- School of Pharmaceutical Science and Technology (SPST) Tianjin University 92 Weijin Road, Building 24, Nankai District Tianjin 300072 P. R. China
| | - Guan Zhou
- School of Pharmaceutical Science and Technology (SPST) Tianjin University 92 Weijin Road, Building 24, Nankai District Tianjin 300072 P. R. China
| | - Jing Tian
- School of Pharmaceutical Science and Technology (SPST) Tianjin University 92 Weijin Road, Building 24, Nankai District Tianjin 300072 P. R. China
| | - Rajavel Srinivasan
- School of Pharmaceutical Science and Technology (SPST) Tianjin University 92 Weijin Road, Building 24, Nankai District Tianjin 300072 P. R. China
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7
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Karageorgis G, Liver S, Nelson A. Activity-Directed Synthesis: A Flexible Approach for Lead Generation. ChemMedChem 2020; 15:1776-1782. [PMID: 32734671 PMCID: PMC7589241 DOI: 10.1002/cmdc.202000524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 11/06/2022]
Abstract
Activity-directed synthesis (ADS) is a structure-blind, functional-driven molecular discovery approach. In this Concept, four case studies highlight the general applicability of ADS and showcase its flexibility to support different medicinal chemistry strategies. ADS deliberately harnesses reactions with multiple possible outcomes, and allows many chemotypes to be evaluated in parallel. Resources are focused on bioactive molecules, which emerge in tandem with associated synthetic routes. Some of the future challenges for ADS are highlighted, including the realisation of an autonomous molecular discovery platform. The prospects for ADS to become a mainstream lead generation approach are discussed.
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Affiliation(s)
- George Karageorgis
- School of Chemistry and Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Samuel Liver
- School of Chemistry and Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- Rosalind Franklin InstituteHarwell CampusDidcotOX11 0FAUK
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- Rosalind Franklin InstituteHarwell CampusDidcotOX11 0FAUK
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Green AI, Hobor F, Tinworth CP, Warriner S, Wilson AJ, Nelson A. Activity-Directed Synthesis of Inhibitors of the p53/hDM2 Protein-Protein Interaction. Chemistry 2020; 26:10682-10689. [PMID: 32458465 PMCID: PMC7496268 DOI: 10.1002/chem.202002153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) provide a rich source of potential targets for drug discovery and biomedical science research. However, the identification of structural-diverse starting points for discovery of PPI inhibitors remains a significant challenge. Activity-directed synthesis (ADS), a function-driven discovery approach, was harnessed in the discovery of the p53/hDM2 PPI. Over two rounds of ADS, 346 microscale reactions were performed, with prioritisation on the basis of the activity of the resulting product mixtures. Four distinct and novel series of PPI inhibitors were discovered that, through biophysical characterisation, were shown to have promising ligand efficiencies. It was thus shown that ADS can facilitate ligand discovery for a target that does not have a defined small-molecule binding site, and can provide distinctive starting points for the discovery of PPI inhibitors.
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Affiliation(s)
- Adam I. Green
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | | | - Stuart Warriner
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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9
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Stepek IA, Cao T, Koetemann A, Shimura S, Wollscheid B, Bode JW. Antibiotic Discovery with Synthetic Fermentation: Library Assembly, Phenotypic Screening, and Mechanism of Action of β-Peptides Targeting Penicillin-Binding Proteins. ACS Chem Biol 2019; 14:1030-1040. [PMID: 30990649 DOI: 10.1021/acschembio.9b00227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In analogy to biosynthetic pathways leading to bioactive natural products, synthetic fermentation generates mixtures of molecules from simple building blocks under aqueous, biocompatible conditions, allowing the resulting cultures to be directly screened for biological activity. In this work, a novel β-peptide antibiotic was successfully identified using the synthetic fermentation platform. Phenotypic screening was carried out in an initially random fashion, allowing simple identification of active cultures. Subsequent deconvolution, focused screening, and structure-activity relationship studies led to the identification of a potent antimicrobial peptide, showing strong selectivity for our model system Bacillus subtilis over human HEK293 cells. To determine the antibacterial mechanism of action, a peptide probe bearing a photoaffinity tag was readily synthesized through the use of appropriate synthetic fermentation building blocks and utilized for target identification using a quantitative mass spectrometry-based strategy. The chemoproteomic approach led to the identification of a number of bacterial membrane proteins as prospective targets. These findings were validated through binding affinity studies with penicillin-binding protein 4 using microscale thermophoresis, with the bioactive peptide showing a dissociation constant ( Kd) in the nanomolar range. Through these efforts, we provide a proof of concept for the synthetic fermentation approach presented here as a new strategy for the phenotypic discovery of novel bioactive compounds.
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Affiliation(s)
- Iain A. Stepek
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Trung Cao
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Anika Koetemann
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, and BioMedical Proteomics Platform (BMPP), ETH Zurich, 8093 Zurich, Switzerland
| | - Satomi Shimura
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, and BioMedical Proteomics Platform (BMPP), ETH Zurich, 8093 Zurich, Switzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
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10
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Pavlinov I, Gerlach EM, Aldrich LN. Next generation diversity-oriented synthesis: a paradigm shift from chemical diversity to biological diversity. Org Biomol Chem 2019; 17:1608-1623. [PMID: 30328455 DOI: 10.1039/c8ob02327a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Diversity-oriented synthesis adds biological performance as a new diversity element.
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Affiliation(s)
- Ivan Pavlinov
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
| | - Erica M. Gerlach
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
| | - Leslie N. Aldrich
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
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12
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Stepek IA, Bode JW. Synthetic fermentation of bioactive molecules. Curr Opin Chem Biol 2018; 46:18-24. [PMID: 29627458 DOI: 10.1016/j.cbpa.2018.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/18/2018] [Accepted: 03/22/2018] [Indexed: 02/08/2023]
Abstract
The concept of synthetic fermentation is to 'grow' complex organic molecules in a controlled and predictable manner by combining small molecule building blocks in water-without the need for reagents, enzymes, or organisms. This approach mimics the production of small mixtures of structurally related natural products by living organisms, particularly microbes, under conditions compatible with direct screening of the cultures for biological activity. This review discusses the development and implementation of this concept, its use for the discovery of protease inhibitors, its basis as a chemistry outreach program allowing non-specialists to make and discover new antibiotics, and highlights of related approaches.
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Affiliation(s)
- Iain A Stepek
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH-Zürich, 8093 Zürich, Switzerland; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan.
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13
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Hubert JG, Stepek IA, Noda H, Bode JW. Synthetic fermentation of β-peptide macrocycles by thiadiazole-forming ring-closing reactions. Chem Sci 2018; 9:2159-2167. [PMID: 29719689 PMCID: PMC5896468 DOI: 10.1039/c7sc05057g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/05/2018] [Indexed: 01/12/2023] Open
Abstract
A new thiadiazole-forming macrocyclization reaction enables the one-pot synthesis of cyclic β-peptide libraries from readily accessible building blocks without additional reagents.
Macrocyclic β-peptides were efficiently prepared using a thiadiazole-forming cyclization reaction between an α-ketoacid and a thiohydrazide. The linear β-peptide precursors were assembled from isoxazolidine monomers by α-ketoacid-hydroxylamine (KAHA) ligations with a bifunctional initiator – a process we have termed ‘synthetic fermentation’ due to the analogy of producing natural product-like molecules from simpler building blocks. The linear synthetic fermentation products underwent Boc-deprotection/thiadiazole-forming macrocyclization under aqueous, acidic conditions to provide the cyclic products in a one-pot process. This reaction sequence proceeds from easily accessed initiator and monomer building blocks without the need for additional catalysts or reagents, enabling facile production of macrocyclic β-peptides, a relatively underexplored structural class.
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Affiliation(s)
- Jonathan G Hubert
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Iain A Stepek
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (Bikaken) , 3-14-23 Kamiosaki, Shinagawa-ku , Tokyo 141-0021 , Japan
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie , Department of Chemistry and Applied Biosciences , ETH Zürich , Zürich , Switzerland 8093 . ; http://www.bode.ethz.ch
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14
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Xin D, Jeffries A, Burgess K. Interplay Of Stereochemistry, Conformational Rigidity, And Ease Of Synthesis For 13-Membered Cyclic Peptidomimetics Containing APC Residues. ACS COMBINATORIAL SCIENCE 2017; 19:414-421. [PMID: 28561582 DOI: 10.1021/acscombsci.7b00041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a program to design small molecules that bind proteins, we require cyclic peptides (or peptidomimetics) that are severely constrained such that they adopt one predominant conformation in solution. This paper describes syntheses of the 13-membered cyclic tetrapeptides 1 containing aminopyrrolidine carboxyl (APC) residues. A linear precursor was prepared and used to determine optimal conditions for cyclization of that substrate. A special linker was prepared to enable cyclization of similar linear peptidomimetics on a solid phase, and the solution-phase cyclization conditions were shown to be appropriate for this too. Stereochemical variations were then used to determine the ideal APC configuration for cyclization of the linear precursors (on a solid phase, using the conditions identified previously). Consequently, a series of compounds were prepared that are representative of compounds 1. Conformational studies of representative compounds in DMSO solution were performed primarily using (i) NOE studies, (ii) quenched molecular dynamics simulations using no constraints from experiment, and (iii) MacroModel calculations with NMR constraints. All three strategies converged to the same conclusion: the backbone of molecules based on 1 tends to adopt one preferential conformation in solution and that conformation can be predicted from the stereochemistries of the α-amino acids involved.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Andrew Jeffries
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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Liu R, Li X, Lam KS. Combinatorial chemistry in drug discovery. Curr Opin Chem Biol 2017; 38:117-126. [PMID: 28494316 PMCID: PMC5645069 DOI: 10.1016/j.cbpa.2017.03.017] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023]
Abstract
Several combinatorial methods have been developed to create focused or diverse chemical libraries with a wide range of linear or macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. Each combinatorial approach has its own unique high-throughput screening and encoding strategy. In this article, we provide a brief overview of combinatorial chemistry in drug discovery with emphasis on recently developed new technologies for design, synthesis, screening and decoding of combinatorial library. Examples of successful application of combinatorial chemistry in hit discovery and lead optimization are given. The limitations and strengths of combinatorial chemistry are also briefly discussed. We are now in a better position to truly leverage the power of combinatorial technologies for the discovery and development of next-generation drugs.
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Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA.
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16
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Karageorgis G, Dow M, Aimon A, Warriner S, Nelson A. Activity-Directed Synthesis with Intermolecular Reactions: Development of a Fragment into a Range of Androgen Receptor Agonists. Angew Chem Int Ed Engl 2015; 54:13538-44. [PMID: 26358926 PMCID: PMC4648041 DOI: 10.1002/anie.201506944] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 11/09/2022]
Abstract
Activity-directed synthesis (ADS), a novel discovery approach in which bioactive molecules emerge in parallel with associated syntheses, was exploited to develop a weakly binding fragment into novel androgen receptor agonists. Harnessing promiscuous intermolecular reactions of carbenoid compounds enabled highly efficient exploration of chemical space. Four substrates were prepared, yet exploited in 326 reactions to explore diverse chemical space; guided by bioactivity alone, the products of just nine of the reactions were purified to reveal diverse novel agonists with up to 125-fold improved activity. Remarkably, one agonist stemmed from a novel enantioselective transformation; this is the first time that an asymmetric reaction has been discovered solely on the basis of the biological activity of the product. It was shown that ADS is a significant addition to the lead generation toolkit, enabling the efficient and rapid discovery of novel, yet synthetically accessible, bioactive chemotypes.
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Affiliation(s)
- George Karageorgis
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT (UK) E-mail:
| | - Mark Dow
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT (UK) E-mail:
| | - Anthony Aimon
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT (UK) E-mail:
| | - Stuart Warriner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT (UK) E-mail:
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT (UK) E-mail:
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17
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Karageorgis G, Dow M, Aimon A, Warriner S, Nelson A. Activity-Directed Synthesis with Intermolecular Reactions: Development of a Fragment into a Range of Androgen Receptor Agonists. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506944] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Affiliation(s)
- Derek B Lowe
- Vertex Pharmaceuticals 50 Northern Avenue, Boston, Massachussets 02210, USA
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Minimalist synthesis. Nat Chem Biol 2014. [DOI: 10.1038/nchembio.1704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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