1
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Tsien J, Hu C, Merchant RR, Qin T. Three-dimensional saturated C(sp 3)-rich bioisosteres for benzene. Nat Rev Chem 2024:10.1038/s41570-024-00623-0. [PMID: 38982260 DOI: 10.1038/s41570-024-00623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Benzenes, the most ubiquitous structural moiety in marketed small-molecule drugs, are frequently associated with poor 'drug-like' properties, including metabolic instability, and poor aqueous solubility. In an effort to overcome these limitations, recent developments in medicinal chemistry have demonstrated the improved physicochemical profiles of C(sp3)-rich bioisosteric scaffolds relative to arenes. In the past two decades, we have witnessed an exponential increase in synthetic methods for accessing saturated bioisosteres of monosubstituted and para-substituted benzenes. However, until recent discoveries, analogous three-dimensional ortho-substituted and meta-substituted biososteres have remained underexplored, owing to their ring strain and increased s-character hybridization. This Review summarizes the emerging synthetic methodologies to access such saturated motifs and their impact on the application of bioisosteres for ortho-substituted, meta-substituted and multi-substituted benzene rings. It concludes with a perspective on the development of next-generation bioisosteres, including those within novel chemical space.
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Affiliation(s)
- Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Hu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rohan R Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Kong D, Fahrenhorst-Jones T, Kuo A, Simmons JL, Tan L, Burns JM, Pierens GK, Li R, West NP, Boyle GM, Smith MT, Savage GP, Williams CM. seco-1-Azacubane-2-carboxylic Acid: Derivative Scope and Comparative Biological Evaluation. J Org Chem 2024; 89:798-803. [PMID: 38131648 DOI: 10.1021/acs.joc.3c02333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The unusual and sterically constrained amino acid, seco-1-azacubane-2-carboxylic acid, was incorporated into a range of bioactive chemical templates, including enalaprilat, perindoprilat, endomorphin-2 and isoniazid, and subjected to biological testing. The endomorphin-2 derivative displayed increased activity at the δ opioid receptor, but a loss in activity was observed in the other cases, although human normal cell line evaluation suggests limited cytotoxic effects.
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Affiliation(s)
- Dehui Kong
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Andy Kuo
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Jacinta L Simmons
- QIMR Berghofer Medical Research Institute, Brisbane, 4029, Queensland, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Jed M Burns
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Rui Li
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, 4029, Queensland, Australia
| | - Maree T Smith
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072, Queensland, Australia
| | - G Paul Savage
- CSIRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168, Victoria, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia
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3
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Donnier-Valentin L, Kassamba S, Legros J, Fressigné C, Vuluga D, Brown RCD, Linclau B, De Paolis M. Photoinduced Formation of Cubyl Aryl Thioethers and Synthesis of Monocubyl Analogue of Dapsone. Org Lett 2023. [PMID: 37991751 DOI: 10.1021/acs.orglett.3c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
1,4-Disubstituted cubyl aryl thioethers were generated from the corresponding iodocubanes and aryl thiolates upon UV irradiation in dimethyl sulfoxide at room temperature. This simple procedure was found to be compatible with a variety of substituted aryl thiolates. This finding paved the way to a synthesis of the monocubyl analogue of dapsone, a key molecule in the treatment of leprosy, also known as Hansen's disease, and of acne.
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Affiliation(s)
| | - Seydou Kassamba
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, 76000 Rouen, France
| | - Julien Legros
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, 76000 Rouen, France
| | | | - Daniela Vuluga
- INSA Rouen, PBS, UMR 6270, CNRS, 76801 Saint-Etienne-du-Rouvray, France
| | - Richard C D Brown
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Bruno Linclau
- Department of Organic and Molecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Ghent, Belgium
| | - Michaël De Paolis
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, 76000 Rouen, France
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4
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Barotcu AZ, Karanfil A, Şahin E, Kelebekli L. Stereoselective synthesis of novel bis-homoinositols with bicyclo[4.2.0]octane motifs. Carbohydr Res 2022; 519:108611. [PMID: 35716487 DOI: 10.1016/j.carres.2022.108611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022]
Abstract
Starting from cyclooctatetraene, bis-homoconduritols with cis-inositol and allo-inositol (or bicyclo[4.2.0]octane motif) structures were synthesized. Photooxygenation of trans-7,8-dibromo-bicyclo[4.2.0]octa-2,4-diene allowed the preparation of tricyclic endoperoxide. The compound diacetate was obtained by reduction of endoperoxide with thiourea followed by acetylation reaction. Removal of halides with zinc dust in acetic acid yielded the dien-diacetate, a key compound of the designed molecules. OsO4 oxidation of diendiacetate followed by acetylation gave the corresponding hexaacetates. Finally, the novel desired bis-homoinositols were obtained in high yield by the ammonolysis of acetate groups. The structures of all synthesized compounds were characterized by spectroscopic methods.
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Affiliation(s)
- Ayşenur Zeren Barotcu
- Department of Chemistry, Faculty of Sciences and Arts, Ordu University, 52200, Ordu, Turkey
| | - Abdullah Karanfil
- Department of Chemistry, Faculty of Sciences and Arts, Ordu University, 52200, Ordu, Turkey
| | - Ertan Şahin
- Department of Chemistry, Faculty of Sciences, Ataturk University, 25240, Erzurum, Turkey
| | - Latif Kelebekli
- Department of Chemistry, Faculty of Sciences and Arts, Ordu University, 52200, Ordu, Turkey.
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5
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Takebe H, Matsubara S. Catalytic Asymmetric Synthesis of 2,6‐Disubstituted Cuneanes via Enantioselective Constitutional Isomerization of 1,4‐Disubstituted Cubanes. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hiyori Takebe
- Kyoto University Faculty of Engineering Graduate School of Engineering: Kyoto Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Material Chemistry JAPAN
| | - Seijiro Matsubara
- Kyoto University Faculty of Engineering Graduate School of Engineering: Kyoto Daigaku Kogakubu Daigakuin Kogaku Kenkyuka Material Chemistry Kyotodaigaku-katsura, Nishikyo 615-8510 Kyoto JAPAN
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6
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Chen X, Furukawa N, Jin DY, Liu Y, Stafford DW, Williams CM, Suhara Y, Tie JK. Naturally occurring UBIAD1 mutations differentially affect menaquinone biosynthesis and vitamin K-dependent carboxylation. FEBS J 2021; 289:2613-2627. [PMID: 34813684 PMCID: PMC9064899 DOI: 10.1111/febs.16291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/15/2021] [Accepted: 11/22/2021] [Indexed: 11/30/2022]
Abstract
UbiA prenyltransferase domain-containing protein-1 (UBIAD1) is responsible for the biosynthesis of menaquinone-4 (MK-4), a cofactor for extrahepatic carboxylation of vitamin K-dependent (VKD) proteins. Genetic variations of UBIAD1 are mainly associated with Schnyder corneal dystrophy (SCD), a disease characterized by abnormal accumulation of cholesterol in the cornea. Results from in vitro studies demonstrate that SCD-associated UBIAD1 mutations are defective in MK-4 biosynthesis. However, SCD patients do not exhibit typical phenotypes associated with defects of MK-4 or VKD carboxylation. Here, we coupled UBIAD1's biosynthetic activity of MK-4 with VKD carboxylation in HEK293 cells that stably express a chimeric VKD reporter protein. The endogenous Ubiad1 gene in these cells was knocked out by CRISPR-Cas9-mediated genome editing. The effect of UBIAD1 mutations on MK-4 biosynthesis and VKD carboxylation was evaluated in Ubiad1-deficient reporter cells by determining the production of MK-4 or by measuring the efficiency of reporter-protein carboxylation. Our results show that the hot-spot mutation N102S has a moderate impact on MK-4 biosynthesis (retained ˜ 82% activity) but does not affect VKD carboxylation. However, the G186R mutation significantly affected both MK-4 biosynthesis and VKD carboxylation. Other mutations exhibit varying degrees of effects on MK-4 biosynthesis and VKD carboxylation. These results are consistent with in vivo results obtained from gene knock-in mice and SCD patients. Our findings suggest that UBIAD1's MK-4 biosynthetic activity does not directly correlate with the phenotypes of SCD patients. The established cell-based assays in this study provide a powerful tool for the functional studies of UBIAD1 in a cellular milieu.
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Affiliation(s)
- Xuejie Chen
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Natsuko Furukawa
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Da-Yun Jin
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Yizhou Liu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Darrel W Stafford
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Yoshitomo Suhara
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Jian-Ke Tie
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
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7
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Kuandykov RR. STRUCTURE AND PROPERTIES OF A NEW CARBON ALLOTROPE BASED ON LADENBURG BENZENE. J STRUCT CHEM+ 2021. [DOI: 10.1134/s002247662110005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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9
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Collin DE, Kovacic K, Light ME, Linclau B. Synthesis of Ortho-Functionalized 1,4-Cubanedicarboxylate Derivatives through Photochemical Chlorocarbonylation. Org Lett 2021; 23:5164-5169. [PMID: 34133174 DOI: 10.1021/acs.orglett.1c01702] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cubane ring has received intense attention as a 3D benzene isostere and scaffold. Mono- and 1,4-disubstituted cubanes are well-described. Here we report a practical procedure for a direct radical-mediated chlorocarbonylation process initially reported by Bashir-Hashemi, to access a range of 2-substituted 1,4-cubanedicarboxylic ester derivatives. A subsequent regioselective ester hydrolysis to give fully differentiated 1,2,4-trisubstituted cubanes is demonstrated.
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Affiliation(s)
- Diego E Collin
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Kristina Kovacic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Mark E Light
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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10
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Fan Q, Zhu L, Ren H, Lin H, Wu G. A new metal-organic framework of 3,9-diazatetraasterane-1,5,7,11-tetracarboxylic acid-3,6,9,12-tetraphenyl with sodium ion: Synthesis, characterization and DFT calculations. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Chen X, Liu Y, Furukawa N, Jin DY, Savage GP, Stafford DW, Suhara Y, Williams CM, Tie JK. A novel vitamin K derived anticoagulant tolerant to genetic variations of vitamin K epoxide reductase. J Thromb Haemost 2021; 19:689-700. [PMID: 33314621 PMCID: PMC7925372 DOI: 10.1111/jth.15209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Vitamin K antagonists (VKAs), such as warfarin, have remained the cornerstone of oral anticoagulation therapy in the prevention and treatment of thromboembolism for more than half a century. They function by impairing the biosynthesis of vitamin K-dependent (VKD) clotting factors through the inhibition of vitamin K epoxide reductase (VKOR). The challenge of VKAs therapy is their narrow therapeutic index and highly variable dosing requirements, which are partially the result of genetic variations of VKOR. OBJECTIVES The goal of this study was to search for an improved VKA that is tolerant to the genetic variations of its target enzyme. METHODS A series of vitamin K derivatives with benzyl and related side-chain substitutions at the 3-position of 1,4-naphthoquinone were synthesized. The role of these compounds in VKD carboxylation was evaluated by mammalian cell-based assays and conventional in vitro activity assays. RESULTS Our results showed that replacing the phytyl side-chain with a methylene cyclooctatetraene (COT) moiety at the 3-position of vitamin K1 converted it from a substrate to an inhibitor for VKD carboxylation. Strikingly, this COT-vitamin K derivative displayed a similar inhibition potency in warfarin-resistant VKOR mutations whose warfarin resistance varied more than 400-fold. Further characterization of COT-vitamin K for the inhibition of VKD carboxylation suggested that this compound targets multiple enzymes in the vitamin K redox cycle. Importantly, the anticoagulation effect of COT-vitamin K can be rescued with high doses of vitamin K1 . CONCLUSION We discovered a vitamin K analogue that functions as a VKA and is tolerant to genetic variations in the target enzyme.
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Affiliation(s)
- Xuejie Chen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yizhou Liu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Natsuko Furukawa
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Da-Yun Jin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - G. Paul Savage
- CSIRO Manufacturing, Ian Wark Laboratory, Melbourne 3168, Victoria, Australia
| | - Darrel W. Stafford
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yoshitomo Suhara
- Laboratory of Organic Synthesis and Medicinal Chemistry, Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Jian-Ke Tie
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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12
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Li W. Targeting multiple enzymes in vitamin K metabolism for anticoagulation. J Thromb Haemost 2021; 19:633-636. [PMID: 33650246 PMCID: PMC8966952 DOI: 10.1111/jth.15212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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13
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De S, Jash M, Chowdhury C. Palladium(ii) catalysed cascade strategy for the synthesis of dibenzo[5,6:7,8]cycloocta[1,2-b]indol-10-ols/-10(15H)-ones: easy access to 1,3,5,7-cyclooctatetraenes (COTs). Chem Commun (Camb) 2020; 56:15659-15662. [PMID: 33289730 DOI: 10.1039/d0cc06538b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An atom-economic Pd(ii)-catalysed cascade cyclisation of 2-(biphenylethynyl)anilines tethered to an aldehyde or cyano group leads to the formation of dibenzo[5,6:7,8]cycloocta[1,2-b]indol-10-ols 6 or dibenzo[5,6:7,8]cycloocta[1,2-b]indol-10(15H)-ones 8 with high yields (up to 95%). The reaction proceeds via amino-palladation of the alkyne followed by nucleophilic addition onto the aldehyde/cyano group. Treatment of 6 with p-TsOH·H2O smoothly provided cyclooctatetraene (COT) derivatives 7.
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Affiliation(s)
- Sukanya De
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata-700032, India.
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14
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Zhang W, Zhou ZX, Zhu XJ, Sun ZH, Dai WM, Li CC. Asymmetric Total Synthesis of the Highly Strained 4β-Acetoxyprobotryane-9β,15α-diol. J Am Chem Soc 2020; 142:19868-19873. [DOI: 10.1021/jacs.0c10116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen Zhang
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zi-Xiong Zhou
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xu-Jiang Zhu
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhang-Hua Sun
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei-Min Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Chuang-Chuang Li
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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15
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Tse EG, Houston SD, Williams CM, Savage GP, Rendina LM, Hallyburton I, Anderson M, Sharma R, Walker GS, Obach RS, Todd MH. Nonclassical Phenyl Bioisosteres as Effective Replacements in a Series of Novel Open-Source Antimalarials. J Med Chem 2020; 63:11585-11601. [PMID: 32678591 DOI: 10.1021/acs.jmedchem.0c00746] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The replacement of one chemical motif with another that is broadly similar is a common method in medicinal chemistry to modulate the physical and biological properties of a molecule (i.e., bioisosterism). In recent years, bioisosteres such as cubane and bicyclo[1.1.1]pentane (BCP) have been used as highly effective phenyl mimics. Herein, we show the successful incorporation of a range of phenyl bioisosteres during the open-source optimization of an antimalarial series. Cubane (19) and closo-carborane (23) analogues exhibited improved in vitro potency against Plasmodium falciparum compared to the parent phenyl compound; however, these changes resulted in a reduction in metabolic stability; unusually, enzyme-mediated oxidation was found to take place on the cubane core. A BCP analogue (22) was found to be equipotent to its parent phenyl compound and showed significantly improved metabolic properties. While these results demonstrate the utility of these atypical bioisosteres when used in a medicinal chemistry program, the search to find a suitable bioisostere may well require the preparation of many candidates, in our case, 32 compounds.
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Affiliation(s)
- Edwin G Tse
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sevan D Houston
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - G Paul Savage
- Ian Wark Laboratory, CSIRO Manufacturing, Melbourne, Victoria 3168, Australia
| | - Louis M Rendina
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Irene Hallyburton
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Mark Anderson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Raman Sharma
- Pfizer Inc., Groton, Connecticut 06340, United States
| | | | - R Scott Obach
- Pfizer Inc., Groton, Connecticut 06340, United States
| | - Matthew H Todd
- School of Pharmacy, University College London, London WC1N 1AX, U.K
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16
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Dallaston MA, Houston SD, Williams CM. Cubane, Bicyclo[1.1.1]pentane and Bicyclo[2.2.2]octane: Impact and Thermal Sensitiveness of Carboxyl-, Hydroxymethyl- and Iodo-substituents. Chemistry 2020; 26:11966-11970. [PMID: 32820575 DOI: 10.1002/chem.202001658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/22/2020] [Indexed: 12/21/2022]
Abstract
With the burgeoning interest in cage motifs for bioactive molecule discovery, and the recent disclosure of 1,4-cubane-dicarboxylic acid impact sensitivity, more research into the safety profiles of cage scaffolds is required. Therefore, the impact sensitivity and thermal decomposition behavior of judiciously selected starting materials and synthetic intermediates of cubane, bicyclo[1.1.1]pentane (BCP), and bicyclo[2.2.2]octane (BCO) were evaluated via hammer test and sealed cell differential scanning calorimetry, respectively. Iodo-substituted systems were found to be more impact sensitive, whereas hydroxymethyl substitution led to more rapid thermodecomposition. Cubane was more likely to be impact sensitive with these substituents, followed by BCP, whereas all BCOs were unresponsive. The majority of derivatives were placed substantially above Yoshida thresholds-a computational indicator of sensitivity.
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Affiliation(s)
- Madeleine A Dallaston
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Sevan D Houston
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
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17
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Yoshino N, Kato Y, Mabit T, Nagata Y, Williams CM, Harada M, Muranaka A, Uchiyama M, Matsubara S. Cubane Chirality via Substitution of a “Hidden” Regular Tetrahedron. Org Lett 2020; 22:4083-4087. [DOI: 10.1021/acs.orglett.0c01142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nana Yoshino
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Yumi Kato
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Thibaud Mabit
- JSPS International Fellowship for Research, Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo, Kyoto 615-8530, Japan
| | - Yuuya Nagata
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Nishi 10, Kita, Sapporo 001-0021, Japan
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mei Harada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsuya Muranaka
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Seijiro Matsubara
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku-Katsura, Nishikyo, Kyoto 615-8510, Japan
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18
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Houston SD, Fahrenhorst-Jones T, Xing H, Chalmers BA, Sykes ML, Stok JE, Farfan Soto C, Burns JM, Bernhardt PV, De Voss JJ, Boyle GM, Smith MT, Tsanaktsidis J, Savage GP, Avery VM, Williams CM. The cubane paradigm in bioactive molecule discovery: further scope, limitations and the cyclooctatetraene complement. Org Biomol Chem 2020; 17:6790-6798. [PMID: 31241113 DOI: 10.1039/c9ob01238a] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cubane phenyl ring bioisostere paradigm was further explored in an extensive study covering a wide range of pharmaceutical and agrochemical templates, which included antibiotics (cefaclor, penicillin G) and antihistamine (diphenhydramine), a smooth muscle relaxant (alverine), an anaesthetic (ketamine), an agrochemical instecticide (triflumuron), an antiparasitic (benznidazole) and an anticancer agent (tamibarotene). This investigation highlights the scope and limitations of incorporating cubane into bioactive molecule discovery, both in terms of synthetic compatibility and physical property matching. Cubane maintained bioisosterism in the case of the Chagas disease antiparasitic benznidazole, although it was less active in the case of the anticancer agent (tamibarotenne). Application of the cyclooctatetraene (COT) (bio)motif complement was found to optimize benznidazole relative to the benzene parent, and augmented anticancer activity relative to the cubane analogue in the case of tamibarotene. Like all bioisosteres, scaffolds and biomotifs, however, there are limitations (e.g. synthetic implementation), and these have been specifically highlighted herein using failed examples. A summary of all templates prepared to date by our group that were biologically evaluated strongly supports the concept that cubane is a valuable tool in bioactive molecule discovery and COT is a viable complement.
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Affiliation(s)
- Sevan D Houston
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Hui Xing
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Benjamin A Chalmers
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Melissa L Sykes
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Clementina Farfan Soto
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Jed M Burns
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, QLD, Australia
| | - Maree T Smith
- School of Biomedical Sciences, Faculty of Medicine, UQ, Brisbane, Australia
| | - John Tsanaktsidis
- CSIRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168, Victoria (VIC), Australia
| | - G Paul Savage
- CSIRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168, Victoria (VIC), Australia
| | - Vicky M Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD), Australia.
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19
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Collin DE, Folgueiras‐Amador AA, Pletcher D, Light ME, Linclau B, Brown RCD. Cubane Electrochemistry: Direct Conversion of Cubane Carboxylic Acids to Alkoxy Cubanes Using the Hofer-Moest Reaction under Flow Conditions. Chemistry 2020; 26:374-378. [PMID: 31593312 PMCID: PMC6973092 DOI: 10.1002/chem.201904479] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Indexed: 12/12/2022]
Abstract
The highly strained cubane system is of great interest as a scaffold and rigid linker in both pharmaceutical and materials chemistry. The first electrochemical functionalisation of cubane by oxidative decarboxylative ether formation (Hofer-Moest reaction) was demonstrated. The mild conditions are compatible with the presence of other oxidisable functional groups, and the use of flow electrochemical conditions allows straightforward upscaling.
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Affiliation(s)
- Diego E. Collin
- School of ChemistryUniversity of SouthamptonHighfield, SouthamptonSO17 1BJUK
| | | | - Derek Pletcher
- School of ChemistryUniversity of SouthamptonHighfield, SouthamptonSO17 1BJUK
| | - Mark E. Light
- School of ChemistryUniversity of SouthamptonHighfield, SouthamptonSO17 1BJUK
| | - Bruno Linclau
- School of ChemistryUniversity of SouthamptonHighfield, SouthamptonSO17 1BJUK
| | - Richard C. D. Brown
- School of ChemistryUniversity of SouthamptonHighfield, SouthamptonSO17 1BJUK
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20
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Sarkar MR, Houston SD, Savage GP, Williams CM, Krenske EH, Bell SG, De Voss JJ. Rearrangement-Free Hydroxylation of Methylcubanes by a Cytochrome P450: The Case for Dynamical Coupling of C–H Abstraction and Rebound. J Am Chem Soc 2019; 141:19688-19699. [DOI: 10.1021/jacs.9b08064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Md. Raihan Sarkar
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Sevan D. Houston
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - G. Paul Savage
- Ian Wark Laboratory, CSIRO Manufacturing, Melbourne, VIC 3168, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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21
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Arachchige KSA, Fahrenhorst-Jones T, Burns JM, Al-Fayaad HA, Behera JN, Rao CNR, Clegg JK, Williams CM. 1,4-Diazacubane crystal structure rectified as piperazinium. Chem Commun (Camb) 2019; 55:11751-11753. [PMID: 31513198 DOI: 10.1039/c9cc06272f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All 21 [n]-azacubanes are proposed by theoreticians to be stable, however, to-date only the synthesis of 1,4-diazacubane has been reported - as a Ni2+ templated Kagome metal organic framework (MOF). Described herein is the structural reassignment of this Kagome MOF on the basis of deducing the precise experimental procedure, and demonstrating that rather than the formation of 1,4-diazacubane, charge is balanced by disordered piperazinium cations across a twelve-fold symmetry site. Furthermore, quantum chemical calculations reveal that 1,4-diazacubane is unlikely to form under the reported conditions due to unfavorable enthalpies for select hypothetical reactions leading to such a product. This significant structure correction upholds the unconquered synthesis status quo of azacubane.
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Affiliation(s)
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Jed M Burns
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Hydar A Al-Fayaad
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Jogendra N Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India and Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India and School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752 050, India
| | - C N R Rao
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064, India and Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Queensland, Australia.
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22
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Determining the necessity of phenyl ring π-character in warfarin. Bioorg Med Chem Lett 2019; 29:1954-1956. [PMID: 31147103 DOI: 10.1016/j.bmcl.2019.05.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/18/2019] [Accepted: 05/18/2019] [Indexed: 11/23/2022]
Abstract
Despite the difficulty in administering a safe dose regimen and reports of emerging resistance, warfarin (1) remains the most widely-used oral anticoagulant for the prevention and treatment of thrombosis in humans globally. Systematic substitution of the warfarin phenyl ring with either 1,3,5,7-cyclooctatetraene (COT) (2), cubane (3), cyclohexane (4) or cyclooctane (5) and subsequent evaluation against the target enzyme, vitamin K epoxide reductase (VKOR), facilitated interrogation of both steric and electronic properties of the phenyl pharmacophore. The tolerance of VKOR to further functional group modification (carboxylate 14, PTAD adduct 15) was also investigated. The results demonstrate the importance of both annulene conferred π-interactions and ring size in the activity of warfarin.
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23
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Houston SD, Chalmers BA, Savage GP, Williams CM. Enantioselective synthesis of (R)-2-cubylglycine including unprecedented rhodium mediated C–H insertion of cubane. Org Biomol Chem 2019; 17:1067-1070. [DOI: 10.1039/c8ob02959h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An enantioselective synthesis of the non-proteinogenic amino acid (R)-2-cubylglycine and the first examples of cubane C–H insertion are reported.
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Affiliation(s)
- Sevan D. Houston
- School of Chemistry and Molecular Biosciences
- University of Queensland
- Brisbane
- Australia
| | - Benjamin A. Chalmers
- School of Chemistry and Molecular Biosciences
- University of Queensland
- Brisbane
- Australia
| | - G. Paul Savage
- CSIRO Manufacturing
- Ian Wark Laboratory
- Melbourne
- Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences
- University of Queensland
- Brisbane
- Australia
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