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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Smyrnov OK, Melnykov KP, Pashenko OY, Volochnyuk DM, Ryabukhin SV. Stellane at the Forefront: Derivatization and Reactivity Studies of a Promising Saturated Bioisostere of ortho-Substituted Benzenes. Org Lett 2024. [PMID: 38804566 DOI: 10.1021/acs.orglett.4c01645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
This work highlights stellane's cage stability and derivatization opportunities. A diverse range of building blocks were synthesized using modern synthesis protocols to demonstrate stellane's reactivity and chemical tolerance across different reaction systems, proving its promise as a bioisosteric scaffold. It can be utilized in scaffold-based molecular design and is superior in terms of topological precision compared to existing ortho isosteres, as well as monosubstituted benzene mimetics, holding the potential to become a robust platform for future medicinal chemistry studies.
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Affiliation(s)
- Oleh K Smyrnov
- Enamine Ltd., 78 Winston Churchill Street, 02094 Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, 01601 Kyiv, Ukraine
| | - Kostiantyn P Melnykov
- Enamine Ltd., 78 Winston Churchill Street, 02094 Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, 01601 Kyiv, Ukraine
| | - Olexandr Ye Pashenko
- Enamine Ltd., 78 Winston Churchill Street, 02094 Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademik Kuhar Street, 02660 Kyiv, Ukraine
| | - Dmytro M Volochnyuk
- Enamine Ltd., 78 Winston Churchill Street, 02094 Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademik Kuhar Street, 02660 Kyiv, Ukraine
| | - Serhiy V Ryabukhin
- Enamine Ltd., 78 Winston Churchill Street, 02094 Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademik Kuhar Street, 02660 Kyiv, Ukraine
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3
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Zhou JL, Xiao Y, He L, Gao XY, Yang XC, Wu WB, Wang G, Zhang J, Feng JJ. Palladium-Catalyzed Ligand-Controlled Switchable Hetero-(5 + 3)/Enantioselective [2σ+2σ] Cycloadditions of Bicyclobutanes with Vinyl Oxiranes. J Am Chem Soc 2024. [PMID: 38739092 DOI: 10.1021/jacs.4c01851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
For nearly 60 years, significant research efforts have been focused on developing strategies for the cycloaddition of bicyclobutanes (BCBs). However, higher-order cycloaddition and catalytic asymmetric cycloaddition of BCBs have been long-standing formidable challenges. Here, we report Pd-catalyzed ligand-controlled, tunable cycloadditions for the divergent synthesis of bridged bicyclic frameworks. The dppb ligand facilitates the formal (5+3) cycloaddition of BCBs and vinyl oxiranes, yielding valuable eight-membered ethers with bridged bicyclic scaffolds in 100% regioselectivity. The Cy-DPEphos ligand promotes selective hetero-[2σ+2σ] cycloadditions to access pharmacologically important 2-oxabicyclo[3.1.1]heptane (O-BCHeps). Furthermore, the corresponding catalytic asymmetric synthesis of O-BCHeps with 94-99% ee has been achieved using chiral (S)-DTBM-Segphos, representing the first catalytic asymmetric cross-dimerization of two strained rings. The obtained O-BCHeps are promising bioisosteres for ortho-substituted benzenes.
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Affiliation(s)
- Jin-Lan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
| | - Yuanjiu Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
| | - Linke He
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China
| | - Xin-Yu Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
| | - Xue-Chun Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
| | - Wen-Biao Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
| | - Guoqiang Wang
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China
| | - Junliang Zhang
- Department of Chemistry, Fudan University, Shanghai 200438, P.R. China
| | - Jian-Jun Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China
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4
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Levterov VV, Panasiuk Y, Shablykin O, Stashkevych O, Sahun K, Rassokhin A, Sadkova I, Lesyk D, Anisiforova A, Holota Y, Borysko P, Bodenchuk I, Voloshchuk NM, Mykhailiuk PK. 2-Oxabicyclo[2.1.1]hexanes: Synthesis, Properties, and Validation as Bioisosteres of ortho- and meta-Benzenes. Angew Chem Int Ed Engl 2024; 63:e202319831. [PMID: 38465464 DOI: 10.1002/anie.202319831] [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: 12/21/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/12/2024]
Abstract
We have developed a general and practical approach towards 2-oxabicyclo[2.1.1]hexanes with two and three exit vectors via an iodocyclization reaction. The obtained compounds have been easily converted into the corresponding building blocks for use in medicinal chemistry. 2-Oxabicyclo[2.1.1]hexanes have been incorporated into the structure of five drugs and three agrochemicals, and validated biologically as bioisosteres of ortho- and meta-benzenes.
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Affiliation(s)
| | | | - Oleh Shablykin
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Academician Kukhar Str. 1, 02094, Kyiv, Ukraine
| | - Oleksandr Stashkevych
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Chemistry Department, Volodymyrska Str. 64, 01601, Kyiv, Ukraine
| | - Kateryna Sahun
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | - Artur Rassokhin
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | - Iryna Sadkova
- Enamine Ltd, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | - Dmytro Lesyk
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Yuliia Holota
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | - Petro Borysko
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Nataliya M Voloshchuk
- National University of Life and Environmental Sciences of Ukraine, V. F. Peresypkin Department of Phytopathology, Heroyiv Oborony Str. 15, 03041, Kyiv, Ukraine
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5
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Diepers HE, Walker JCL. (Bio)isosteres of ortho- and meta-substituted benzenes. Beilstein J Org Chem 2024; 20:859-890. [PMID: 38655554 PMCID: PMC11035989 DOI: 10.3762/bjoc.20.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Saturated bioisosteres of substituted benzenes offer opportunities to fine-tune the properties of drug candidates in development. Bioisosteres of para-benzenes, such as those based on bicyclo[1.1.1]pentane, are now very common and can be used to increase aqueous solubility and improve metabolic stability, among other benefits. Bioisosteres of ortho- and meta-benzenes were for a long time severely underdeveloped by comparison. This has begun to change in recent years, with a number of potential systems being reported that can act as bioisosteres for these important fragments. In this review, we will discuss these recent developments, summarizing the synthetic approaches to the different bioisosteres as well as the impact they have on the physiochemical and biological properties of pharmaceuticals and agrochemicals.
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Affiliation(s)
- H Erik Diepers
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Johannes C L Walker
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
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6
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Cuadros S, Paut J, Anselmi E, Dagousset G, Magnier E, Dell'Amico L. Light-Driven Synthesis and Functionalization of Bicycloalkanes, Cubanes and Related Bioisosteres. Angew Chem Int Ed Engl 2024; 63:e202317333. [PMID: 38179801 DOI: 10.1002/anie.202317333] [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: 11/14/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
Bicycloalkanes, cubanes and their structural analogues have emerged as bioisosteres of (hetero)arenes. To meet increasing demand, the chemical community has developed a plethora of novel synthetic methods. In this review, we assess the progress made in the field of light-driven construction and functionalization of such relevant molecules. We have focused on diverse structural targets, as well as on reaction processes giving access to: (i) [1.1.1]-bicyclopentanes (BCPs); (ii) [2.2.1]-bicyclohexanes (BCHs); (iii) [3.1.1]-bicycloheptanes (BCHeps); and (iv) cubanes; as well as other structurally related scaffolds. Finally, future perspectives dealing with the identification of novel reaction manifolds to access new functionalized bioisosteric units are discussed.
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Affiliation(s)
- Sara Cuadros
- Department of Chemical Sciences, University of Padova, Via Francesco Marzolo 1, 35131, Padova, Italy
| | - Julien Paut
- Department of Chemical Sciences, University of Padova, Via Francesco Marzolo 1, 35131, Padova, Italy
- Institut Lavoisier de Versailles, University of Paris-Saclay, 45 Avenue des Etats-Unis, 78035, Versailles, France
| | - Elsa Anselmi
- Institut Lavoisier de Versailles, University of Paris-Saclay, 45 Avenue des Etats-Unis, 78035, Versailles, France
- Université de Tours, Faculté des Sciences et Techniques, 37200, Tours, France
| | - Guillaume Dagousset
- Institut Lavoisier de Versailles, University of Paris-Saclay, 45 Avenue des Etats-Unis, 78035, Versailles, France
| | - Emmanuel Magnier
- Institut Lavoisier de Versailles, University of Paris-Saclay, 45 Avenue des Etats-Unis, 78035, Versailles, France
| | - Luca Dell'Amico
- Department of Chemical Sciences, University of Padova, Via Francesco Marzolo 1, 35131, Padova, Italy
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7
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Fu Q, Cao S, Wang J, Lv X, Wang H, Zhao X, Jiang Z. Enantioselective [2π + 2σ] Cycloadditions of Bicyclo[1.1.0]butanes with Vinylazaarenes through Asymmetric Photoredox Catalysis. J Am Chem Soc 2024; 146:8372-8380. [PMID: 38499472 DOI: 10.1021/jacs.3c14077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Here we present a highly enantioselective [2π + 2σ] photocycloaddition of bicyclo[1.1.0]butanes (BCBs). The reaction uses a variety of vinylazaarenes as partners and is catalyzed by a polycyclic aromatic hydrocarbon (PAH)-containing chiral phosphoric acid as a bifunctional chiral photosensitizer. A wide array of pharmaceutically important bicyclo[2.1.1]hexane (BCH) derivatives have been synthesized with high yields, enantioselectivity, and diastereoselectivity. In addition to the diverse 1-ketocarbonyl-3-substituted BCBs, α/β-substituted vinylazaarenes are compatible with such an unprecedented photoredox catalytic pathway, resulting in the successful assembly of an all-carbon quaternary stereocenter or two adjacent tertiary stereocenters on the product.
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Affiliation(s)
- Qianqian Fu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Shanshan Cao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Jiahao Wang
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Xinxin Lv
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Hao Wang
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Xiaowei Zhao
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng 475004, Henan,P. R. China
| | - Zhiyong Jiang
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, P. R. China
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng 475004, Henan,P. R. China
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8
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Pattison G. Assessing the rigidity of cubanes and bicyclo(1.1.1)pentanes as benzene bioisosteres. Bioorg Med Chem 2024; 102:117652. [PMID: 38442523 DOI: 10.1016/j.bmc.2024.117652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Aromatic rings are critical core substructures in the majority of pharmaceutical compounds. There is much recent interest in replacing aromatic structures with saturated bioisosteres of benzene, which are generally fused or bridged ring systems. These bioisosteres often show improved solubility properties compared to benzene, and may also undergo fewer unwanted metabolic processes. One key reason why aromatic rings have proven so successful in drug design is their rigidity. This paper uses molecular dynamics simulations supported by crystallographic data to assess the rigidity of bicyclopentane and cubane ring systems as two of the most common benzene bioisosteres and compares this to benzene. Whilst a benzene ring is shown to be more flexible than these two bioisosteres in terms of its dihedral ring flexibility, substituents around the ring tend to behave in a much more similar way in both benzene and the bioisosteric systems.
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Affiliation(s)
- Graham Pattison
- School of Chemistry, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, UK LN6 7DL.
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9
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Ma X, Chen JL, Gaskins BE. Decarboxylative C-N Coupling of 2,2-Difluorobicyclo[1.1.1]pentane (BCP-F 2) Building Blocks. Org Lett 2024; 26:1947-1951. [PMID: 38386927 DOI: 10.1021/acs.orglett.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Described herein is our effort toward achieving the decarboxylative functionalization of 2,2-difluorobicyclo[1.1.1]pentane (BCP-F2) building blocks. When compared with the nonfluorinated bicyclo[1.1.1]pentane (BCP) analogues, we discovered divergent reactivities. This is the first successful decarboxylative coupling of BCP-F2 building blocks reported via the photoredox mechanism.
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Affiliation(s)
- Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Joanna L Chen
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Bryce E Gaskins
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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10
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Prysiazhniuk K, Datsenko OP, Polishchuk O, Shulha S, Shablykin O, Nikandrova Y, Horbatok K, Bodenchuk I, Borysko P, Shepilov D, Pishel I, Kubyshkin V, Mykhailiuk PK. Spiro[3.3]heptane as a Saturated Benzene Bioisostere. Angew Chem Int Ed Engl 2024; 63:e202316557. [PMID: 38251921 DOI: 10.1002/anie.202316557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/23/2024]
Abstract
The spiro[3.3]heptane core, with the non-coplanar exit vectors, was shown to be a saturated benzene bioisostere. This scaffold was incorporated into the anticancer drug sonidegib (instead of the meta-benzene), the anticancer drug vorinostat (instead of the phenyl ring), and the anesthetic drug benzocaine (instead of the para-benzene). The patent-free saturated analogs obtained showed a high potency in the corresponding biological assays.
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Affiliation(s)
| | | | | | | | - Oleh Shablykin
- Enamine Ltd., Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, 02094, Kyiv, Ukraine
| | | | | | | | - Petro Borysko
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Iryna Pishel
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
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11
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Anderson JM, Poole DL, Cook GC, Murphy JA, Measom ND. Organometallic Bridge Diversification of Bicyclo[1.1.1]pentanes. Chemistry 2024; 30:e202304070. [PMID: 38117748 DOI: 10.1002/chem.202304070] [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: 12/07/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Bicyclo[1.1.1]pentane (BCP) derivatives have attracted significant recent interest in drug discovery as alkyne, tert-butyl and arene bioisosteres, where their incorporation is frequently associated with increased compound solubility and metabolic stability. While strategies for functionalisation of the bridgehead (1,3) positions are extensively developed, platforms allowing divergent substitution at the bridge (2,4,5) positions remain limited. Recent reports have introduced 1-electron strategies for arylation and incorporation of a small range of other substituents, but are limited in terms of scope, yields or practical complexity. Herein, we show the synthesis of diverse 1,2,3-trifunctionalised BCPs through lithium-halogen exchange of a readily accessible BCP bromide. When coupled with medicinally relevant product derivatisations, our developed 2-electron "late stage" approach provides rapid and straightforward access to unprecedented BCP structural diversity (>20 hitherto-unknown motifs reported). Additionally, we describe a method for the synthesis of enantioenriched "chiral-at-BCP" bicyclo[1.1.1]pentanes through a novel stereoselective bridgehead desymmetrisation.
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Affiliation(s)
- Joseph M Anderson
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK, G1 1XL
| | - Darren L Poole
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
| | - Gemma C Cook
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
| | - John A Murphy
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK, G1 1XL
| | - Nicholas D Measom
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
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12
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Semeno VV, Vasylchenko VO, Fesun IM, Ruzhylo LY, Kipriianov MO, Melnykov KP, Skreminskyi A, Iminov R, Mykhailiuk P, Vashchenko BV, Grygorenko OO. Bicyclo[m.n.k]alkane Building Blocks as Promising Benzene and Cycloalkane Isosteres: Multigram Synthesis, Physicochemical and Structural Characterization. Chemistry 2024; 30:e202303859. [PMID: 38149408 DOI: 10.1002/chem.202303859] [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: 11/20/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 12/28/2023]
Abstract
Electrophilic double bond functionalization - intramolecular enolate alkylation sequence was used to obtain a series of bridged and fused bicyclo[m.n.k]alkane derivatives (i. e., bicyclo[4.1.1]octanes, bicyclo[2.2.1]heptanes, bicyclo[3.2.1]octanes, bicyclo[3.1.0]hexanes, and bicyclo[4.2.0]heptanes). The scope and limitations of the method were established, and applicability to the multigram synthesis of target bicyclic compounds was illustrated. Using the developed protocols, over 50 mono- and bifunctional building blocks relevant to medicinal chemistry were prepared. The synthesized compounds are promising isosteres of benzene and cycloalkane rings, which is confirmed by their physicochemical and structural characterization (pKa , LogP, and exit vector parameters (EVP)). "Rules of thumb" for the upcoming isosteric replacement studies were proposed.
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Affiliation(s)
- Volodymyr V Semeno
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | | | - Ihor M Fesun
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
| | - Liudmyla Yu Ruzhylo
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- National Technical University of Ukraine " Igor Sikorsky Kyiv Polytechnic Institute", Beresteiskyi Ave. 37, Kyїv, 03056, Ukraine
| | - Mykhailo O Kipriianov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- National Technical University of Ukraine " Igor Sikorsky Kyiv Polytechnic Institute", Beresteiskyi Ave. 37, Kyїv, 03056, Ukraine
| | - Kostiantyn P Melnykov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | | | - Rustam Iminov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
| | | | - Bohdan V Vashchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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13
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Yang Y, Tsien J, Dykstra R, Chen SJ, Wang JB, Merchant RR, Hughes JME, Peters BK, Gutierrez O, Qin T. Programmable late-stage functionalization of bridge-substituted bicyclo[1.1.1]pentane bis-boronates. Nat Chem 2024; 16:285-293. [PMID: 37884667 PMCID: PMC10922318 DOI: 10.1038/s41557-023-01342-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/08/2023] [Indexed: 10/28/2023]
Abstract
Modular functionalization enables versatile exploration of chemical space and has been broadly applied in structure-activity relationship (SAR) studies of aromatic scaffolds during drug discovery. Recently, the bicyclo[1.1.1]pentane (BCP) motif has increasingly received attention as a bioisosteric replacement of benzene rings due to its ability to improve the physicochemical properties of prospective drug candidates, but studying the SARs of C2-substituted BCPs has been heavily restricted by the need for multistep de novo synthesis of each analogue of interest. Here we report a programmable bis-functionalization strategy to enable late-stage sequential derivatization of BCP bis-boronates, opening up opportunities to explore the SARs of drug candidates possessing multisubstituted BCP motifs. Our approach capitalizes on the inherent chemoselectivity exhibited by BCP bis-boronates, enabling highly selective activation and functionalization of bridgehead (C3)-boronic pinacol esters (Bpin), leaving the C2-Bpin intact and primed for subsequent derivatization. These selective transformations of both BCP bridgehead (C3) and bridge (C2) positions enable access to C1,C2-disubstituted and C1,C2,C3-trisubstituted BCPs that encompass previously unexplored chemical space.
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Affiliation(s)
- Yangyang Yang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ryan Dykstra
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Si-Jie Chen
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - James B Wang
- 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
| | - Jonathan M E Hughes
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Byron K Peters
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Osvaldo Gutierrez
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Harwood LA, Xiong Z, Christensen KE, Wang R, Wong LL, Robertson J. Selective P450 BM3 Hydroxylation of Cyclobutylamine and Bicyclo[1.1.1]pentylamine Derivatives: Underpinning Synthetic Chemistry for Drug Discovery. J Am Chem Soc 2023; 145:27767-27773. [PMID: 38051939 PMCID: PMC10740007 DOI: 10.1021/jacs.3c10542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Achieving single-step syntheses of a set of related compounds divergently and selectively from a common starting material affords substantial efficiency gains when compared with preparing those same compounds by multiple individual syntheses. In order for this approach to be realized, complementary reagent systems must be available; here, a panel of engineered P450BM3 enzymes is shown to fulfill this remit in the selective C-H hydroxylation of cyclobutylamine derivatives at chemically unactivated sites. The oxidations can proceed with high regioselectivity and stereoselectivity, producing valuable bifunctional intermediates for synthesis and applications in fragment-based drug discovery. The process also applies to bicyclo[1.1.1]pentyl (BCP) amine derivatives to achieve the first direct enantioselective functionalization of the bridging methylenes and open a short and efficient route to chiral BCP bioisosteres for medicinal chemistry. The combination of substrate, enzyme, and reaction engineering provides a powerful general platform for small-molecule elaboration and diversification.
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Affiliation(s)
- Lucy A. Harwood
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ziyue Xiong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
| | - Kirsten E. Christensen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ruiyao Wang
- Wisdom
Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool
University, Suzhou Industrial
Park, Suzhou, Jiangsu, 215123, P. R. China
| | - Luet L. Wong
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K.
| | - Jeremy Robertson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Oxford
Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
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15
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Denisenko A, Garbuz P, Makovetska Y, Shablykin O, Lesyk D, Al-Maali G, Korzh R, Sadkova IV, Mykhailiuk PK. 1,2-Disubstituted bicyclo[2.1.1]hexanes as saturated bioisosteres of ortho-substituted benzene. Chem Sci 2023; 14:14092-14099. [PMID: 38098705 PMCID: PMC10718076 DOI: 10.1039/d3sc05121h] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 12/17/2023] Open
Abstract
Bicyclo[2.1.1]hexanes have been synthesized, characterized, and biologically validated as saturated bioisosteres of the ortho-substituted benzene ring. The incorporation of the 1,2-disubstituted bicyclo[2.1.1]hexane core into the structure of fungicides boscalid (BASF), bixafen (Bayer CS), and fluxapyroxad (BASF) gave saturated patent-free analogs with high antifungal activity.
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Affiliation(s)
- Aleksandr Denisenko
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
| | - Pavel Garbuz
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
| | | | - Oleh Shablykin
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the NAS of Ukraine 02094 Kyiv Ukraine
| | - Dmytro Lesyk
- Bienta Winston Churchill st. 78 02094 Kyiv Ukraine
| | - Galeb Al-Maali
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
- Institute of Botany of the National Academy of Sciences of Ukraine 02094 Kyiv Ukraine
| | - Rodion Korzh
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
| | - Iryna V Sadkova
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
| | - Pavel K Mykhailiuk
- Enamine Ltd Winston Churchill st. 78 02094 Kyiv Ukraine www.mykhailiukchem.org
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16
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Meanwell NA. Applications of Bioisosteres in the Design of Biologically Active Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18087-18122. [PMID: 36961953 DOI: 10.1021/acs.jafc.3c00765] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.
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Affiliation(s)
- Nicholas A Meanwell
- The Baruch S. Blumberg Institute, 3805 Old Easton Rd, Doylestown, Pennsylvania 18902, United States
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17
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Tang L, Xiao Y, Wu F, Zhou JL, Xu TT, Feng JJ. Silver-Catalyzed Dearomative [2π+2σ] Cycloadditions of Indoles with Bicyclobutanes: Access to Indoline Fused Bicyclo[2.1.1]hexanes. Angew Chem Int Ed Engl 2023; 62:e202310066. [PMID: 37822277 DOI: 10.1002/anie.202310066] [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: 07/14/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
Bicyclo[2.1.1]hexanes (BCHs) are becoming ever more important in drug design and development as bridged scaffolds that provide underexplored chemical space, but are difficult to access. Here a silver-catalyzed dearomative [2π+2σ] cycloaddition strategy for the synthesis of indoline fused BCHs from N-unprotected indoles and bicyclobutane precursors is described. The strain-release dearomative cycloaddition operates under mild conditions, tolerating a wide range of functional groups. It is capable of forming BCHs with up to four contiguous quaternary carbon centers, achieving yields of up to 99 %. In addition, a scale-up experiment and the synthetic transformations of the cycloadducts further highlighted the synthetic utility.
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Affiliation(s)
- Lei Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
| | - Yuanjiu Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
| | - Feng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
| | - Jin-Lan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
| | - Tong-Tong Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
| | - Jian-Jun Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan, 410082, P. R. China
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18
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Abstract
The concept of strain in organic compounds is as old as modern organic chemistry and was initially introduced to justify the synthetic setbacks along the synthesis of small ring systems (pars construens of strain). In the last decades, chemists have developed an arsenal of strain-release reactions (pars destruens of strain) which can generate─with significant driving force─rigid aliphatic systems that can act as three-dimensional alternatives to (hetero)arenes. Photocatalysis added an additional dimension to strain-release processes by leveraging the energy of photons to create chemical complexity under mild conditions. This perspective presents the latest advancements in strain-release photocatalysis─with emphases on mechanisms, catalytic cycles, and current limitations─the unique chemical architectures that can be produced, and possible future directions.
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Affiliation(s)
- Peter Bellotti
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York 10021, New York United States
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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19
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Reinhold M, Steinebach J, Golz C, Walker JCL. Synthesis of polysubstituted bicyclo[2.1.1]hexanes enabling access to new chemical space. Chem Sci 2023; 14:9885-9891. [PMID: 37736652 PMCID: PMC10510755 DOI: 10.1039/d3sc03083k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Saturated bridged-bicyclic compounds are currently under intense investigation as building blocks for pharmaceutical drug design. However, the most common methods for their preparation only provide access to bridgehead-substituted structures. The synthesis of bridge-functionalised species is highly challenging but would open up many new opportunities for molecular design. We describe a photocatalytic cycloaddition reaction that provides unified access to bicyclo[2.1.1]hexanes with 11 distinct substitution patterns. Bridge-substituted structures that represent ortho-, meta-, and polysubstituted benzene bioisosteres, as well as those that enable the investigation of chemical space inaccessible to aromatic motifs can all be prepared using this operationally simple protocol. Proof-of-concept examples of the application of the method to the synthesis of saturated analogues of biorelevant trisubstituted benzenes are also presented.
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Affiliation(s)
- Marius Reinhold
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Justin Steinebach
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Christopher Golz
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Johannes C L Walker
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen Tammannstr. 2 37077 Göttingen Germany
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20
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Lu Y, Chen C. Exceptional reactivity of the bridgehead amine on bicyclo[1.1.1]pentane. ARKIVOC 2023; 2023:202312003. [PMID: 37786812 PMCID: PMC10544781 DOI: 10.24820/ark.5550190.p012.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Bicyclo[1.1.1]pentane (BCP) has received substantial interest in the field of synthetic chemistry recently for its potential use as a benzene isostere in medicinal chemistry. Whereas bicyclo[2.2.2]octane (BCO) has also been used as a bioisostere of benzene, the condensation of BCP-amine with nadic anhydride is significantly easier than that of BCO-amine. Analyses of the geometries and the frontier molecular orbitals of these amines suggest that the low steric hindrance and high intrinsic nucleophilicity of BCP-amine together contribute to its exceptional reactivity.
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Affiliation(s)
- Yong Lu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038
| | - Chuo Chen
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038
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21
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Radhoff N, Daniliuc CG, Studer A. Lewis Acid Catalyzed Formal (3+2)-Cycloaddition of Bicyclo[1.1.0]butanes with Ketenes. Angew Chem Int Ed Engl 2023; 62:e202304771. [PMID: 37166141 DOI: 10.1002/anie.202304771] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
Abstract
Design, synthesis and application of benzene bioisosteres have attracted a lot of attention in the past 20 years. Recently, bicyclo[2.1.1]hexanes have emerged as highly attractive bioisosteres for ortho- and meta-substituted benzenes. Herein we report a mild, scalable and transition-metal-free protocol for the construction of highly substituted bicyclo[2.1.1]hexan-2-ones through Lewis acid catalyzed (3+2)-cycloaddition of bicyclo[1.1.0]-butane ketones with disubstituted ketenes. The reaction shows high functional group tolerance as documented by the successful preparation of various 3-alkyl-3-aryl as well as 3,3-bisalkyl bicyclo[2.1.1]hexan-2-ones (26 examples, up to 89 % yield). Postfunctionalization of the exocyclic ketone moiety is also demonstrated.
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Affiliation(s)
- Niklas Radhoff
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
| | - Armido Studer
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
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22
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Liang Y, Paulus F, Daniliuc CG, Glorius F. Catalytic Formal [2π+2σ] Cycloaddition of Aldehydes with Bicyclobutanes: Expedient Access to Polysubstituted 2-Oxabicyclo[2.1.1]hexanes. Angew Chem Int Ed Engl 2023; 62:e202305043. [PMID: 37307521 DOI: 10.1002/anie.202305043] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Synthesis of bicyclic scaffolds has attracted tremendous attention because they are playing an important role as saturated bioisosteres of benzenoids in modern drug discovery. Here, we report a BF3 -catalyzed [2π+2σ] cycloaddition of aldehydes with bicyclo[1.1.0]butanes (BCBs) to access polysubstituted 2-oxabicyclo[2.1.1]hexanes. A new kind of BCB containing an acyl pyrazole group was invented, which not only significantly facilitates the reactions, but can also serve as a handle for diverse downstream transformations. Furthermore, aryl and vinyl epoxides can also be utilized as substrates which undergo cycloaddition with BCBs after in situ rearrangement to aldehydes. We anticipate that our results will promote access to challenging sp3 -rich bicyclic frameworks and the exploration of BCB-based cycloaddition chemistry.
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Affiliation(s)
- Yujie Liang
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Fritz Paulus
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149, Münster, Germany
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23
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Shire B, Anderson EA. Conquering the Synthesis and Functionalization of Bicyclo[1.1.1]pentanes. JACS AU 2023; 3:1539-1553. [PMID: 37388694 PMCID: PMC10301682 DOI: 10.1021/jacsau.3c00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 07/01/2023]
Abstract
Bicyclo[1.1.1]pentanes (BCPs) have become established as attractive bioisosteres for para-substituted benzene rings in drug design. Conferring various beneficial properties compared with their aromatic "parents," BCPs featuring a wide array of bridgehead substituents can now be accessed by an equivalent variety of methods. In this perspective, we discuss the evolution of this field and focus on the most enabling and general methods for BCPs synthesis, considering both scope and limitation. Recent breakthroughs on the synthesis of bridge-substituted BCPs are described, as well as methodologies for postsynthesis functionalization. We further explore new challenges and directions for the field, such as the emergence of other rigid small ring hydrocarbons and heterocycles possessing unique substituent exit vectors.
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24
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Denisenko A, Garbuz P, Voloshchuk NM, Holota Y, Al-Maali G, Borysko P, Mykhailiuk PK. 2-Oxabicyclo[2.1.1]hexanes as saturated bioisosteres of the ortho-substituted phenyl ring. Nat Chem 2023:10.1038/s41557-023-01222-0. [PMID: 37277469 PMCID: PMC10396955 DOI: 10.1038/s41557-023-01222-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/25/2023] [Indexed: 06/07/2023]
Abstract
The ortho-substituted phenyl ring is a basic structural element in chemistry. It is found in more than three hundred drugs and agrochemicals. During the past decade, scientists have tried to replace the phenyl ring in bioactive compounds with saturated bioisosteres to obtain novel patentable structures. However, most of the research in this area has been devoted to the replacement of the para-substituted phenyl ring. Here we have developed saturated bioisosteres of the ortho-substituted phenyl ring with improved physicochemical properties: 2-oxabicyclo[2.1.1]hexanes. Crystallographic analysis revealed that these structures and the ortho-substituted phenyl ring indeed have similar geometric properties. Replacement of the phenyl ring in marketed agrochemicals fluxapyroxad (BASF) and boscalid (BASF) with 2-oxabicyclo[2.1.1]hexanes dramatically improved their water solubility, reduced lipophilicity and most importantly retained bioactivity. This work suggests an opportunity for chemists to replace the ortho-substituted phenyl ring in bioactive compounds with saturated bioisosteres in medicinal chemistry and agrochemistry.
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Affiliation(s)
| | | | | | | | - Galeb Al-Maali
- Bienta, Kyiv, Ukraine
- M.G. Kholodny Institute of Botany of the National Academy of Sciences of Ukraine, Kyiv, Ukraine
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25
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Wiesenfeldt MP, Rossi-Ashton JA, Perry IB, Diesel J, Garry OL, Bartels F, Coote SC, Ma X, Yeung CS, Bennett DJ, MacMillan DWC. General access to cubanes as benzene bioisosteres. Nature 2023; 618:513-518. [PMID: 37015289 PMCID: PMC10680098 DOI: 10.1038/s41586-023-06021-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
The replacement of benzene rings with sp3-hybridized bioisosteres in drug candidates generally improves pharmacokinetic properties while retaining biological activity1-5. Rigid, strained frameworks such as bicyclo[1.1.1]pentane and cubane are particularly well suited as the ring strain imparts high bond strength and thus metabolic stability on their C-H bonds. Cubane is the ideal bioisostere as it provides the closest geometric match to benzene6,7. At present, however, all cubanes in drug design, like almost all benzene bioisosteres, act solely as substitutes for mono- or para-substituted benzene rings1-7. This is owing to the difficulty of accessing 1,3- and 1,2-disubstituted cubane precursors. The adoption of cubane in drug design has been further hindered by the poor compatibility of cross-coupling reactions with the cubane scaffold, owing to a competing metal-catalysed valence isomerization8-11. Here we report expedient routes to 1,3- and 1,2-disubstituted cubane building blocks using a convenient cyclobutadiene precursor and a photolytic C-H carboxylation reaction, respectively. Moreover, we leverage the slow oxidative addition and rapid reductive elimination of copper to develop C-N, C-C(sp3), C-C(sp2) and C-CF3 cross-coupling protocols12,13. Our research enables facile elaboration of all cubane isomers into drug candidates, thus enabling ideal bioisosteric replacement of ortho-, meta- and para-substituted benzenes.
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Affiliation(s)
| | | | - Ian B Perry
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
| | - Johannes Diesel
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
| | - Olivia L Garry
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
| | - Florian Bartels
- Merck Center for Catalysis at Princeton University, Princeton, NJ, USA
| | | | - Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - Charles S Yeung
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
| | - David J Bennett
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, MA, USA
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26
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Wright BA, Matviitsuk A, Black MJ, García-Reynaga P, Hanna LE, Herrmann AT, Ameriks MK, Sarpong R, Lebold TP. Skeletal Editing Approach to Bridge-Functionalized Bicyclo[1.1.1]pentanes from Azabicyclo[2.1.1]hexanes. J Am Chem Soc 2023; 145:10960-10966. [PMID: 37145091 PMCID: PMC10281541 DOI: 10.1021/jacs.3c02616] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Azabicyclo[2.1.1]hexanes (aza-BCHs) and bicyclo[1.1.1]pentanes (BCPs) have emerged as attractive classes of sp3-rich cores for replacing flat, aromatic groups with metabolically resistant, three-dimensional frameworks in drug scaffolds. Strategies to directly convert, or "scaffold hop", between these bioisosteric subclasses through single-atom skeletal editing would enable efficient interpolation within this valuable chemical space. Herein, we describe a strategy to "scaffold hop" between aza-BCH and BCP cores through a nitrogen-deleting skeletal edit. Photochemical [2+2] cycloadditions, used to prepare multifunctionalized aza-BCH frameworks, are coupled with a subsequent deamination step to afford bridge-functionalized BCPs, for which few synthetic solutions currently exist. The modular sequence provides access to various privileged bridged bicycles of pharmaceutical relevance.
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Affiliation(s)
- Brandon A Wright
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Michael J Black
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Luke E Hanna
- Janssen Research and Development, San Diego, California 92121, United States
| | - Aaron T Herrmann
- Janssen Research and Development, San Diego, California 92121, United States
| | - Michael K Ameriks
- Janssen Research and Development, San Diego, California 92121, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Terry P Lebold
- Janssen Research and Development, San Diego, California 92121, United States
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27
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Dong W, Keess S, Molander GA. Nickel-Mediated Alkyl-, Acyl-, and Sulfonylcyanation of [1.1.1]Propellane. CHEM CATALYSIS 2023; 3:100608. [PMID: 37840854 PMCID: PMC10572913 DOI: 10.1016/j.checat.2023.100608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The replacement of traditional functional groups with polycyclic scaffolds has been increasingly rewarding in medicinal chemistry programs. Over the decades, 1,3-disubstituted bicyclo[1.1.1]pentanes (BCPs) have demonstrated the potential for being competent bioisosteres for aryl-, alkyl- and alkynyl substructures. Although highly desired, mild and versatile synthetic methods to access synthetically valuable BCP-containing building blocks remain limited. Herein, a versatile way to access bridgehead substituted BCP nitriles, a useful BCP building block, is described, enabled by the unexpected selectivity of nickel in the multi-component radical cyanation. Commodity materials including carboxylic acids, amines, sulfonyl chlorides, and alkyl chlorides are engaged to provide a broad spectrum of substituted BCP nitriles in a single-step, multi-component fashion.
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Affiliation(s)
- Weizhe Dong
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Sebastian Keess
- Medicinal Chemistry Department, Neuroscience Discovery Research, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Gary A. Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
- Lead contact
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28
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Kim MJ, Wang DJ, Targos K, Garcia UA, Harris AF, Guzei IA, Wickens ZK. Diastereoselective Synthesis of Cyclopropanes from Carbon Pronucleophiles and Alkenes. Angew Chem Int Ed Engl 2023; 62:e202303032. [PMID: 36929023 PMCID: PMC10189787 DOI: 10.1002/anie.202303032] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Cyclopropanes are desirable structural motifs with valuable applications in drug discovery and beyond. Established alkene cyclopropanation methods give rise to cyclopropanes with a limited array of substituents, are difficult to scale, or both. Herein, we disclose a new cyclopropane synthesis through the formal coupling of abundant carbon pronucleophiles and unactivated alkenes. This strategy exploits dicationic adducts derived from electrolysis of thianthrene in the presence of alkene substrates. We find that these dielectrophiles undergo cyclopropanation with methylene pronucleophiles via alkenyl thianthrenium intermediates. This protocol is scalable, proceeds with high diastereoselectivity, and tolerates diverse functional groups on both the alkene and pronucleophile coupling partners. To validate the utility of this new procedure, we prepared an array of substituted analogs of an established cyclopropane that is en route to multiple pharmaceuticals.
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Affiliation(s)
- Min Ji Kim
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Diana J. Wang
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Karina Targos
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Uriel A. Garcia
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Alison F. Harris
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
| | - Zachary K. Wickens
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, 53706, United States
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29
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Anderson JM, Measom ND, Murphy JA, Poole DL. Bridge Heteroarylation of Bicyclo[1.1.1]pentane Derivatives. Org Lett 2023; 25:2053-2057. [PMID: 36929825 DOI: 10.1021/acs.orglett.3c00412] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Herein, we report the decarboxylative Minisci heteroarylation of bicyclo[1.1.1]pentane (BCP) and 2-oxabicyclo[2.1.1]hexane (oBCH) derivatives at the bridge positions. In an operationally simple, photocatalyst-free process, free bridge carboxylic acids are directly coupled with nonprefunctionalized heteroarenes to provide rare examples of polysubstituted BCP and oBCH derivatives in synthetically useful yields. Additionally, the impact of the BCP core on the physicochemical properties of a representative example compared to those of its all-aromatic ortho- and meta-substituted analogues is evaluated.
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Affiliation(s)
- Joseph M Anderson
- Medicinal Chemistry, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K.,Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Nicholas D Measom
- Medicinal Chemistry, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - John A Murphy
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Darren L Poole
- Medicinal Chemistry, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
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30
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Agasti S, Beltran F, Pye E, Kaltsoyannis N, Crisenza GEM, Procter DJ. A catalytic alkene insertion approach to bicyclo[2.1.1]hexane bioisosteres. Nat Chem 2023; 15:535-541. [PMID: 36781910 DOI: 10.1038/s41557-023-01135-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/12/2023] [Indexed: 02/15/2023]
Abstract
C(sp3)-rich bicyclic hydrocarbon scaffolds, as exemplified by bicyclo[1.1.1]pentanes, play an increasingly high-profile role as saturated bioisosteres of benzenoids in medicinal chemistry and crop science. Substituted bicyclo[2.1.1]hexanes (BCHs) are emerging bicyclic hydrocarbon bioisosteres for ortho- and meta-substituted benzenes, but are difficult to access. Therefore, a general synthetic route to BCHs is needed if their potential as bioisosteres is to be realized. Here we describe a broadly applicable catalytic approach that delivers substituted BCHs by intermolecular coupling between olefins and bicyclo[1.1.0]butyl (BCB) ketones. The SmI2-catalysed process works for a wide range of electron-deficient alkenes and substituted BCB ketones, operates with SmI2 loadings as low as 5 mol% and is underpinned by a radical relay mechanism that is supported by density functional theory calculations. The product BCH ketones have been shown to be versatile synthetic intermediates through selective downstream manipulation and the expedient synthesis of a saturated hydrocarbon analogue of the broad-spectrum antimicrobial, phthalylsulfathiazole.
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Affiliation(s)
- Soumitra Agasti
- Department of Chemistry, The University of Manchester, Manchester, UK
| | - Frédéric Beltran
- Department of Chemistry, The University of Manchester, Manchester, UK
| | - Emma Pye
- Department of Chemistry, The University of Manchester, Manchester, UK
| | | | | | - David J Procter
- Department of Chemistry, The University of Manchester, Manchester, UK.
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31
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Garry OL, Heilmann M, Chen J, Liang Y, Zhang X, Ma X, Yeung CS, Bennett DJ, MacMillan DWC. Rapid Access to 2-Substituted Bicyclo[1.1.1]pentanes. J Am Chem Soc 2023; 145:3092-3100. [PMID: 36696089 PMCID: PMC10680143 DOI: 10.1021/jacs.2c12163] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The replacement of aryl rings with saturated carbocyclic structures has garnered significant interest in drug discovery due to the potential for improved pharmacokinetic properties upon substitution. In particular, 1,3-difunctionalized bicyclo[1.1.1]pentanes (BCPs) have been widely adopted as bioisosteres for parasubstituted arene rings, appearing in a number of lead pharmaceutical candidates. However, despite the pharmaceutical value of 2-substituted BCPs as replacements for ortho- or meta-substituted arene rings, general and rapid syntheses of these scaffolds remain elusive. Current approaches to 2-substituted BCPs rely on installation of the bridge substituent prior to BCP core construction, leading to lengthy step counts and often nonmodular sequences. While challenging, direct functionalization of the strong bridge BCP C-H bonds would offer a more streamlined pathway to diverse 2-substituted BCPs. Here, we report a generalizable synthetic linchpin strategy for bridge functionalization via radical C-H abstraction of the BCP core. Through mild generation of a strong hydrogen atom abstractor, we rapidly synthesize novel 2-substituted BCP synthetic linchpins in one pot. These synthetic linchpins then serve as common precursors to complex 2-substituted BCPs, allowing one-step access to a number of previously inaccessible electrophile and nucleophile fragments at the 2-position via two new metallaphotoredox protocols. Altogether, this platform enables the expedient synthesis of four pharmaceutical analogues, all of which show similar or improved properties compared to their aryl-containing equivalents, demonstrating the potential of these 2-substituted BCPs in drug development.
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Affiliation(s)
- Olivia L Garry
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Michael Heilmann
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Jingjia Chen
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Yufan Liang
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Xiaheng Zhang
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Charles S Yeung
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - David Jonathan Bennett
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
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32
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Ma X, Jiang Y. Synthesis of gem-Diboromethyl-Substituted Bicyclo[1.1.1]pentanes and Their Application in Palladium-Catalyzed Cross Couplings. J Org Chem 2023; 88:1665-1694. [PMID: 36695785 DOI: 10.1021/acs.joc.2c02701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We describe the first general transition-metal-free synthesis of gem-diboromethyl-substituted bicyclo[1.1.1]pentane (BCP) and other related C(sp3)-rich carbocyclic benzene bioisosteres from their corresponding p-tosylhydrazones. These novel functionalized benzene bioisosteres demonstrated unique reactivities toward palladium-catalyzed C(sp2)-C(sp3) cross couplings. The overall transformation can be applied to relatively complex substrates with potential utility in drug discovery.
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Affiliation(s)
- Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc. 33 Ave. Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Yuan Jiang
- Department of Analytical Research and Development, Merck & Co., Inc. 33 Ave. Louis Pasteur, Boston, Massachusetts 02115, United States
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33
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Iida T, Kanazawa J, Matsunaga T, Miyamoto K, Hirano K, Uchiyama M. Practical and Facile Access to Bicyclo[3.1.1]heptanes: Potent Bioisosteres of meta-Substituted Benzenes. J Am Chem Soc 2022; 144:21848-21852. [PMID: 36342862 DOI: 10.1021/jacs.2c09733] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is increasing interest in replacement of the planar aromatic rings of drug candidates with three-dimensional caged scaffolds in order to improve the physical properties, but bioisosteres of meta-substituted benzenes have remained elusive. We focused on the bicyclo[3.1.1]heptane (BCH) scaffold as a novel bioisostere of meta-substituted benzenes, anticipating that [3.1.1]propellane (2) would be a versatile precursor of diversely functionalized BCHs. Here, we describe a practical preparative method for [3.1.1]propellane from newly developed 1,5-diiodobicyclo[3.1.1]heptane (1), as well as difunctionalization reactions of 2 leading to functionalized BCHs. We also report postfunctionalization reactions of these products.
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Affiliation(s)
- Toranosuke Iida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junichiro Kanazawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tadafumi Matsunaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiichi Hirano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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34
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Frank N, Nugent J, Shire BR, Pickford HD, Rabe P, Sterling AJ, Zarganes-Tzitzikas T, Grimes T, Thompson AL, Smith RC, Schofield CJ, Brennan PE, Duarte F, Anderson EA. Synthesis of meta-substituted arene bioisosteres from [3.1.1]propellane. Nature 2022; 611:721-726. [PMID: 36108675 DOI: 10.1038/s41586-022-05290-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022]
Abstract
Small-ring cage hydrocarbons are popular bioisosteres (molecular replacements) for commonly found para-substituted benzene rings in drug design1. The utility of these cage structures derives from their superior pharmacokinetic properties compared with their parent aromatics, including improved solubility and reduced susceptibility to metabolism2,3. A prime example is the bicyclo[1.1.1]pentane motif, which is mainly synthesized by ring-opening of the interbridgehead bond of the strained hydrocarbon [1.1.1]propellane with radicals or anions4. By contrast, scaffolds mimicking meta-substituted arenes are lacking because of the challenge of synthesizing saturated isosteres that accurately reproduce substituent vectors5. Here we show that bicyclo[3.1.1]heptanes (BCHeps), which are hydrocarbons for which the bridgehead substituents map precisely onto the geometry of meta-substituted benzenes, can be conveniently accessed from [3.1.1]propellane. We found that [3.1.1]propellane can be synthesized on a multigram scale, and readily undergoes a range of radical-based transformations to generate medicinally relevant carbon- and heteroatom-substituted BCHeps, including pharmaceutical analogues. Comparison of the absorption, distribution, metabolism and excretion (ADME) properties of these analogues reveals enhanced metabolic stability relative to their parent arene-containing drugs, validating the potential of this meta-arene analogue as an sp3-rich motif in drug design. Collectively, our results show that BCHeps can be prepared on useful scales using a variety of methods, offering a new surrogate for meta-substituted benzene rings for implementation in drug discovery programmes.
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Affiliation(s)
- Nils Frank
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeremy Nugent
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Bethany R Shire
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Helena D Pickford
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Alistair J Sterling
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Thomas Grimes
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Russell C Smith
- Abbvie Drug Discovery Science & Technology (DDST), North Chicago, IL, USA
| | | | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
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35
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[2]-Ladderanes as isosteres for meta-substituted aromatic rings and rigidified cyclohexanes. Nat Commun 2022; 13:6056. [PMID: 36229621 PMCID: PMC9561113 DOI: 10.1038/s41467-022-33827-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/04/2022] [Indexed: 01/05/2023] Open
Abstract
Aromatic ring isosteres and rigidified saturated hydrocarbons are important motifs to enable drug discovery. Herein we disclose [2]-ladderanes as a class of meta-substituted aromatic ring isosteres and rigidified cyclohexanes. A straightforward synthesis of the building blocks is presented along with representative derivatization. Preliminary studies reveal that the [2]-ladderanes offer similar metabolic and physicochemical properties thus establishing this class of molecules as interesting motifs.
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36
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Bychek R, Mykhailiuk PK. A Practical and Scalable Approach to Fluoro-Substituted Bicyclo[1.1.1]pentanes. Angew Chem Int Ed Engl 2022; 61:e202205103. [PMID: 35638404 PMCID: PMC9401599 DOI: 10.1002/anie.202205103] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Indexed: 12/27/2022]
Abstract
After more than 20 years of trials, a practical scalable approach to fluoro‐substituted bicyclo[1.1.1]pentanes (F‐BCPs) has been developed. The physicochemical properties of the F‐BCPs have been studied, and the core was incorporated into the structure of the anti‐inflammatory drug Flurbiprofen in place of the fluorophenyl ring.
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Affiliation(s)
- Roman Bychek
- Enamine Ltd., Chervonotkatska 60, 02094, Kyiv, Ukraine
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37
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Bychek R, Mykhailiuk PK. A Practical and Scalable Approach to Fluoro‐Substituted Bicyclo[1.1.1]pentanes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205103] [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)
- Roman Bychek
- Enamine Ltd. Chervonotkatska 60 02094 Kyiv Ukraine
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38
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Lasányi D, Máth D, Tolnai GL. Synthesis and Use of Bicyclo[1.1.1]pentylaldehyde Building Blocks. J Org Chem 2022; 87:2393-2401. [DOI: 10.1021/acs.joc.1c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dániel Lasányi
- Institute of Chemistry, Eotvos Lorand University, Pazmany P. stny. 1/a, Budapest H1117, Hungary
| | - Dániel Máth
- Institute of Chemistry, Eotvos Lorand University, Pazmany P. stny. 1/a, Budapest H1117, Hungary
| | - Gergely L. Tolnai
- Institute of Chemistry, Eotvos Lorand University, Pazmany P. stny. 1/a, Budapest H1117, Hungary
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39
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Harmata AS, Spiller TE, Sowden MJ, Stephenson CRJ. Photochemical Formal (4 + 2)-Cycloaddition of Imine-Substituted Bicyclo[1.1.1]pentanes and Alkenes. J Am Chem Soc 2021; 143:21223-21228. [PMID: 34902245 PMCID: PMC9241356 DOI: 10.1021/jacs.1c10541] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Amines containing bridged bicyclic carbon skeletons are desirable building blocks for medicinal chemistry. Herein, we report the conversion of bicyclo[1.1.1]pentan-1-amines to a wide range of polysubstituted bicyclo[3.1.1]heptan-1-amines through a photochemical, formal (4 + 2)-cycloaddition of an intermediate imine diradical. To our knowledge, this is the first reported method to convert the bicyclo[1.1.1]pentane skeleton to the bicyclo[3.1.1]heptane skeleton. Hydrolysis of the imine products gives complex, sp3-rich primary amine building blocks.
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Affiliation(s)
| | | | | | - Corey R. J. Stephenson
- Corresponding Author Corey R. J. Stephenson – Department of Chemistry, University of Michigan, 940 North University Avenue, Ann Arbor, Michigan 48109, United States;
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40
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Grygorenko OO, Volochnyuk DM, Vashchenko BV. Emerging Building Blocks for Medicinal Chemistry: Recent Synthetic Advances. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100857] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Oleksandr O. Grygorenko
- Enamine Ltd. Chervonotkatska 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
| | - Dmitriy M. Volochnyuk
- Enamine Ltd. Chervonotkatska 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
- Institute of Organic Chemistry National Academy of Sciences of Ukraine Murmanska Street 5 Kyiv 02094 Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd. Chervonotkatska 78 Kyiv 02094 Ukraine
- Taras Shevchenko National University of Kyiv Volodymyrska Street 60 Kyiv 01601 Ukraine
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41
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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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42
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Yang Y, Tsien J, Hughes JME, Peters BK, Merchant RR, Qin T. An intramolecular coupling approach to alkyl bioisosteres for the synthesis of multisubstituted bicycloalkyl boronates. Nat Chem 2021; 13:950-955. [PMID: 34584254 PMCID: PMC8739920 DOI: 10.1038/s41557-021-00786-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Bicyclic hydrocarbons, and bicyclo[1.1.1]pentanes (BCPs) in particular, are playing an emerging role as saturated bioisosteres in pharmaceutical, agrochemical and materials chemistry. Taking advantage of strain-release strategies, prior synthetic studies have featured the synthesis of bridgehead-substituted (C1, C3) BCPs from [1.1.1]propellane. Here, we describe an approach to access multisubstituted BCPs via intramolecular cyclization. In addition to C1,C3-disubstituted BCPs, this method also enables the construction of underexplored multisubstituted (C1, C2 and C3) BCPs from readily accessible cyclobutanones. The broad generality of this method has also been examined through the synthesis of a variety of other caged bicyclic molecules, ranging from [2.1.1] to [3.2.1] scaffolds. The modularity afforded by the pendant bridgehead boron pinacol esters generated during the cyclization reaction has been demonstrated through several downstream functionalizations, highlighting the ability of this approach to enable the programmed and divergent synthesis of multisubstituted bicyclic hydrocarbons.
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Affiliation(s)
- Yangyang Yang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States
| | - Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States
| | - Jonathan M. E. Hughes
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Byron K. Peters
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rohan R. Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, United States.,Correspondence to:
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Fominova K, Diachuk T, Granat D, Savchuk T, Vilchynskyi V, Svitlychnyi O, Meliantsev V, Kovalchuk I, Litskan E, Levterov VV, Badlo VR, Vaskevych RI, Vaskevych AI, Bolbut AV, Semeno VV, Iminov R, Shvydenko K, Kuznetsova AS, Dmytriv YV, Vysochyn D, Ripenko V, Tolmachev AA, Pavlova O, Kuznietsova H, Pishel I, Borysko P, Mykhailiuk PK. Oxa-spirocycles: synthesis, properties and applications. Chem Sci 2021; 12:11294-11305. [PMID: 34667540 PMCID: PMC8447932 DOI: 10.1039/d1sc03615g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/20/2021] [Indexed: 12/27/2022] Open
Abstract
A general approach to a new generation of spirocyclic molecules – oxa-spirocycles – was developed. The key synthetic step was iodocyclization. More than 150 oxa-spirocyclic compounds were prepared. Incorporation of an oxygen atom into the spirocyclic unit dramatically improved water solubility (by up to 40 times) and lowered lipophilicity. More potent oxa-spirocyclic analogues of antihypertensive drug terazosin were synthesized and studied in vivo. A general practical approach to a new generation of spirocyclic molecules – oxa-spirocycles – is developed.![]()
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Affiliation(s)
- Kateryna Fominova
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Taras Diachuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Dmitry Granat
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Taras Savchuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Vladyslav Vilchynskyi
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Oleksiy Svitlychnyi
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Vladyslav Meliantsev
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Igor Kovalchuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Eduard Litskan
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Vadym V Levterov
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Valentyn R Badlo
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Ruslan I Vaskevych
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine Murmanska St. 5 02094 Kyiv Ukraine
| | - Alla I Vaskevych
- National Technical University of Ukraine, Igor Sikorsky Kiev Polytechnic Institute Prosp. Peremohy 37 03056 Kyiv Ukraine
| | - Andrii V Bolbut
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine Murmanska St. 5 02094 Kyiv Ukraine
| | - Volodymyr V Semeno
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Rustam Iminov
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Kostiantyn Shvydenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine Murmanska St. 5 02094 Kyiv Ukraine
| | | | - Yurii V Dmytriv
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org.,National Technical University of Ukraine, Igor Sikorsky Kiev Polytechnic Institute Prosp. Peremohy 37 03056 Kyiv Ukraine
| | - Daniil Vysochyn
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Vasyl Ripenko
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | - Andrei A Tolmachev
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
| | | | | | - Iryna Pishel
- Bienta Chervonotkatska 78 02094 Kyiv Ukraine http://www.bienta.net
| | - Petro Borysko
- Bienta Chervonotkatska 78 02094 Kyiv Ukraine http://www.bienta.net
| | - Pavel K Mykhailiuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine http://www.enamine.net http://www.mykhailiukchem.org
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Zhao JX, Chang YX, He C, Burke BJ, Collins MR, Del Bel M, Elleraas J, Gallego GM, Montgomery TP, Mousseau JJ, Nair SK, Perry MA, Spangler JE, Vantourout JC, Baran PS. 1,2-Difunctionalized bicyclo[1.1.1]pentanes: Long-sought-after mimetics for ortho/ meta-substituted arenes. Proc Natl Acad Sci U S A 2021; 118:e2108881118. [PMID: 34244445 PMCID: PMC8285974 DOI: 10.1073/pnas.2108881118] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of a versatile platform for the synthesis of 1,2-difunctionalized bicyclo[1.1.1]pentanes to potentially mimic ortho/meta-substituted arenes is described. The syntheses of useful building blocks bearing alcohol, amine, and carboxylic acid functional handles have been achieved from a simple common intermediate. Several ortho- and meta-substituted benzene analogs, as well as simple molecular matched pairs, have also been prepared using this platform. The results of in-depth ADME (absorption, distribution, metabolism, and excretion) investigations of these systems are presented, as well as computational studies which validate the ortho- or meta-character of these bioisosteres.
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Affiliation(s)
- Jin-Xin Zhao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Yu-Xuan Chang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Chi He
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Benjamin J Burke
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - Michael R Collins
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121;
| | - Matthew Del Bel
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - Jeff Elleraas
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - Gary M Gallego
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - T Patrick Montgomery
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - James J Mousseau
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research, Development and Medical, Groton, CT 06340
| | - Sajiv K Nair
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | - Matthew A Perry
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research, Development and Medical, Groton, CT 06340
| | - Jillian E Spangler
- Oncology Medicinal Chemistry, Pfizer Worldwide Research, Development and Medical, San Diego, CA 92121
| | | | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037;
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