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Pereira O, Ruth M, Gerbig D, Wende RC, Schreiner PR. Leveraging Limited Experimental Data with Machine Learning: Differentiating a Methyl from an Ethyl Group in the Corey-Bakshi-Shibata Reduction. J Am Chem Soc 2024; 146:14576-14586. [PMID: 38752849 DOI: 10.1021/jacs.4c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
We present a case study on how to improve an existing metal-free catalyst for a particularly difficult reaction, namely, the Corey-Bakshi-Shibata (CBS) reduction of butanone, which constitutes the classic and prototypical challenge of being able to differentiate a methyl from an ethyl group. As there are no known strategies on how to address this challenge, we leveraged the power of machine learning by constructing a realistic (for a typical laboratory) small, albeit high-quality, data set of about 100 reactions (run in triplicate) that we used to train a model in combination with a key-intermediate graph (of substrate and catalyst) to predict the differences in Gibbs activation energies ΔΔG‡ of the enantiomeric reaction paths. With the help of this model, we were able to select and subsequently screen a small selection of catalysts and increase the selectivity for the CBS reduction of butanone to 80% enantiomeric excess (ee), the highest possible value achieved to date for this substrate with a metal-free catalyst, thereby also exceeding the best available enzymatic systems (64% ee) and the selectivity with Corey's original catalyst (60% ee). This translates into a >50% improvement in relative ΔG‡ from 0.9 to 1.4 kcal mol-1. We underscore the transformative potential of machine learning in accelerating catalyst design because we rely on a manageable small data set and a key-intermediate graph representing a combination of catalyst and substrate graphs in lieu of a transition-state model. Our results highlight the synergy of synthetic chemistry and data-centric approaches and provide a blueprint for future catalyst optimization.
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Affiliation(s)
- Oliver Pereira
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marcel Ruth
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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2
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Sağırlı A, Acar H, Özçal HE, Büyükbayram M. Microwave-assisted synthesis and odor characteristics of some new isoxazolidines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2130079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Akın Sağırlı
- Faculty of Arts & Sciences, Department of Chemistry, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Havva Acar
- Faculty of Arts & Sciences, Department of Chemistry, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Hakan Emre Özçal
- Faculty of Arts & Sciences, Department of Chemistry, Bolu Abant Izzet Baysal University, Bolu, Turkey
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3
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Bethi V, Tanaka F. Organocatalytic Enantioselective γ-Position-Selective Mannich Reactions of β-Ketocarbonyl Derivatives. Org Lett 2022; 24:6711-6715. [PMID: 36096488 PMCID: PMC9513800 DOI: 10.1021/acs.orglett.2c02433] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Catalytic asymmetric Mannich reactions of β-ketocarbonyl
derivatives (such as β-ketoesters and (2-oxopropyl)phosphonate),
resulting in the formation of a C–C bond at the γ-position
of the β-ketocarbonyl derivatives with high enantioselectivities,
are reported. The bond formation at the α-position of the β-ketoester
was reversible, and the γ-position-reacted product δ-amino
β-ketoester derivative was kinetically formed and was stable.
The dynamic kinetic process was key for the direct access to the γ-position-reacted
products from β-ketocarbonyls under catalytic conditions.
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Affiliation(s)
- Venkati Bethi
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Fujie Tanaka
- Chemistry and Chemical Bioengineering Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
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4
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Narita K, Yoshida S, Satoh H, Watanabe K, Yoshimura Y. Synthetic route for optically active tetracyclic hexahydrobenzofurobenzopyran skeleton of bisabosquals. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Ohashi E, Karanjit S, Nakayama A, Takeuchi K, Emam SE, Ando H, Ishida T, Namba K. Efficient construction of the hexacyclic ring core of palau'amine: the p K a concept for proceeding with unfavorable equilibrium reactions. Chem Sci 2021; 12:12201-12210. [PMID: 34667586 PMCID: PMC8457368 DOI: 10.1039/d1sc03260g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/10/2021] [Indexed: 11/21/2022] Open
Abstract
Palau'amine has received a great deal of attention as an attractive synthetic target due to its intriguing molecular architecture and significant immunosuppressive activity, and we achieved its total synthesis in 2015. However, the synthesized palau'amine has not been readily applicable to the mechanistic study of immunosuppressive activity, because it requires 45 longest linear steps from a commercially available compound. Here, we report the short-step construction of the ABCDEF hexacyclic ring core of palau'amine. The construction of the CDE tricyclic ring core in a single step is achieved by our pKa concept for proceeding with unfavorable equilibrium reactions, and a palau'amine analog without the aminomethyl and chloride groups is synthesized in 20 longest linear steps from the same starting material. The palau'amine analog is confirmed to retain the immunosuppressive activity. The present synthetic approach for a palau'amine analog has the potential for use in the development of palau'amine probes for mechanistic elucidation. A palau'amine analog (2) was synthesized from 2-cyclopentenone in 20 steps. The construction of the CDE tricyclic ring core in a single step is achieved by our pKa concept for proceeding with the unfavorable equilibrium reactions.![]()
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Affiliation(s)
- Eisaku Ohashi
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Sangita Karanjit
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan .,Research Cluster on "Innovative Chemical Sensing", Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Atsushi Nakayama
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan .,Research Cluster on "Innovative Chemical Sensing", Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Kohei Takeuchi
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Sherif E Emam
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Hidenori Ando
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Tatsuhiro Ishida
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
| | - Kosuke Namba
- Graduate School of Pharmaceutical Sciences, Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan .,Research Cluster on "Innovative Chemical Sensing", Tokushima University 1-78 Shomachi Tokushima 770-8505 Japan
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Marine Heterocyclic Compounds That Modulate Intracellular Calcium Signals: Chemistry and Synthesis Approaches. Mar Drugs 2021; 19:md19020078. [PMID: 33572583 PMCID: PMC7911796 DOI: 10.3390/md19020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 11/21/2022] Open
Abstract
Intracellular Ca2+ plays a pivotal role in the control of a large series of cell functions in all types of cells, from neurotransmitter release and muscle contraction to gene expression, cell proliferation and cell death. Ca2+ is transported through specific channels and transporters in the plasma membrane and subcellular organelles such as the endoplasmic reticulum and mitochondria. Therefore, dysregulation of intracellular Ca2+ homeostasis may lead to cell dysfunction and disease. Accordingly, chemical compounds from natural origin and/or synthesis targeting directly or indirectly these channels and proteins may be of interest for the treatment of cell dysfunction and disease. In this review, we show an overview of a group of marine drugs that, from the structural point of view, contain one or various heterocyclic units in their core structure, and from the biological side, they have a direct influence on the transport of calcium in the cell. The marine compounds covered in this review are divided into three groups, which correspond with their direct biological activity, such as compounds with a direct influence in the calcium channel, compounds with a direct effect on the cytoskeleton and drugs with an effect on cancer cell proliferation. For each target, we describe its bioactive properties and synthetic approaches. The wide variety of chemical structures compiled in this review and their significant medical properties may attract the attention of many different researchers.
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Shao H, Fang K, Wang YP, Zhang XM, Ding TM, Zhang SY, Chen ZM, Tu YQ. Total Synthesis of Fawcettimine-Type Alkaloid, Lycojaponicumin A. Org Lett 2020; 22:3775-3779. [PMID: 32330061 DOI: 10.1021/acs.orglett.0c00961] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The efficient total synthesis of lycojaponicumin A (1) has been accomplished for the first time. The remarkable features of this novel strategy include the following: (1) rapid construction of tricyclic intermediate 4 through a regio- and stereoselective semipinacol ring expansion, which simplified the construction of rings A and B of 1; (2) the subsequent regio- and stereoselective formation of the highly strained rings C-E of 1 through a tandem oxa-hetero [3 + 2] cycloaddition/N-cycloalkylation.
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Affiliation(s)
- Hui Shao
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Kun Fang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China, 730000
| | - Yun-Peng Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Xiao-Ming Zhang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China, 730000
| | - Tong-Mei Ding
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Zhi-Min Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240
| | - Yong-Qiang Tu
- School of Chemistry and Chemical Engineering, Frontiers Science Center of Transformative Molecules, Shanghai Jiao Tong University, Shanghai, P. R. China, 200240.,State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China, 730000
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J. Lovely C, Ray A, Mukherjee S, Das J, Bhandari M, Herath A, Yousufuddin M. Heterosubstituted 4-Vinylimidazoles – Preparation and Diels-Alder Reactions. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Ray A, Yousufuddin M, Gout D, Lovely CJ. Intramolecular Diels-Alder Reaction of a Silyl-Substituted Vinylimidazole en Route to the Fully Substituted Cyclopentane Core of Oroidin Dimers. Org Lett 2018; 20:5964-5968. [PMID: 30192150 DOI: 10.1021/acs.orglett.8b02675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An intramolecular Diels-Alder reaction of a silyl-substituted vinylimidazole delivers a diastereomeric mixture of C4-silyl functionalized dihydrobenzimidazoles. Subsequent diastereoselective reduction and elaboration of the lactone gives rise to a polysubstituted tetrahydrobenzimidazole, which, upon oxidative rearrangement, affords a single spirofused imidazolone containing all of the relevant functionality for an approach to the oroidin dimers axinellamine, massadine, and palau'amine.
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Affiliation(s)
- Abhisek Ray
- Department of Chemistry and Biochemistry , University of Texas-Arlington , Arlington , Texas 76019-0065 , United States
| | - Muhammed Yousufuddin
- Department of Chemistry and Biochemistry , University of Texas-Arlington , Arlington , Texas 76019-0065 , United States
| | - Delphine Gout
- Department of Chemistry and Biochemistry , University of Texas-Arlington , Arlington , Texas 76019-0065 , United States
| | - Carl J Lovely
- Department of Chemistry and Biochemistry , University of Texas-Arlington , Arlington , Texas 76019-0065 , United States
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Podunavac M, Lacharity JJ, Jones KE, Zakarian A. Stereodivergence in the Ireland–Claisen Rearrangement of α-Alkoxy Esters. Org Lett 2018; 20:4867-4870. [DOI: 10.1021/acs.orglett.8b02011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Maša Podunavac
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Jacob J. Lacharity
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Kerry E. Jones
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Armen Zakarian
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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