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Huo T, Zhao X, Cheng Z, Wei J, Zhu M, Dou X, Jiao N. Late-stage modification of bioactive compounds: Improving druggability through efficient molecular editing. Acta Pharm Sin B 2024; 14:1030-1076. [PMID: 38487004 PMCID: PMC10935128 DOI: 10.1016/j.apsb.2023.11.021] [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: 08/21/2023] [Revised: 10/14/2023] [Accepted: 11/13/2023] [Indexed: 03/17/2024] Open
Abstract
Synthetic chemistry plays an indispensable role in drug discovery, contributing to hit compounds identification, lead compounds optimization, candidate drugs preparation, and so on. As Nobel Prize laureate James Black emphasized, "the most fruitful basis for the discovery of a new drug is to start with an old drug"1. Late-stage modification or functionalization of drugs, natural products and bioactive compounds have garnered significant interest due to its ability to introduce diverse elements into bioactive compounds promptly. Such modifications alter the chemical space and physiochemical properties of these compounds, ultimately influencing their potency and druggability. To enrich a toolbox of chemical modification methods for drug discovery, this review focuses on the incorporation of halogen, oxygen, and nitrogen-the ubiquitous elements in pharmacophore components of the marketed drugs-through late-stage modification in recent two decades, and discusses the state and challenges faced in these fields. We also emphasize that increasing cooperation between chemists and pharmacists may be conducive to the rapid discovery of new activities of the functionalized molecules. Ultimately, we hope this review would serve as a valuable resource, facilitating the application of late-stage modification in the construction of novel molecules and inspiring innovative concepts for designing and building new drugs.
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Affiliation(s)
- Tongyu Huo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinyi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zengrui Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jialiang Wei
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
| | - Minghui Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Changping Laboratory, Beijing 102206, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, East China Normal University, Shanghai 200062, China
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2
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Kosteczka GL, Soek RN, Richter WE, Campos RB. Substituent effects on intramolecular Schmidt reactions: a theoretical study on the formation of bridged lactams. Org Biomol Chem 2023; 21:4114-4122. [PMID: 37129005 DOI: 10.1039/d3ob00532a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The competitive formation of isomeric bridged lactams via acid-catalyzed intramolecular Schmidt reactions from 3-azidoethylcyclopentanones is explored using density functional theory (DFT) calculations, primarily performed at the M06-2X/6-311++G(d,p) level of theory. The results indicate that specific substituents installed at α-carbons can efficiently control the regioselectivity of the reaction by lone pair-cation interactions or steric hindrance reversing the main product preference, whereas cation-π interactions are not so effective.
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Affiliation(s)
- Guilherme L Kosteczka
- Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, PR, Brazil.
| | - Rafael N Soek
- Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, PR, Brazil.
| | - Wagner E Richter
- Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, PR, Brazil.
| | - Renan B Campos
- Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, PR, Brazil.
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3
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Sun Q, Lu X, Tantillo DJ. Dynamic Effects in Intramolecular Schmidt Reactions: Entropy, Electrostatic Drag, and Selectivity Prediction. Chemphyschem 2021; 22:649-656. [PMID: 33567140 DOI: 10.1002/cphc.202100033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Electrostatic drag in the intramolecular Schmidt reactions of azidopropylcyclohexanones is characterized using density functional theory (DFT) calculations and direct dynamics simulations. Despite resulting from enthalpically favorable interactions, electrostatic drag slows down N2 loss during formation of bridged lactam products, an effect with implications for controlling product selectivity.
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Affiliation(s)
- Qing Sun
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, China
| | - Xin Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
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4
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Pandey AK, Kirberger SE, Johnson JA, Kimbrough JR, Partridge DKD, Pomerantz WCK. Efficient Synthesis of 1,4-Thiazepanones and 1,4-Thiazepanes as 3D Fragments for Screening Libraries. Org Lett 2020; 22:3946-3950. [PMID: 32347732 PMCID: PMC8324318 DOI: 10.1021/acs.orglett.0c01230] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
1,4-Thiazepanes and 1,4-thiazepanones represent seven-membered ring systems with highly 3D character and are currently underrepresented in fragment screening libraries. A nuclear magnetic resonance (NMR) fragment screen identified 1,4-acylthiazepanes as new BET (bromodomain and extraterminal domain) bromodomain ligands; however, an efficient and readily diversified synthesis for library development has not been reported. Here we report a one-pot synthesis using α,β-unsaturated esters and 1,2-amino thiols to form 1,4-thiazepanones as precursors to 1,4-thiazepanes with high 3D character. This reaction proceeds in reasonable time (0.5-3 h) and in good yield and tolerates a broad scope of α,β-unsaturated esters. Several 1,4-thiazepanes were synthesized by a two-step transformation and were characterized as new BET bromodomain ligands using protein-observed 19F NMR. This synthesis should provide ready access to diverse 3D fragments for screening libraries.
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Affiliation(s)
- Anil K Pandey
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steven E Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jennifer R Kimbrough
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Danika K D Partridge
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Kennedy CR, Lin S, Jacobsen EN. The Cation-π Interaction in Small-Molecule Catalysis. Angew Chem Int Ed Engl 2016; 55:12596-624. [PMID: 27329991 PMCID: PMC5096794 DOI: 10.1002/anie.201600547] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
Catalysis by small molecules (≤1000 Da, 10(-9) m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.
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Affiliation(s)
- C Rose Kennedy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA
| | - Song Lin
- Department of Chemistry, University of California, Berkeley, 535 Latimer Hall, Berkeley, CA, 94720, USA
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA.
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Kennedy CR, Lin S, Jacobsen EN. Die Kation-π-Wechselwirkung in der Katalyse mit niedermolekularen Verbindungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600547] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C. Rose Kennedy
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| | - Song Lin
- Department of Chemistry; University of California, Berkeley; 535 Latimer Hall Berkeley CA 94720 USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
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Szostak R, Aubé J, Szostak M. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C–N Rotational Pathway. J Org Chem 2015; 80:7905-27. [DOI: 10.1021/acs.joc.5b00881] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roman Szostak
- Department of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Jeffrey Aubé
- Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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Bhuma N, Vangala M, Nair RJ, Sabharwal SG, Dhavale DD. Halogenated d-xylono-δ-lactams: synthesis and enzyme inhibition study. Carbohydr Res 2015; 402:215-24. [DOI: 10.1016/j.carres.2014.10.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/18/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
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9
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Sun X, Gao C, Zhang F, Song Z, Kong L, Wen X, Sun H. Electronic and steric effects on the intramolecular Schmidt reaction of alkyl azides with secondary benzyl alcohols. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, Delbert M. Shankel Structural Biology Center, 2034 Becker Drive, Lawrence, Kansas 66047
| | - Jeffrey Aubé
- Department of Medicinal Chemistry, University of Kansas, Delbert M. Shankel Structural Biology Center, 2034 Becker Drive, Lawrence, Kansas 66047
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11
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An efficient synthesis of δ-glyconolactams by intramolecular Schmidt–Boyer reaction under microwave radiation. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.10.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Gutierrez O, Tantillo DJ. Analogies between Synthetic and Biosynthetic Reactions in Which [1,2]-Alkyl Shifts Are Combined with Other Events: Dyotropic, Schmidt, and Carbocation Rearrangements. J Org Chem 2012; 77:8845-50. [DOI: 10.1021/jo301864h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Osvaldo Gutierrez
- Department of Chemistry, Univeristy of California−Davis, 1 Shields Avenue, Davis, California
95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, Univeristy of California−Davis, 1 Shields Avenue, Davis, California
95616, United States
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13
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Gutierrez O, Aubé J, Tantillo DJ. Mechanism of the Acid-Promoted Intramolecular Schmidt Reaction: Theoretical Assessment of the Importance of Lone Pair–Cation, Cation−π, and Steric Effects in Controlling Regioselectivity. J Org Chem 2011; 77:640-7. [DOI: 10.1021/jo202338m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Osvaldo Gutierrez
- Department of Chemistry, University of California at Davis, Davis, California
95616, United States
| | - Jeffrey Aubé
- Department
of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United
States
| | - Dean J. Tantillo
- Department of Chemistry, University of California at Davis, Davis, California
95616, United States
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Abstract
Medium-bridged twisted lactams, in which a non-planar amide bond is achieved by incorporating the nitrogen atom at the bridgehead position in a medium-sized heterocycle, offer an attractive setting in which to study the properties of distorted amide linkages. This Emerging Area article will describe progress in the preparation and study of these compounds. This work shows that compounds containing an even moderately distorted amide bond display useful and unusual chemical properties while retaining a measure of stability that enables their study.
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, Structural Biology Center, 2121 Simons Drive, West Campus, Lawrence, KS 66047, USA
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15
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Szostak M, Yao L, Day VW, Powell DR, Aubé J. Structural characterization of N-protonated amides: regioselective N-activation of medium-bridged twisted lactams. J Am Chem Soc 2010; 132:8836-7. [PMID: 20536127 DOI: 10.1021/ja101690u] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The straightforward protonation of lactams by treatment with acid and the full structural characterization of three resulting N-protonated lactams are disclosed. This work provides experimental evidence that N-protonation of amide bonds results in a dramatic increase in nonplanarity about the C-N amide bond. The resulting compounds are discussed in structural, spectroscopic, and reactivity terms. The data suggest that distortion of these amide bonds by approximately 50 degrees is sufficient for their effective N-activation.
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, Delbert M. Shankel Structural Biology Center, 2034 Becker Drive, Lawrence, Kansas 66047, USA
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16
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Szostak M, Aubé J. Synthesis, structural analysis, and reactivity of bridged orthoamides by intramolecular Schmidt reaction. J Am Chem Soc 2010; 132:2530-1. [PMID: 20128606 DOI: 10.1021/ja910654t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intramolecular Schmidt reactions can be reliably steered toward bridged heterocycles containing orthoamides in high yields. The ketal tether enhances the control of regioselectivity in the migration of the bond distal to the reactive azide nucleophile, thus providing the first examples of the intramolecular Schmidt reaction proceeding with a complete regioselectivity en route to bridged products. The method is broad in scope and allows for systematic study of compounds that are analogous to elusive tetrahedral intermediates of amide addition reactions. Some initial reactivity and structural profiling of these compounds are also reported.
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, Structural Biology Center, 2121 Simons Drive, West Campus, Lawrence, Kansas 66047, USA
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Szostak M, Yao L, Aubé J. Synthesis of medium-bridged twisted lactams via cation-pi control of the regiochemistry of the intramolecular Schmidt reaction. J Org Chem 2010; 75:1235-43. [PMID: 20095596 DOI: 10.1021/jo902574m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Medium-bridged twisted amides can be synthesized by the intramolecular Schmidt reaction of 2-azidoalkyl ketones. In these reactions, the regiochemistry of the Schmidt reaction is diverted into a typically disfavored pathway by the presence of an aromatic group at the alpha-position adjacent to the ketone, which stabilizes the predominantly reactive conformation of the azidohydrin intermediate by engaging in a nonbonded cation-pi interaction with the positively charged diazonium cation. This results in the rarely observed rearrangement of the C-C bond distal to the azidoalkyl chain. This reaction pathway also requires the azide-containing tether to be situated in the axial orientation in the key azidohydrin intermediate. Examination of the effect of substitution of aromatic rings on the regiochemistry of the Schmidt reaction shows an increase in the migratory selectivity with more electron-rich aromatic groups. The selectivity is lower when an electron-withdrawing substituent is placed on the aromatic ring. The ability of cation-pi interactions to act as a controlling element decreases when Lewis acids coordinate to substituents on the aromatic ring. The developed version of the Schmidt reaction provides a direct access to a family of medium-bridged twisted amides with a [4.3.1] bicyclic system, compounds which are very difficult to access with use of other currently available methods.
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Malott Hall, Room 4070, Lawrence, Kansas 66045-7852, USA
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Szostak M, Yao L, Aubé J. Proximity effects in nucleophilic addition reactions to medium-bridged twisted lactams: remarkably stable tetrahedral intermediates. J Am Chem Soc 2010; 132:2078-84. [PMID: 20095610 PMCID: PMC2820158 DOI: 10.1021/ja909792h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reactions of a series of strained bicyclic and tricyclic one-carbon bridged lactams with organometallic reagents have been investigated. These amides permit isolation of a number of remarkably stable hemiaminals upon nucleophilic addition to the twisted amide bonds present in the lactam precursors. The factors that affect the stability of the resulting bridged hemiaminals are presented. In some cases, the hemiaminals were found to collapse to the open-form amino ketones in a manner expected for traditional carboxylic acid derivatives. Transannular N...C=O interactions were also observed in some nine-membered amino ketones. Additionally, tricyclic bridged lactams were found to react with some nucleophiles that typically react with ketones but not with planar amides. The effect of geometry on the reactivity of amide bonds and the amide bond distortion range that marks the boundary of amide-like and ketone-like carbonyl reactivity of lactams are also discussed.
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Malott Hall, Room 4070, Lawrence, Kansas 66045-7852
| | - Lei Yao
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Malott Hall, Room 4070, Lawrence, Kansas 66045-7852
| | - Jeffrey Aubé
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Malott Hall, Room 4070, Lawrence, Kansas 66045-7852
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Szostak M, Aubé J. Synthesis and rearrangement of a bridged thioamide. Chem Commun (Camb) 2009:7122-4. [DOI: 10.1039/b917508c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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