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Shee Y, Li H, Zhang P, Nikolic AM, Lu W, Kelly HR, Manee V, Sreekumar S, Buono FG, Song JJ, Newhouse TR, Batista VS. Site-specific template generative approach for retrosynthetic planning. Nat Commun 2024; 15:7818. [PMID: 39251606 PMCID: PMC11385523 DOI: 10.1038/s41467-024-52048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/26/2024] [Indexed: 09/11/2024] Open
Abstract
Retrosynthesis, the strategy of devising laboratory pathways by working backwards from the target compound, is crucial yet challenging. Enhancing retrosynthetic efficiency requires overcoming the vast complexity of chemical space, the limited known interconversions between molecules, and the challenges posed by limited experimental datasets. This study introduces generative machine learning methods for retrosynthetic planning. The approach features three innovations: generating reaction templates instead of reactants or synthons to create novel chemical transformations, allowing user selection of specific bonds to change for human-influenced synthesis, and employing a conditional kernel-elastic autoencoder (CKAE) to measure the similarity between generated and known reactions for chemical viability insights. These features form a coherent retrosynthetic framework, validated experimentally by designing a 3-step synthetic pathway for a challenging small molecule, demonstrating a significant improvement over previous 5-9 step approaches. This work highlights the utility and robustness of generative machine learning in addressing complex challenges in chemical synthesis.
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Affiliation(s)
- Yu Shee
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Haote Li
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Pengpeng Zhang
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Wenxin Lu
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - H Ray Kelly
- Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Vidhyadhar Manee
- Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Sanil Sreekumar
- Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Frederic G Buono
- Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Jinhua J Song
- Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
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2
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Martínez‐Lara F, Suárez A, Velasco N, Suárez‐Pantiga S, Sanz R. Gold‐Catalyzed Reactions of 2‐Alkynyl‐1‐indolyl‐1,2‐diols with Thiols: Stereoselective Synthesis of (
Z
)‐α‐Indol‐3‐yl α‐(2‐Thioalkenyl) Ketones. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202100930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fernando Martínez‐Lara
- Área de Química Orgánica, Departamento de Química, Facultad de Ciencias Universidad de Burgos Pza. Misael Bañuelos s/n 09001- Burgos Spain
| | - Anisley Suárez
- Área de Química Orgánica, Departamento de Química, Facultad de Ciencias Universidad de Burgos Pza. Misael Bañuelos s/n 09001- Burgos Spain
| | - Noelia Velasco
- Área de Química Orgánica, Departamento de Química, Facultad de Ciencias Universidad de Burgos Pza. Misael Bañuelos s/n 09001- Burgos Spain
| | - Samuel Suárez‐Pantiga
- Área de Química Orgánica, Departamento de Química, Facultad de Ciencias Universidad de Burgos Pza. Misael Bañuelos s/n 09001- Burgos Spain
| | - Roberto Sanz
- Área de Química Orgánica, Departamento de Química, Facultad de Ciencias Universidad de Burgos Pza. Misael Bañuelos s/n 09001- Burgos Spain
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3
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Holzschneider K, Kirsch SF. [1, 2]-Migration Reactions Catalyzed by Gold Complexes and their Applications in Total Synthesis. Isr J Chem 2018. [DOI: 10.1002/ijch.201700081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Stefan F. Kirsch
- Organic Chemistry; Bergische Universität Wuppertal; Gaußstr. 20 42119 Wuppertal Germany
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4
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Bertocco P, Derendorf J, Jenne C, Kirsch C. Improving the Solubility of Halogenated 1-Ammonio-closo-dodecaborate Anions. Inorg Chem 2017; 56:3459-3466. [DOI: 10.1021/acs.inorgchem.6b03006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp Bertocco
- Fakultät für Mathematik und
Naturwissenschaften, Anorganische Chemie, Bergische Universität Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
| | - Janis Derendorf
- Fakultät für Mathematik und
Naturwissenschaften, Anorganische Chemie, Bergische Universität Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
| | - Carsten Jenne
- Fakultät für Mathematik und
Naturwissenschaften, Anorganische Chemie, Bergische Universität Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
| | - Christoph Kirsch
- Fakultät für Mathematik und
Naturwissenschaften, Anorganische Chemie, Bergische Universität Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
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Hosseyni S, Wojtas L, Li M, Shi X. Intermolecular Homopropargyl Alcohol Addition to Alkyne and a Sequential 1,6-Enyne Cycloisomerization with Triazole-Gold Catalyst. J Am Chem Soc 2016; 138:3994-7. [DOI: 10.1021/jacs.6b00882] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Seyedmorteza Hosseyni
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Lukasz Wojtas
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Minyong Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Xiaodong Shi
- Department
of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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Thummanapelli SK, Hosseyni S, Su Y, Akhmedov NG, Shi X. Ligand-controlled gold-catalyzed cycloisomerization of 1,n-enyne esters toward synthesis of dihydronaphthalene. Chem Commun (Camb) 2016; 52:7687-90. [PMID: 27231053 DOI: 10.1039/c6cc03032g] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We describe herein a gold-catalyzed rearrangement of propargyl esters followed by allene–ene cyclization to afford substituted bicyclic [4.4.0] dihydronaphthalene compounds.
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Affiliation(s)
| | | | - Yijin Su
- C.Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | - Novruz G. Akhmedov
- C.Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | - Xiaodong Shi
- Department of Chemistry
- University of South Florida
- Tampa
- USA
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