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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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König JA, Morgenstern B, Jauch J. The Total Synthesis of Hyperfirin via a Cyclooctadiene Strategy. Org Lett 2024; 26:7083-7087. [PMID: 38996193 DOI: 10.1021/acs.orglett.4c01836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Polycyclic polyprenylated acylphloroglucinols (PPAPs) combine compelling structural complexity with effective biological activity. The total synthesis of Hyperfirin is reported as one linear sequence. Key to this novel modular strategy is to access the bicyclo[3.3.1]nonane-2,4,9-trione framework via transannular acylation of a decorated eight-membered ring, followed by late stage bridgehead substitution. The described route adds flexibility to PPAP construction and broadens the scope of eight-membered ring chemistry.
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Affiliation(s)
- Julien A König
- Organic Chemistry II, Saarland University, 66123 Saarbrücken, Germany
| | - Bernd Morgenstern
- Service Center X-ray Diffraction, Saarland University, 66123 Saarbrücken, Germany
| | - Johann Jauch
- Organic Chemistry II, Saarland University, 66123 Saarbrücken, Germany
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3
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Ji Y, Hong B, Franzoni I, Wang M, Guan W, Jia H, Li H. Enantioselective Total Synthesis of Hyperforin and Pyrohyperforin. Angew Chem Int Ed Engl 2022; 61:e202116136. [DOI: 10.1002/anie.202116136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Yunpeng Ji
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Benke Hong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Ivan Franzoni
- NuChem Sciences Inc. 2350 rue Cohen Suite 201 Saint-Laurent Quebec H4R 2N6 Canada
| | - Mengyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Weiqiang Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Houhua Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
- State Key Laboratory of Medicinal Chemical Biology Nankai University 38 Tongyan Rd Tianjin 300350 China
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4
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Ji Y, Hong B, Franzoni I, Wang M, Guan W, Jia H, Li H. Enantioselective Total Synthesis of Hyperforin and Pyrohyperforin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yunpeng Ji
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Benke Hong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Ivan Franzoni
- NuChem Sciences Inc. 2350 rue Cohen Suite 201 Saint-Laurent Quebec H4R 2N6 Canada
| | - Mengyang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Weiqiang Guan
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
| | - Houhua Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center School of Pharmaceutical Sciences Peking University Xue Yuan Road No. 38 Beijing 100191 China
- State Key Laboratory of Medicinal Chemical Biology Nankai University 38 Tongyan Rd Tianjin 300350 China
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