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Moskal M, Beker W, Szymkuć S, Grzybowski BA. Scaffold‐Directed Face Selectivity Machine‐Learned from Vectors of Non‐covalent Interactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Martyna Moskal
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Wiktor Beker
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Sara Szymkuć
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry Polish Academy of Sciences Ul. Kasprzaka 44/52 01-224 Warsaw Poland
- Allchemy, Inc. Highland IN USA
- IBS Center for Soft and Living Matter and Department of Chemistry UNIST 50, UNIST-gil, Eonyang-eup, Ulju-gun Ulsan South Korea
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Moskal M, Beker W, Szymkuć S, Grzybowski BA. Scaffold-Directed Face Selectivity Machine-Learned from Vectors of Non-covalent Interactions. Angew Chem Int Ed Engl 2021; 60:15230-15235. [PMID: 33876554 DOI: 10.1002/anie.202101986] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/29/2021] [Indexed: 11/06/2022]
Abstract
This work describes a method to vectorize and Machine-Learn, ML, non-covalent interactions responsible for scaffold-directed reactions important in synthetic chemistry. Models trained on this representation predict correct face of approach in ca. 90 % of Michael additions or Diels-Alder cycloadditions. These accuracies are significantly higher than those based on traditional ML descriptors, energetic calculations, or intuition of experienced synthetic chemists. Our results also emphasize the importance of ML models being provided with relevant mechanistic knowledge; without such knowledge, these models cannot easily "transfer-learn" and extrapolate to previously unseen reaction mechanisms.
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Affiliation(s)
- Martyna Moskal
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Wiktor Beker
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Sara Szymkuć
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Ul. Kasprzaka 44/52, 01-224, Warsaw, Poland.,Allchemy, Inc., Highland, IN, USA.,IBS Center for Soft and Living Matter and Department of Chemistry, UNIST, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea
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Szymkuć S, Gajewska EP, Klucznik T, Molga K, Dittwald P, Startek M, Bajczyk M, Grzybowski BA. Computer-Assisted Synthetic Planning: The End of the Beginning. Angew Chem Int Ed Engl 2016; 55:5904-37. [PMID: 27062365 DOI: 10.1002/anie.201506101] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/14/2015] [Indexed: 11/07/2022]
Abstract
Exactly half a century has passed since the launch of the first documented research project (1965 Dendral) on computer-assisted organic synthesis. Many more programs were created in the 1970s and 1980s but the enthusiasm of these pioneering days had largely dissipated by the 2000s, and the challenge of teaching the computer how to plan organic syntheses earned itself the reputation of a "mission impossible". This is quite curious given that, in the meantime, computers have "learned" many other skills that had been considered exclusive domains of human intellect and creativity-for example, machines can nowadays play chess better than human world champions and they can compose classical music pleasant to the human ear. Although there have been no similar feats in organic synthesis, this Review argues that to concede defeat would be premature. Indeed, bringing together the combination of modern computational power and algorithms from graph/network theory, chemical rules (with full stereo- and regiochemistry) coded in appropriate formats, and the elements of quantum mechanics, the machine can finally be "taught" how to plan syntheses of non-trivial organic molecules in a matter of seconds to minutes. The Review begins with an overview of some basic theoretical concepts essential for the big-data analysis of chemical syntheses. It progresses to the problem of optimizing pathways involving known reactions. It culminates with discussion of algorithms that allow for a completely de novo and fully automated design of syntheses leading to relatively complex targets, including those that have not been made before. Of course, there are still things to be improved, but computers are finally becoming relevant and helpful to the practice of organic-synthetic planning. Paraphrasing Churchill's famous words after the Allies' first major victory over the Axis forces in Africa, it is not the end, it is not even the beginning of the end, but it is the end of the beginning for the computer-assisted synthesis planning. The machine is here to stay.
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Affiliation(s)
- Sara Szymkuć
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Ewa P Gajewska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Tomasz Klucznik
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Karol Molga
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Piotr Dittwald
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Michał Startek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, 02-097 Warszawa, Poland
| | - Michał Bajczyk
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 02-224, Poland. , .,Center for Soft and Living Matter of Korea's Institute for Basic Science (IBS), Department of Chemistry, Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, South Korea. ,
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Szymkuć S, Gajewska EP, Klucznik T, Molga K, Dittwald P, Startek M, Bajczyk M, Grzybowski BA. Computergestützte Syntheseplanung: Das Ende vom Anfang. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201506101] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sara Szymkuć
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Ewa P. Gajewska
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Tomasz Klucznik
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Karol Molga
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Piotr Dittwald
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Michał Startek
- Faculty of Mathematics, Informatics, and Mechanics University of Warsaw Banacha 2 02-097 Warszawa Poland
| | - Michał Bajczyk
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
| | - Bartosz A. Grzybowski
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw 02-224 Polen
- Center for Soft and Living Matter of Korea's Institute for Basic Science (IBS) Department of Chemistry Ulsan National Institute of Science and Technology 50, UNIST-gil, Eonyang-eup, Ulju-gun Ulsan Südkorea
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