Literature DB >> 33049755

Computational planning of the synthesis of complex natural products.

Barbara Mikulak-Klucznik1, Patrycja Gołębiowska1, Alison A Bayly2, Oskar Popik1, Tomasz Klucznik1, Sara Szymkuć1, Ewa P Gajewska1, Piotr Dittwald1, Olga Staszewska-Krajewska1, Wiktor Beker1, Tomasz Badowski1, Karl A Scheidt2, Karol Molga3, Jacek Mlynarski4, Milan Mrksich5, Bartosz A Grzybowski6,7,8.   

Abstract

Training algorithms to computationally plan multistep organic syntheses has been a challenge for more than 50 years1-7. However, the field has progressed greatly since the development of early programs such as LHASA1,7, for which reaction choices at each step were made by human operators. Multiple software platforms6,8-14 are now capable of completely autonomous planning. But these programs 'think' only one step at a time and have so far been limited to relatively simple targets, the syntheses of which could arguably be designed by human chemists within minutes, without the help of a computer. Furthermore, no algorithm has yet been able to design plausible routes to complex natural products, for which much more far-sighted, multistep planning is necessary15,16 and closely related literature precedents cannot be relied on. Here we demonstrate that such computational synthesis planning is possible, provided that the program's knowledge of organic chemistry and data-based artificial intelligence routines are augmented with causal relationships17,18, allowing it to 'strategize' over multiple synthetic steps. Using a Turing-like test administered to synthesis experts, we show that the routes designed by such a program are largely indistinguishable from those designed by humans. We also successfully validated three computer-designed syntheses of natural products in the laboratory. Taken together, these results indicate that expert-level automated synthetic planning is feasible, pending continued improvements to the reaction knowledge base and further code optimization.

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Year:  2020        PMID: 33049755     DOI: 10.1038/s41586-020-2855-y

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  32 in total

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Authors:  Zhengfeng Yang; Chenghai Li; Xiu Wang; Chunyan Zhai; Zhengfang Yi; Lei Wang; Bisheng Liu; Bing Du; Huihui Wu; Xizhi Guo; Mingyao Liu; Dali Li; Jian Luo
Journal:  J Cell Physiol       Date:  2010-10       Impact factor: 6.384

Review 2.  Computer-aided organic synthesis.

Authors:  Matthew H Todd
Journal:  Chem Soc Rev       Date:  2005-02-08       Impact factor: 54.564

3.  Empirical Explorations of SYNCHEM.

Authors:  H L Gelernter; A F Sanders; D L Larsen; K K Agarwal; R H Boivie; G A Spritzer; J E Searleman
Journal:  Science       Date:  1977-09-09       Impact factor: 47.728

4.  Computer-assisted design of complex organic syntheses.

Authors:  E J Corey; W T Wipke
Journal:  Science       Date:  1969-10-10       Impact factor: 47.728

Review 5.  Data-driven computer aided synthesis design.

Authors:  Orr Ravitz
Journal:  Drug Discov Today Technol       Date:  2013-09

6.  A robotic platform for flow synthesis of organic compounds informed by AI planning.

Authors:  Connor W Coley; Dale A Thomas; Justin A M Lummiss; Jonathan N Jaworski; Christopher P Breen; Victor Schultz; Travis Hart; Joshua S Fishman; Luke Rogers; Hanyu Gao; Robert W Hicklin; Pieter P Plehiers; Joshua Byington; John S Piotti; William H Green; A John Hart; Timothy F Jamison; Klavs F Jensen
Journal:  Science       Date:  2019-08-09       Impact factor: 47.728

7.  Planning chemical syntheses with deep neural networks and symbolic AI.

Authors:  Marwin H S Segler; Mike Preuss; Mark P Waller
Journal:  Nature       Date:  2018-03-28       Impact factor: 49.962

8.  Predicting the outcomes of organic reactions via machine learning: are current descriptors sufficient?

Authors:  G Skoraczyński; P Dittwald; B Miasojedow; S Szymkuć; E P Gajewska; B A Grzybowski; A Gambin
Journal:  Sci Rep       Date:  2017-06-15       Impact factor: 4.379

9.  Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans.

Authors:  Tomasz Badowski; Karol Molga; Bartosz A Grzybowski
Journal:  Chem Sci       Date:  2019-03-01       Impact factor: 9.825

10.  Computational design of syntheses leading to compound libraries or isotopically labelled targets.

Authors:  Karol Molga; Piotr Dittwald; Bartosz A Grzybowski
Journal:  Chem Sci       Date:  2019-08-16       Impact factor: 9.825

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1.  Chemistry-informed molecular graph as reaction descriptor for machine-learned retrosynthesis planning.

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4.  Bayesian Optimization of Computer-Proposed Multistep Synthetic Routes on an Automated Robotic Flow Platform.

Authors:  Anirudh M K Nambiar; Christopher P Breen; Travis Hart; Timothy Kulesza; Timothy F Jamison; Klavs F Jensen
Journal:  ACS Cent Sci       Date:  2022-06-10       Impact factor: 18.728

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Authors:  Mohammed AlQuraishi; Peter K Sorger
Journal:  Nat Methods       Date:  2021-10-04       Impact factor: 28.547

6.  Reinforcing the supply chain of umifenovir and other antiviral drugs with retrosynthetic software.

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Journal:  Nat Commun       Date:  2021-12-16       Impact factor: 14.919

Review 7.  Intelligent host engineering for metabolic flux optimisation in biotechnology.

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Journal:  Biochem J       Date:  2021-10-29       Impact factor: 3.857

Review 8.  The Combination of Tradition and Future: Data-Driven Natural-Product-Based Treatments for Parkinson's Disease.

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Journal:  Evid Based Complement Alternat Med       Date:  2021-07-14       Impact factor: 2.629

Review 9.  Functional and Material Properties in Nanocatalyst Design: A Data Handling and Sharing Problem.

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Journal:  Int J Mol Sci       Date:  2021-05-13       Impact factor: 5.923

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Journal:  Front Microbiol       Date:  2021-12-09       Impact factor: 5.640

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