Merging enzymatic and synthetic chemistry with computational synthesis planning

[1]  Connor W. Coley,et al.  Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP , 2022, Nature Communications.

[2]  Connor W. Coley,et al.  Similarity based enzymatic retrosynthesis , 2022, Chemical science.

[3]  T. Laino,et al.  Biocatalysed synthesis planning using data-driven learning , 2022, Nature Communications.

[4]  A. Ignatchenko,et al.  Rhea, the reaction knowledgebase in 2022 , 2021, Nucleic Acids Res..

[5]  W. Green,et al.  Influence of Template Size, Canonicalization, and Exclusivity for Retrosynthesis and Reaction Prediction Applications , 2021, J. Chem. Inf. Model..

[6]  Connor W. Coley,et al.  Machine learning modeling of family wide enzyme-substrate specificity screens , 2021, PLoS Comput. Biol..

[7]  Hongwu Ma,et al.  Cell-free chemoenzymatic starch synthesis from carbon dioxide , 2021, Science.

[8]  Philippe Y. Ayala,et al.  Artificial Intelligence in Chemistry: Current Trends and Future Directions , 2021, J. Chem. Inf. Model..

[9]  Richmond Sarpong,et al.  Automation and computer-assisted planning for chemical synthesis , 2021, Nature Reviews Methods Primers.

[10]  Alison R. H. Narayan,et al.  Chemoenzymatic Total Synthesis of Natural Products. , 2021, Accounts of chemical research.

[11]  Lorna J. Hepworth,et al.  RetroBioCat as a computer-aided synthesis planning tool for biocatalytic reactions and cascades , 2021, Nature Catalysis.

[12]  Dieter Jahn,et al.  BRENDA, the ELIXIR core data resource in 2021: new developments and updates , 2020, Nucleic Acids Res..

[13]  M. Pagni,et al.  MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models , 2020, Nucleic acids research.

[14]  Piotr Dittwald,et al.  Computational planning of the synthesis of complex natural products , 2020, Nature.

[15]  Nicholas G Jentsch,et al.  Efficient Synthesis of Cannabigerol, Grifolin, and Piperogalin via Alumina-Promoted Allylation. , 2020, Journal of natural products.

[16]  J. Bowie,et al.  A bio-inspired cell-free system for cannabinoid production from inexpensive inputs , 2020, Nature Chemical Biology.

[17]  B. Shen,et al.  Divergent synthesis of complex diterpenes through a hybrid oxidative approach , 2020, Science.

[18]  U. Bornscheuer,et al.  Biocatalysis: Enzymatic Synthesis for Industrial Applications , 2020, Angewandte Chemie.

[19]  Ola Engkvist,et al.  AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning , 2020, Journal of Cheminformatics.

[20]  Christopher C. Nawrat,et al.  Synthesis of Islatravir Enabled by a Catalytic, Enantioselective Alkynylation of a Ketone. , 2020, Organic letters.

[21]  Regina Barzilay,et al.  Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis , 2020, Journal of medicinal chemistry.

[22]  Brian C. Barnes,et al.  Machine Learned Prediction of Reaction Template Applicability for Data-Driven Retrosynthetic Predictions of Energetic Materials , 2020, SHOCK COMPRESSION OF CONDENSED MATTER - 2019: Proceedings of the Conference of the American Physical Society Topical Group on Shock Compression of Condensed Matter.

[23]  Anna Fryszkowska,et al.  Biocatalysis in drug discovery and development. , 2020, Current opinion in chemical biology.

[24]  Riccardo Petraglia,et al.  Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy† , 2020, Chemical science.

[25]  Christopher C. Nawrat,et al.  Nine-Step Stereoselective Synthesis of Islatravir from Deoxyribose. , 2020, Organic letters.

[26]  Jian Li,et al.  Recent advances in the chemoenzymatic synthesis of bioactive natural products. , 2020, Current opinion in chemical biology.

[27]  Roger A Sheldon,et al.  The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis , 2020, Chemical science.

[28]  Brian C. Barnes,et al.  Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning , 2020, J. Chem. Inf. Model..

[29]  Yuedong Yang,et al.  Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks , 2019, ArXiv.

[30]  Alán Aspuru-Guzik,et al.  Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models , 2018, Frontiers in Pharmacology.

[31]  Mathilde Koch,et al.  Reinforcement Learning for Bio-Retrosynthesis. , 2019, ACS synthetic biology.

[32]  Shane T. Grosser,et al.  Design of an in vitro biocatalytic cascade for the manufacture of islatravir , 2019, Science.

[33]  Ola Engkvist,et al.  AI-assisted synthesis prediction. , 2019, Drug discovery today. Technologies.

[34]  Bartosz A Grzybowski,et al.  Synergy Between Expert and Machine-Learning Approaches Allows for Improved Retrosynthetic Planning. , 2019, Angewandte Chemie.

[35]  Eman Abdelraheem,et al.  Biocatalysis explained: from pharmaceutical to bulk chemical production , 2019, Reaction Chemistry & Engineering.

[36]  Pieter P. Plehiers,et al.  A robotic platform for flow synthesis of organic compounds informed by AI planning , 2019, Science.

[37]  Suzanne M. Paley,et al.  The BioCyc collection of microbial genomes and metabolic pathways , 2019, Briefings Bioinform..

[38]  Connor W. Coley,et al.  RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application , 2019, J. Chem. Inf. Model..

[39]  Christopher A. Voigt,et al.  Retrosynthetic design of metabolic pathways to chemicals not found in nature , 2019, Current Opinion in Systems Biology.

[40]  Adrian T. Grzybowski,et al.  Complete biosynthesis of cannabinoids and their unnatural analogues in yeast , 2019, Nature.

[41]  D. Lupton,et al.  Enantioselective Total Synthesis of (-)-Δ9-Tetrahydrocannabinol via N-Heterocyclic Carbene Catalysis. , 2019, Organic letters.

[42]  Pablo Carbonell,et al.  RetroRules: a database of reaction rules for engineering biology , 2018, Nucleic Acids Res..

[43]  Louis J Diorazio,et al.  Route design, the foundation of successful chemical development. , 2018, Bioorganic & medicinal chemistry.

[44]  Ljubisa Miskovic,et al.  Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors , 2017, bioRxiv.

[45]  Connor W. Coley,et al.  Machine Learning in Computer-Aided Synthesis Planning. , 2018, Accounts of chemical research.

[46]  Nicholas J Turner,et al.  Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. , 2018, Chemical reviews.

[47]  J. Jacobson,et al.  Enantioselective Total Synthesis of Cannabinoids-A Route for Analogue Development. , 2018, Organic letters.

[48]  Pablo Carbonell,et al.  RetroPath2.0: A retrosynthesis workflow for metabolic engineers. , 2018, Metabolic engineering.

[49]  Mike Preuss,et al.  Learning to Plan Chemical Syntheses , 2017, ArXiv.

[50]  Christian Templin,et al.  40 Years on , 2017, European heart journal.

[51]  Bowen Liu,et al.  Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models , 2017, ACS central science.

[52]  Paul H Opgenorth,et al.  A synthetic biochemistry platform for cell free production of monoterpenes from glucose , 2017, Nature Communications.

[53]  Marwin H. S. Segler,et al.  Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction. , 2017, Chemistry.

[54]  Matthew D Truppo,et al.  Biocatalysis in the Pharmaceutical Industry: The Need for Speed. , 2017, ACS medicinal chemistry letters.

[55]  Hsu-Min Chiang,et al.  Current Trends and Future Directions , 2017 .

[56]  Piotr Dittwald,et al.  Computer-Assisted Synthetic Planning: The End of the Beginning. , 2016, Angewandte Chemie.

[57]  Christoph Steinbeck,et al.  Reaction Decoder Tool (RDT): extracting features from chemical reactions , 2016, Bioinform..

[58]  A. Usobiaga,et al.  Evolution of the Cannabinoid and Terpene Content during the Growth of Cannabis sativa Plants from Different Chemotypes. , 2016, Journal of natural products.

[59]  Landon J. Durak,et al.  Late-Stage Diversification of Biologically Active Molecules via Chemoenzymatic C-H Functionalization. , 2016, ACS catalysis.

[60]  John J. Irwin,et al.  ZINC 15 – Ligand Discovery for Everyone , 2015, J. Chem. Inf. Model..

[61]  V. Hatzimanikatis,et al.  Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. , 2015, Current opinion in chemical biology.

[62]  Jürgen Schmidhuber,et al.  Training Very Deep Networks , 2015, NIPS.

[63]  Michael G. Hutchings,et al.  Route Design in the 21st Century: The ICSYNTH Software Tool as an Idea Generator for Synthesis Prediction , 2015 .

[64]  E. Carreira,et al.  Stereodivergent total synthesis of Δ9-tetrahydrocannabinols. , 2014, Angewandte Chemie.

[65]  S. Ke,et al.  Large-Scale Domain Motions and Pyridoxal-5′-Phosphate Assisted Radical Catalysis in Coenzyme B12-Dependent Aminomutases† , 2014, International journal of molecular sciences.

[66]  Nicholas J. Turner,et al.  Biocatalytic Approaches to the Synthesis of Enantiomerically Pure Chiral Amines , 2014, Topics in Catalysis.

[67]  Erich Leitner,et al.  Inversion of enantioselectivity of a mononuclear non-heme iron(II)-dependent hydroxylase by tuning the interplay of metal-center geometry and protein structure. , 2013, Angewandte Chemie.

[68]  Orr Ravitz,et al.  Data-driven computer aided synthesis design. , 2013, Drug discovery today. Technologies.

[69]  Yong Chen,et al.  Enantioselective total synthesis of (-)-Δ8-THC and (-)-Δ9-THC via catalytic asymmetric hydrogenation and S(N)Ar cyclization. , 2013, Organic letters.

[70]  A. Takeuchi,et al.  Structure and function of ∆1-tetrahydrocannabinolic acid (THCA) synthase, the enzyme controlling the psychoactivity of Cannabis sativa. , 2012, Journal of molecular biology.

[71]  Bruce J Tromberg,et al.  The need for speed , 2012, Smart Structures.

[72]  Lei Shi,et al.  SABIO-RK—database for biochemical reaction kinetics , 2011, Nucleic Acids Res..

[73]  Anthony P. F. Cook,et al.  Computer‐aided synthesis design: 40 years on , 2012 .

[74]  Manfred T Reetz,et al.  Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution , 2011, Nature Chemistry.

[75]  Dietmar Schomburg,et al.  BKM-react, an integrated biochemical reaction database , 2011, BMC Biochemistry.

[76]  B. Feringa,et al.  Aminomutases: mechanistic diversity, biotechnological applications and future perspectives. , 2011, Trends in biotechnology.

[77]  Paul N. Devine,et al.  Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture , 2010, Science.

[78]  B. Bachmann.  Biosynthesis: is it time to go retro? , 2010, Nature chemical biology.

[79]  Yang Liu,et al.  Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation , 2009, J. Chem. Inf. Model..

[80]  K. Kantardjieff,et al.  Inverting the enantioselectivity of a carbonyl reductase via substrate-enzyme docking-guided point mutation. , 2008, Organic letters.

[81]  B. Trost,et al.  Synthesis of (-)-Delta9-trans-tetrahydrocannabinol: stereocontrol via Mo-catalyzed asymmetric allylic alkylation reaction. , 2007, Organic letters.

[82]  F. Campos,et al.  An efficient enantioselective synthesis of (R,R)-formoterol, a potent bronchodilator, using lipases , 2000 .

[83]  H. Leemhuis,et al.  Characterization of the Gene Cluster Involved in Isoprene Metabolism in Rhodococcus sp. Strain AD45 , 2000, Journal of bacteriology.

[84]  Frances H. Arnold,et al.  Inverting enantioselectivity by directed evolution of hydantoinase for improved production of l-methionine , 2000, Nature Biotechnology.

[85]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[86]  Scott J. Miller,et al.  Bis(oxazoline) and Bis(oxazolinyl)pyridine Copper Complexes as Enantioselective Diels−Alder Catalysts: Reaction Scope and Synthetic Applications , 1999 .

[87]  C. Senanayake,et al.  Large-Scale Synthesis of Enantio- and Diastereomerically Pure (R,R)-Formoterol† , 1998 .

[88]  S. Morimoto,et al.  First direct evidence for the mechanism of .DELTA.1-tetrahydrocannabinolic acid biosynthesis , 1995 .

[89]  S. Segawa,et al.  End of the beginning , 1990, Nature.

[90]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[91]  E. Corey,et al.  Computer-assisted analysis in organic synthesis. , 1985, Science.

[92]  Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .