A genetic optimization strategy with generality in asymmetric organocatalysis as a primary target

A catalyst possessing a broad substrate scope, in terms of both turnover and enantioselectivity, is sometimes called “general”. Despite their great utility in asymmetric synthesis, truly general catalysts are difficult or expensive to discover via traditional high-throughput screening and are, therefore, rare. Existing computational tools accelerate the evaluation of reaction conditions from a pre-defined set of experiments to identify the most general ones, but cannot generate entirely new catalysts with enhanced substrate breadth. For these reasons, we report an inverse design strategy based on the open-source genetic algorithm NaviCatGA and on the OSCAR database of organocatalysts to simultaneously probe the catalyst and substrate scope and optimize generality as a primary target. We apply this strategy to the Pictet–Spengler condensation, for which we curate a database of 820 reactions, used to train statistical models of selectivity and activity. Starting from OSCAR, we define a combinatorial space of millions of catalyst possibilities, and perform evolutionary experiments on a diverse substrate scope that is representative of the whole chemical space of tetrahydro-β-carboline products. While privileged catalysts emerge, we show how genetic optimization can address the broader question of generality in asymmetric synthesis, extracting structure–performance relationships from the challenging areas of chemical space.

[1]  Qiongqiong Wan,et al.  Ultra-high-throughput mapping of the chemical space of asymmetric catalysis enables accelerated reaction discovery , 2023, Nature communications.

[2]  Andrew F. Zahrt,et al.  A machine-learning tool to predict substrate-adaptive conditions for Pd-catalyzed C–N couplings , 2023, Science.

[3]  K. Rissanen,et al.  Machine Learning-Guided Development of Trialkylphosphine Ni(I) Dimers and Applications in Site-Selective Catalysis. , 2023, Journal of the American Chemical Society.

[4]  Jolene P. Reid,et al.  A Data-Driven Workflow for Assigning and Predicting Generality in Asymmetric Catalysis. , 2023, Journal of the American Chemical Society.

[5]  Scott J. Miller,et al.  Generality-oriented optimization of enantioselective aminoxyl radical catalysis , 2023, Science.

[6]  Dylan M. Anstine,et al.  Generative Models as an Emerging Paradigm in the Chemical Sciences , 2023, Journal of the American Chemical Society.

[7]  V. Gandon,et al.  Collective Total Synthesis of Mavacuran Alkaloids through Intermolecular 1,4-Addition of an Organolithium Reagent. , 2023, Angewandte Chemie.

[8]  F. Toste,et al.  Data Science Enables the Development of a New Class of Chiral Phosphoric Acid Catalysts. , 2023, Chem.

[9]  Jieping Zhu,et al.  Divergent Asymmetric Total Synthesis of (-)-Voacafricines A & B. , 2023, Angewandte Chemie.

[10]  Bojana Ranković,et al.  Bayesian Optimization for Chemical Reactions. , 2023, Chimia.

[11]  C. Corminboeuf,et al.  Genetic Algorithms for the Discovery of Homogeneous Catalysts. , 2023, Chimia.

[12]  Jan H. Jensen,et al.  Computational Evolution Of New Catalysts For The Morita-Baylis-Hillman Reaction. , 2023, Angewandte Chemie.

[13]  Chen Zhao,et al.  Mechanism of a Dually Catalyzed Enantioselective Oxa-Pictet-Spengler Reaction and the Development of a Stereodivergent Variant. , 2023, ACS catalysis.

[14]  A. Varnek,et al.  Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors. , 2023, Angewandte Chemie.

[15]  Anup Biswas Organocatalyzed Asymmetric Pictet‐Spengler Reactions , 2023, ChemistrySelect.

[16]  F. Gosselin,et al.  Data-Driven Multi-Objective Optimization Tactics for Catalytic Asymmetric Reactions Using Bisphosphine Ligands. , 2022, Journal of the American Chemical Society.

[17]  Brennan T. Rose,et al.  High-Level Data Fusion Enables the Chemoinformatically Guided Discovery of Chiral Disulfonimide Catalysts for Atropselective Iodination of 2-Amino-6-arylpyridines. , 2022, Journal of the American Chemical Society.

[18]  Andrew F. Zahrt,et al.  Machine-Learning-Guided Discovery of Electrochemical Reactions , 2022, Journal of the American Chemical Society.

[19]  M. Sigman,et al.  Exploring Structure-Function Relationships of Aryl Pyrrolidine-Based Hydrogen-Bond Donors in Asymmetric Catalysis Using Data-Driven Techniques. , 2022, ACS catalysis.

[20]  Jieping Zhu,et al.  Organocatalytic Enantioselective Pictet-Spengler Reaction of α-Ketoesters: Development and Application to the Total Synthesis of (+)-Alstratine A. , 2022, Angewandte Chemie.

[21]  F. Gosselin,et al.  Atroposelective Negishi Coupling Optimization Guided by Multivariate Linear Regression Analysis: Asymmetric Synthesis of KRAS G12C Covalent Inhibitor GDC-6036. , 2022, Journal of the American Chemical Society.

[22]  B. Grzybowski,et al.  Closed-loop optimization of general reaction conditions for heteroaryl Suzuki-Miyaura coupling , 2022, Science.

[23]  Ryan P. Adams,et al.  A Multi-Objective Active Learning Platform and Web App for Reaction Optimization. , 2022, Journal of the American Chemical Society.

[24]  Connor W. Coley,et al.  Computer-aided multi-objective optimization in small molecule discovery , 2022, Patterns.

[25]  Eugene E. Kwan,et al.  Screening for generality in asymmetric catalysis , 2022, Nature.

[26]  B. List,et al.  A Catalytic Asymmetric Pictet–Spengler Platform as a Biomimetic Diversification Strategy toward Naturally Occurring Alkaloids , 2022, Journal of the American Chemical Society.

[27]  Matthew D. Wodrich,et al.  Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes , 2022, Nature Protocols.

[28]  Shuo-qing Zhang,et al.  When machine learning meets molecular synthesis , 2022, Trends in Chemistry.

[29]  F. Glorius,et al.  Machine Learning for Chemical Reactivity The Importance of Failed Experiments. , 2022, Angewandte Chemie.

[30]  D. MacMillan,et al.  Accelerating reaction generality and mechanistic insight through additive mapping , 2022, Science.

[31]  A. Bahamonde,et al.  Predicting relative efficiency of amide bond formation using multivariate linear regression , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[32]  B. Grzybowski,et al.  Machine Learning May Sometimes Simply Capture Literature Popularity Trends: A Case Study of Heterocyclic Suzuki–Miyaura Coupling , 2022, Journal of the American Chemical Society.

[33]  Shiqiang Ma,et al.  Enantioselective Pictet–Spengler Condensation to Access the Total Synthesis of (+)‐Tabertinggine , 2022, European Journal of Organic Chemistry.

[34]  C. Corminboeuf,et al.  Genetic Optimization of Homogeneous Catalysts , 2022, Chemistry–Methods.

[35]  Jieping Zhu,et al.  Catalytic Enantioselective Pictet–Spengler Reaction of α‐Ketoamides Catalyzed by a Single H‐Bond Donor Organocatalyst , 2022, Angewandte Chemie.

[36]  Shuichi Nakamura,et al.  Enantioselective Pictet-Spengler Reaction of Acyclic α-Ketoesters Using Chiral Imidazoline-Phosphoric Acid Catalysts. , 2022, Organic letters.

[37]  K. Rissanen,et al.  Accelerated dinuclear palladium catalyst identification through unsupervised machine learning , 2021, Science.

[38]  Katrina W. Lexa,et al.  Application of Machine Learning and Reaction Optimization for the Iterative Improvement of Enantioselectivity of Cinchona-Derived Phase Transfer Catalysts , 2021, Organic Process Research & Development.

[39]  Scott J. Miller,et al.  "Tunable and Cooperative Catalysis for Enantioselective Pictet-Spengler Reaction with Varied Nitrogen-Containing Heterocyclic Carboxaldehydes". , 2021, Angewandte Chemie.

[40]  A. Żurański,et al.  Using Data Science To Guide Aryl Bromide Substrate Scope Analysis in a Ni/Photoredox-Catalyzed Cross-Coupling with Acetals as Alcohol-Derived Radical Sources. , 2021, Journal of the American Chemical Society.

[41]  E. Jacobsen,et al.  A Case Study in Catalyst Generality: Simultaneous, Highly-Enantioselective Brønsted- and Lewis-Acid Mechanisms in Hydrogen-Bond-Donor Catalyzed Oxetane Openings. , 2021, Journal of the American Chemical Society.

[42]  S. Snyder,et al.  Synthesis of aza-quaternary centers via Pictet–Spengler reactions of ketonitrones† , 2021, Chemical science.

[43]  Matthew D. Wodrich,et al.  The Genesis of Molecular Volcano Plots. , 2021, Accounts of chemical research.

[44]  Peter C. St. John,et al.  Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties. , 2021, Accounts of chemical research.

[45]  Ryan P. Adams,et al.  Bayesian reaction optimization as a tool for chemical synthesis , 2021, Nature.

[46]  M. Sigman,et al.  Connecting and Analyzing Enantioselective Bifunctional Hydrogen Bond Donor Catalysis using Data Science Tools. , 2020, Journal of the American Chemical Society.

[47]  Jieping Zhu,et al.  Asymmetric Total Synthesis of (-)-Arborisidine and (-)-19-epi-Arborisidine Enabled by a Catalytic Enantioselective Pictet-Spengler Reaction. , 2020, Journal of the American Chemical Society.

[48]  Matthew D. Wodrich,et al.  Data-Driven Advancement of Homogeneous Nickel Catalyst Activity for Aryl Ether Cleavage , 2020 .

[49]  Guilian Luchini,et al.  GoodVibes: automated thermochemistry for heterogeneous computational chemistry data , 2020, F1000Research.

[50]  S. You,et al.  Exploring the Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development: Asymmetric Pictet-Spengler-type Reactions and Beyond. , 2020, Accounts of chemical research.

[51]  Wenhao Gao,et al.  The Synthesizability of Molecules Proposed by Generative Models , 2020, J. Chem. Inf. Model..

[52]  Antonia Iazzetti,et al.  The Pictet-Spengler Reaction Updates Its Habits , 2020, Molecules.

[53]  Andrew F. Zahrt,et al.  Quantitative Structure-Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future. , 2019, Chemical reviews.

[54]  F. Glorius,et al.  A Structure-Based Platform for Predicting Chemical Reactivity , 2019, Chem.

[55]  Vidar R. Jensen,et al.  DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules , 2019, J. Chem. Inf. Model..

[56]  Peter Chen,et al.  A Universal Quantitative Descriptor of the Dispersion Interaction Potential. , 2019, Angewandte Chemie.

[57]  Matthew D. Wodrich,et al.  Activity-Based Screening of Homogeneous Catalysts through the Rapid Assessment of Theoretically Derived Turnover Frequencies , 2019, ACS Catalysis.

[58]  V. Batista,et al.  Search for Catalysts by Inverse Design: Artificial Intelligence, Mountain Climbers, and Alchemists. , 2019, Chemical reviews.

[59]  R. Paton,et al.  Retooling Asymmetric Conjugate Additions for Sterically Demanding Substrates with an Iterative Data-Driven Approach , 2019, ACS catalysis.

[60]  C. Farés,et al.  A multi-substrate screening approach for the identification of a broadly applicable Diels–Alder catalyst , 2019, Nature Communications.

[61]  S. Grimme Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations. , 2019, Journal of chemical theory and computation.

[62]  Yang Wang,et al.  Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning , 2019, Science.

[63]  Christopher A. Hunter,et al.  Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction , 2018, ACS central science.

[64]  C. Bannwarth,et al.  GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions. , 2018, Journal of chemical theory and computation.

[65]  S. Snyder,et al.  Mannich-type Reactions of Cyclic Nitrones: Effective Methods for the Enantioselective Synthesis of Piperidine-containing Alkaloids. , 2018, Angewandte Chemie.

[66]  H. Araki,et al.  Insights into the Structure and Function of a Chiral Conjugate‐Base‐Stabilized Brønsted Acid Catalyst , 2018, European Journal of Organic Chemistry.

[67]  Steven E Wheeler,et al.  AARON: An Automated Reaction Optimizer for New Catalysts. , 2018, Journal of chemical theory and computation.

[68]  S. You,et al.  Unified Mechanistic Understandings of Pictet-Spengler Reactions , 2018, Chem.

[69]  Alán Aspuru-Guzik,et al.  Inverse molecular design using machine learning: Generative models for matter engineering , 2018, Science.

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

[71]  Alán Aspuru-Guzik,et al.  Chimera: enabling hierarchy based multi-objective optimization for self-driving laboratories , 2018, Chemical science.

[72]  Derek T. Ahneman,et al.  Predicting reaction performance in C–N cross-coupling using machine learning , 2018, Science.

[73]  M. Sigman,et al.  Predictive and mechanistic multivariate linear regression models for reaction development , 2018, Chemical science.

[74]  E. Jacobsen,et al.  Chiral Thioureas Promote Enantioselective Pictet-Spengler Cyclization by Stabilizing Every Intermediate and Transition State in the Carboxylic Acid-Catalyzed Reaction. , 2017, Journal of the American Chemical Society.

[75]  Mike Preuss,et al.  Planning chemical syntheses with deep neural networks and symbolic AI , 2017, Nature.

[76]  S. You,et al.  Construction of Chiral Tetrahydro-β-Carbolines: Asymmetric Pictet-Spengler Reaction of Indolyl Dihydropyridines. , 2017, Angewandte Chemie.

[77]  Regina Barzilay,et al.  Prediction of Organic Reaction Outcomes Using Machine Learning , 2017, ACS central science.

[78]  Alán Aspuru-Guzik,et al.  Neural Networks for the Prediction of Organic Chemistry Reactions , 2016, ACS central science.

[79]  W. Thiel,et al.  Nitrated Confined Imidodiphosphates Enable a Catalytic Asymmetric Oxa-Pictet-Spengler Reaction. , 2016, Journal of the American Chemical Society.

[80]  Jonas Boström,et al.  Analysis of Past and Present Synthetic Methodologies on Medicinal Chemistry: Where Have All the New Reactions Gone? , 2016, Journal of medicinal chemistry.

[81]  Anat Milo,et al.  The Development of Multidimensional Analysis Tools for Asymmetric Catalysis and Beyond. , 2016, Accounts of chemical research.

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

[83]  Xavier Guinchard,et al.  Stereoselective Synthesis of Chiral Polycyclic Indolic Architectures through Pd(0) -Catalyzed Tandem Deprotection/Cyclization of Tetrahydro-β-carbolines on Allenes. , 2015, Chemistry.

[84]  Matthew N. Grayson,et al.  Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction. , 2015, The Journal of organic chemistry.

[85]  Anat Milo,et al.  Interrogating selectivity in catalysis using molecular vibrations , 2014, Nature.

[86]  D. Seidel,et al.  Conjugate-base-stabilized Brønsted acids: catalytic enantioselective Pictet-Spengler reactions with unmodified tryptamine. , 2014, Organic letters.

[87]  D. Seidel,et al.  Conjugate-base-stabilized Brønsted acids as asymmetric catalysts: enantioselective Povarov reactions with secondary aromatic amines. , 2013, Angewandte Chemie.

[88]  Steven E. Wheeler,et al.  Origin of the superior performance of (thio)squaramides over (thio)ureas in organocatalysis. , 2013, Chemistry.

[89]  D. Dixon,et al.  Gold and BINOL-Phosphoric Acid Catalyzed Enantioselective Hydroamination/N-Sulfonyliminium Cyclization Cascade , 2013, Organic letters.

[90]  Frank Glorius,et al.  A robustness screen for the rapid assessment of chemical reactions , 2013, Nature Chemistry.

[91]  D. Dixon,et al.  Enantioselective Michael Addition/Iminium Ion Cyclization Cascades of Tryptamine-Derived Ureas , 2013, Organic letters.

[92]  S. You,et al.  An olefin isomerization/asymmetric Pictet-Spengler cascade via sequential catalysis of ruthenium alkylidene and chiral phosphoric acid. , 2013, Organic & biomolecular chemistry.

[93]  S. Grimme Supramolecular binding thermodynamics by dispersion-corrected density functional theory. , 2012, Chemistry.

[94]  Vidar R. Jensen,et al.  An evolutionary algorithm for de novo optimization of functional transition metal compounds. , 2012, Journal of the American Chemical Society.

[95]  Yanguang Wang,et al.  Highly enantioselective Pictet-Spengler reaction catalyzed by SPINOL-phosphoric acids. , 2012, Chemistry.

[96]  E. Jacobsen,et al.  Thiourea-catalyzed enantioselective iso-Pictet-Spengler reactions. , 2011, Organic letters.

[97]  H. Waldmann,et al.  The Pictet-Spengler reaction in nature and in organic chemistry. , 2011, Angewandte Chemie.

[98]  D. Dixon,et al.  Direct Enantioselective Broensted Acid Catalyzed N‐Acyliminium Cyclization Cascades of Tryptamines and Ketoacids. , 2011 .

[99]  S. Shaik,et al.  How to conceptualize catalytic cycles? The energetic span model. , 2011, Accounts of chemical research.

[100]  M. Hahn,et al.  Extended-Connectivity Fingerprints , 2010, J. Chem. Inf. Model..

[101]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[102]  Y. Tao,et al.  Asymmetric Cooperative Catalysis of Strong Brønsted Acid–Promoted Reactions Using Chiral Ureas , 2010, Science.

[103]  D. Dixon,et al.  Enantioselective Brønsted acid-catalyzed N-acyliminium cyclization cascades. , 2009, Journal of the American Chemical Society.

[104]  B. Govaerts,et al.  Design of a genetic algorithm for the simulated evolution of a library of asymmetric transfer hydrogenation catalysts. , 2009, Chemistry.

[105]  P. Schreiner,et al.  (Thio)urea organocatalysis--what can be learnt from anion recognition? , 2009, Chemical Society reviews.

[106]  E. Jacobsen,et al.  Weak Brønsted acid-thiourea co-catalysis: enantioselective, catalytic protio-Pictet-Spengler reactions. , 2009, Organic letters.

[107]  J. V. van Maarseveen,et al.  Enantioselective BINOL-phosphoric acid catalyzed Pictet-Spengler reactions of N-benzyltryptamine. , 2008, The Journal of organic chemistry.

[108]  B. Trout,et al.  Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme. , 2008, Journal of the American Chemical Society.

[109]  D. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .

[110]  Donald G Truhlar,et al.  Density functionals with broad applicability in chemistry. , 2008, Accounts of chemical research.

[111]  I. Raheem,et al.  Enantioselective Pictet-Spengler-type cyclizations of hydroxylactams: H-bond donor catalysis by anion binding. , 2007, Journal of the American Chemical Society.

[112]  H. Hiemstra,et al.  Catalytic Asymmetric Pictet–Spengler Reactions via Sulfenyliminium Ions† , 2007 .

[113]  Yuxue Liang,et al.  A Vaulted Biaryl Phosphoric Acid-Catalyzed Reduction of α-Imino Esters: The Highly Enantioselective Preparation of α-Amino Esters , 2007 .

[114]  B. List,et al.  Catalytic asymmetric Pictet-Spengler reaction. , 2006, Journal of the American Chemical Society.

[115]  H. Tokuyama,et al.  Stereocontrolled total synthesis of (-)-eudistomin C. , 2005, Journal of the American Chemical Society.

[116]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[117]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[118]  H. Kagan,et al.  The Multi-Substrate Screening of Asymmetric Catalysts , 2005 .

[119]  Mark S. Taylor,et al.  Highly enantioselective catalytic acyl-pictet-spengler reactions. , 2004, Journal of the American Chemical Society.

[120]  Kevin Burgess,et al.  New Catalysts and Conditions for a CH Insertion Reaction Identified by High Throughput Catalyst Screening , 1996 .

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

[122]  K. Fukui The path of chemical reactions - the IRC approach , 1981 .

[123]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[124]  H. L. Morgan The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. , 1965 .

[125]  A. Pictet,et al.  Über die Bildung von Isochinolin‐derivaten durch Einwirkung von Methylal auf Phenyl‐äthylamin, Phenyl‐alanin und Tyrosin , 1911 .

[126]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[127]  H. Kagan,et al.  One‐pot multi‐substrate screening in asymmetric catalysis , 1998 .