1
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Liu C, Zhang H. Data processing for high-throughput mass spectrometry in drug discovery. Expert Opin Drug Discov 2024; 19:815-825. [PMID: 38785418 DOI: 10.1080/17460441.2024.2354871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION High-throughput mass spectrometry that could deliver > 10 times faster sample readout speed than traditional LC-based platforms has emerged as a powerful analytical technique, enabling the rapid analysis of complex biological samples. This increased speed of MS data acquisition has brought a critical demand for automatic data processing capabilities that should match or surpass the speed of data acquisition. Those data processing capabilities should serve the different requirements of drug discovery workflows. AREAS COVERED This paper introduced the key steps of the automatic data processing workflows for high-throughput MS technologies. Specific examples and requirements are detailed for different drug discovery applications. EXPERT OPINION The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications.
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Affiliation(s)
| | - Hui Zhang
- Iambic Therapeutics, San Diego, CA, USA
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2
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Polev K, Paneru G, Visyn V, Cybulski O, Lach S, Kolygina DV, Edel E, Grzybowski BA. Light-Driven, Dynamic Assembly of Micron-To-Centimeter Parts, Micromachines and Microbot Swarms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402263. [PMID: 38924658 DOI: 10.1002/advs.202402263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/27/2024] [Indexed: 06/28/2024]
Abstract
This work describes light-driven assembly of dynamic formations and functional particle swarms controlled by appropriately programmed light patterns. The system capitalizes on the use of a fluidic bed whose low thermal conductivity assures that light-generated heat remains "localized" and sets strong convective flows in the immediate vicinity of the particles being irradiated. In this way, even low-power laser light or light from a desktop slide projector can be used to organize dynamic formations of objects spanning four orders of magnitude in size (from microns to centimeters) and over nine orders of magnitude in terms of mass. These dynamic assemblies include open-lattice structures with individual particles performing intricate translational and/or rotational motions, density-gradient particle arrays, nested architectures of mechanical components (e.g., planetary gears), or swarms of light-actuated microbots controlling assembly of other objects.
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Affiliation(s)
- Konstantin Polev
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Govind Paneru
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Valentin Visyn
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
| | - Olgierd Cybulski
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
| | - Slawomir Lach
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
| | - Diana V Kolygina
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Evelyn Edel
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
| | - Bartosz A Grzybowski
- Center for Algorithmic and Robotized Synthesis (CARS), Korea's Institute for Basic Science (IBS), Ulsan, 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
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3
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Strieth-Kalthoff F, Hao H, Rathore V, Derasp J, Gaudin T, Angello NH, Seifrid M, Trushina E, Guy M, Liu J, Tang X, Mamada M, Wang W, Tsagaantsooj T, Lavigne C, Pollice R, Wu TC, Hotta K, Bodo L, Li S, Haddadnia M, Wołos A, Roszak R, Ser CT, Bozal-Ginesta C, Hickman RJ, Vestfrid J, Aguilar-Granda A, Klimareva EL, Sigerson RC, Hou W, Gahler D, Lach S, Warzybok A, Borodin O, Rohrbach S, Sanchez-Lengeling B, Adachi C, Grzybowski BA, Cronin L, Hein JE, Burke MD, Aspuru-Guzik A. Delocalized, asynchronous, closed-loop discovery of organic laser emitters. Science 2024; 384:eadk9227. [PMID: 38753786 DOI: 10.1126/science.adk9227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Contemporary materials discovery requires intricate sequences of synthesis, formulation, and characterization that often span multiple locations with specialized expertise or instrumentation. To accelerate these workflows, we present a cloud-based strategy that enabled delocalized and asynchronous design-make-test-analyze cycles. We showcased this approach through the exploration of molecular gain materials for organic solid-state lasers as a frontier application in molecular optoelectronics. Distributed robotic synthesis and in-line property characterization, orchestrated by a cloud-based artificial intelligence experiment planner, resulted in the discovery of 21 new state-of-the-art materials. Gram-scale synthesis ultimately allowed for the verification of best-in-class stimulated emission in a thin-film device. Demonstrating the asynchronous integration of five laboratories across the globe, this workflow provides a blueprint for delocalizing-and democratizing-scientific discovery.
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Affiliation(s)
- Felix Strieth-Kalthoff
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Han Hao
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
| | - Vandana Rathore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joshua Derasp
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Théophile Gaudin
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Nicholas H Angello
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Martin Seifrid
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | | | - Mason Guy
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Junliang Liu
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Xun Tang
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Masashi Mamada
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Wesley Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tuul Tsagaantsooj
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Cyrille Lavigne
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Robert Pollice
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Tony C Wu
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Kazuhiro Hotta
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Mitsubishi Chemical Corporation Science & Innovation Center, Kanagawa, Japan
| | - Leticia Bodo
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Shangyu Li
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mohammad Haddadnia
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Agnieszka Wołos
- Allchemy Inc., Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Rafał Roszak
- Allchemy Inc., Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Cher Tian Ser
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Carlota Bozal-Ginesta
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Catalonia Institute for Energy Research, Barcelona, Spain
| | - Riley J Hickman
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jenya Vestfrid
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Andrés Aguilar-Granda
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | | | - Wenduan Hou
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Daniel Gahler
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Slawomir Lach
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Adrian Warzybok
- School of Chemistry, University of Glasgow, Glasgow, UK
- Department of Chemical Physics, Jagiellonian University, Krakow, Poland
| | - Oleg Borodin
- School of Chemistry, University of Glasgow, Glasgow, UK
| | | | | | - Chihaya Adachi
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Center for Algorithmic and Robotized Synthesis, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Chemistry, Ulsan Institute of Science and Technology, Ulsan, Republic of Korea
| | - Leroy Cronin
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Jason E Hein
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of Bergen, Bergen, Norway
| | - Martin D Burke
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Materials Science and Engineering, University of Toronto, Toronto, ON, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
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4
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Heinrich G, Kondratiuk M, Gooßen LJ, Wiesenfeldt MP. Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy. Nat Protoc 2024; 19:1529-1556. [PMID: 38409535 DOI: 10.1038/s41596-023-00951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/16/2023] [Indexed: 02/28/2024]
Abstract
The instrumental analysis of reaction mixtures is usually the rate-determining step in the optimization of chemical processes. Traditionally, reactions are analyzed by gas chromatography, HPLC or quantitative NMR spectroscopy on high-field spectrometers. However, chromatographic methods require elaborate work-up and calibration protocols, and high-field NMR spectrometers are expensive to purchase and operate. This protocol describes an inexpensive and highly effective analysis method based on low-field benchtop NMR spectroscopy. Its key feature is the use of fluorine-labeled model substrates that, because of the wide chemical shift range and high sensitivity of 19F, enable separate, quantitative detection of product and by-product signals even on low-field, permanent magnet spectrometers. An external lock/shim device obviates the need for deuterated solvents, permitting the direct, noninvasive measurement of crude reaction mixtures with minimal workup. The low field-strength facilitates a homogeneous excitation over a wide chemical shift range, minimizing systematic integration errors. The addition of the optimal amount of the nonshifting relaxation agent tris(acetylacetonato) iron(III) minimizes relaxation delays at full resolution, reducing the analysis time to 32 s per sample. The correct choice of processing parameters is also crucial. A step-by-step guideline is provided, the influence of all parameters, including adjustments needed when using high-field spectrometers, is discussed and potential pitfalls are highlighted. The wide applicability of the analytical protocol for reaction optimization is illustrated by three examples: a Buchwald-Hartwig amination, a Suzuki coupling and a C-H arylation reaction.
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Affiliation(s)
- G Heinrich
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M Kondratiuk
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - L J Gooßen
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M P Wiesenfeldt
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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5
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Liu DH, Pflüger PM, Outlaw A, Lückemeier L, Zhang F, Regan C, Rashidi Nodeh H, Cernak T, Ma J, Glorius F. Late-Stage Saturation of Drug Molecules. J Am Chem Soc 2024; 146:11866-11875. [PMID: 38621677 PMCID: PMC11066876 DOI: 10.1021/jacs.4c00807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
The available methods of chemical synthesis have arguably contributed to the prevalence of aromatic rings, such as benzene, toluene, xylene, or pyridine, in modern pharmaceuticals. Many such sp2-carbon-rich fragments are now easy to synthesize using high-quality cross-coupling reactions that click together an ever-expanding menu of commercially available building blocks, but the products are flat and lipophilic, decreasing their odds of becoming marketed drugs. Converting flat aromatic molecules into saturated analogues with a higher fraction of sp3 carbons could improve their medicinal properties and facilitate the invention of safe, efficacious, metabolically stable, and soluble medicines. In this study, we show that aromatic and heteroaromatic drugs can be readily saturated under exceptionally mild rhodium-catalyzed hydrogenation, acid-mediated reduction, or photocatalyzed-hydrogenation conditions, converting sp2 carbon atoms into sp3 carbon atoms and leading to saturated molecules with improved medicinal properties. These methods are productive in diverse pockets of chemical space, producing complex saturated pharmaceuticals bearing a variety of functional groups and three-dimensional architectures. The rhodium-catalyzed method tolerates traces of dimethyl sulfoxide (DMSO) or water, meaning that pharmaceutical compound collections, which are typically stored in wet DMSO, can finally be reformatted for use as substrates for chemical synthesis. This latter application is demonstrated through the late-stage saturation (LSS) of 768 complex and densely functionalized small-molecule drugs.
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Affiliation(s)
- De-Hai Liu
- Frontiers
Science Center for Transformative Molecules, Shanghai Key Laboratory
for Molecular Engineering of Chiral Drugs, School of Chemistry and
Chemical Engineering and Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Philipp M. Pflüger
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität
Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Andrew Outlaw
- Department
of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lukas Lückemeier
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität
Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Fuhao Zhang
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität
Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Clinton Regan
- Department
of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hamid Rashidi Nodeh
- Department
of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tim Cernak
- Department
of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jiajia Ma
- Frontiers
Science Center for Transformative Molecules, Shanghai Key Laboratory
for Molecular Engineering of Chiral Drugs, School of Chemistry and
Chemical Engineering and Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität
Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität
Münster, Corrensstraße 40, 48149 Münster, Germany
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6
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Phelps J, Kumar R, Robinson JD, Chu JCK, Flodén NJ, Beaton S, Gaunt MJ. Multicomponent Synthesis of α-Branched Amines via a Zinc-Mediated Carbonyl Alkylative Amination Reaction. J Am Chem Soc 2024; 146:9045-9062. [PMID: 38488310 PMCID: PMC10996026 DOI: 10.1021/jacs.3c14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024]
Abstract
Methods for the synthesis of α-branched alkylamines are important due to their ubiquity in biologically active molecules. Despite the development of many methods for amine preparation, C(sp3)-rich nitrogen-containing compounds continue to pose challenges for synthesis. While carbonyl reductive amination (CRA) between ketones and alkylamines is the cornerstone method for α-branched alkylamine synthesis, it is sometimes limited by the sterically demanding condensation step between dialkyl ketones and amines and the more restricted availability of ketones compared to aldehydes. We recently reported a "higher-order" variant of this transformation, carbonyl alkylative amination (CAA), which utilized a halogen atom transfer (XAT)-mediated radical mechanism, enabling the streamlined synthesis of complex α-branched alkylamines. Despite the efficacy of this visible-light-driven approach, it displayed scalability issues, and competitive reductive amination was a problem for certain substrate classes, limiting applicability. Here, we report a change in the reaction regime that expands the CAA platform through the realization of an extremely broad zinc-mediated CAA reaction. This new strategy enabled elimination of competitive CRA, simplified purification, and improved reaction scope. Furthermore, this new reaction harnessed carboxylic acid derivatives as alkyl donors and facilitated the synthesis of α-trialkyl tertiary amines, which cannot be accessed via CRA. This Zn-mediated CAA reaction can be carried out at a variety of scales, from a 10 μmol setup in microtiter plates enabling high-throughput experimentation, to the gram-scale synthesis of medicinally-relevant compounds. We believe that this transformation enables robust, efficient, and economical access to α-branched alkylamines and provides a viable alternative to the current benchmark methods.
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Affiliation(s)
| | | | | | | | - Nils J. Flodén
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sarah Beaton
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Matthew J. Gaunt
- Yusuf Hamied Department of
Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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7
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Wagner F, Sagmeister P, Jusner CE, Tampone TG, Manee V, Buono FG, Williams JD, Kappe CO. A Slug Flow Platform with Multiple Process Analytics Facilitates Flexible Reaction Optimization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308034. [PMID: 38273711 PMCID: PMC10987115 DOI: 10.1002/advs.202308034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Flow processing offers many opportunities to optimize reactions in a rapid and automated manner, yet often requires relatively large quantities of input materials. To combat this, the use of a flexible slug flow reactor, equipped with two analytical instruments, for low-volume optimization experiments are reported. A Buchwald-Hartwig amination toward the drug olanzapine, with 6 independent optimizable variables, is optimized using three different automated approaches: self-optimization, design of experiments, and kinetic modeling. These approaches are complementary and provide differing information on the reaction: pareto optimal operating points, response surface models, and mechanistic models, respectively. The results are achieved using <10% of the material that would be required for standard flow operation. Finally, a chemometric model is built utilizing automated data handling and three subsequent validation experiments demonstrate good agreement between the slug flow reactor and a standard (larger scale) flow reactor.
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Affiliation(s)
- Florian Wagner
- Center for Continuous Flow Synthesis and Processing (CC FLOW)Research Center Pharmaceutical Engineering GmbH (RCPE)Inffeldgasse 13Graz8010Austria
- Institute of ChemistryUniversity of GrazNAWI Graz, Heinrichstrasse 28Graz8010Austria
| | - Peter Sagmeister
- Center for Continuous Flow Synthesis and Processing (CC FLOW)Research Center Pharmaceutical Engineering GmbH (RCPE)Inffeldgasse 13Graz8010Austria
- Institute of ChemistryUniversity of GrazNAWI Graz, Heinrichstrasse 28Graz8010Austria
| | - Clemens E. Jusner
- Center for Continuous Flow Synthesis and Processing (CC FLOW)Research Center Pharmaceutical Engineering GmbH (RCPE)Inffeldgasse 13Graz8010Austria
- Institute of ChemistryUniversity of GrazNAWI Graz, Heinrichstrasse 28Graz8010Austria
| | - Thomas G. Tampone
- Boehringer Ingelheim Pharmaceuticals, Inc900 Ridgebury RoadRidgefieldCT06877USA
| | - Vidhyadhar Manee
- Boehringer Ingelheim Pharmaceuticals, Inc900 Ridgebury RoadRidgefieldCT06877USA
| | - Frederic G. Buono
- Boehringer Ingelheim Pharmaceuticals, Inc900 Ridgebury RoadRidgefieldCT06877USA
| | - Jason D. Williams
- Center for Continuous Flow Synthesis and Processing (CC FLOW)Research Center Pharmaceutical Engineering GmbH (RCPE)Inffeldgasse 13Graz8010Austria
- Institute of ChemistryUniversity of GrazNAWI Graz, Heinrichstrasse 28Graz8010Austria
| | - C. Oliver Kappe
- Center for Continuous Flow Synthesis and Processing (CC FLOW)Research Center Pharmaceutical Engineering GmbH (RCPE)Inffeldgasse 13Graz8010Austria
- Institute of ChemistryUniversity of GrazNAWI Graz, Heinrichstrasse 28Graz8010Austria
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8
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Yu J, Liu J, Li C, Huang J, Zhu Y, You H. Recent advances and applications in high-throughput continuous flow. Chem Commun (Camb) 2024; 60:3217-3225. [PMID: 38436212 DOI: 10.1039/d3cc06180a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
High-throughput continuous flow technology has emerged as a revolutionary approach in chemical synthesis, offering accelerated experimentation and improved efficiency. With the aid of process analytical technology and automation, this system not only enables rapid optimisation of reaction conditions at the millimole to the picomole scale, but also facilitates automated scale-up synthesis. It can even achieve the self-planning and self-synthesis of small drug molecules with artificial intelligence incorporated in the system. The versatility of the system is highlighted by its compatibility with both electrochemistry and photochemistry, and its significant applications in organic synthesis and drug discovery. This highlight summarises its recent developments and applications, emphasising its significant impact on advancing research across multiple disciplines.
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Affiliation(s)
- Jiaping Yu
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China.
| | - Jiaying Liu
- Institute of Advanced Technology of Heilongjiang Academy of Sciences, Harbin, 150000, China
| | - Chaoyi Li
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China.
| | - Junrong Huang
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China.
| | - Yuxiang Zhu
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Hengzhi You
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China.
- Green Pharmaceutical Engineering Research Centre, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
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9
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Xin Y, Foster SW, Makey DM, Parker D, Bradow J, Wang X, Berritt S, Mongillo R, Grinias JP, Kennedy RT. High-Throughput Capillary Liquid Chromatography Using a Droplet Injection and Application to Reaction Screening. Anal Chem 2024; 96:4693-4701. [PMID: 38442211 PMCID: PMC11001260 DOI: 10.1021/acs.analchem.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The cycle time of a standard liquid chromatography (LC) system is the sum of the time for the chromatographic run and the autosampler injection sequence. Although LC separation times in the 1-10 s range have been demonstrated, injection sequences are commonly >15 s, limiting throughput possible with LC separations. Further, such separations are performed on relatively large bore columns requiring flow rates of ≥5 mL/min, thus generating large volumes of mobile phase waste when used for large scale screening and increasing the difficulty in interfacing to mass spectrometry. Here, a droplet injector system was established that replaces the autosampler with a four-port, two-position valve equipped with a 20 nL internal loop interfaced to a syringe pump and a three-axis positioner to withdraw sample droplets from a well plate. In the system, sample and immiscible fluid are pulled alternately from a well plate into a capillary and then through the injection valve. The valve is actuated when sample fills the loop to allow sequential injection of samples at high throughput. Capillary LC columns with 300 μm inner diameter were used to reduce the consumption of mobile phase and sample. The system achieved 96 separations of 20 nL droplet samples containing 3 components in as little as 8.1 min with 5-s cycle time. This system was coupled to a mass spectrometer through an electrospray ionization source for high-throughput chemical reaction screening.
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Affiliation(s)
- Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel W Foster
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Deklin Parker
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - James Bradow
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Xiaochun Wang
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Simon Berritt
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - Robert Mongillo
- Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06415, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
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10
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Gesmundo NJ, Rago AJ, Young JM, Keess S, Wang Y. At the Speed of Light: The Systematic Implementation of Photoredox Cross-Coupling Reactions for Medicinal Chemistry Research. J Org Chem 2024. [PMID: 38442262 DOI: 10.1021/acs.joc.3c02351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The adoption of new and emerging techniques in organic synthesis is essential to promote innovation in drug discovery. In this Perspective, we detail the strategy we used for the systematic deployment of photoredox-mediated, metal-catalyzed cross-coupling reactions in AbbVie's medicinal chemistry organization, focusing on topics such as assessment, evaluation, implementation, and accessibility. The comprehensive evaluation of photoredox reaction setups and published methods will be discussed, along with internal efforts to build expertise and photoredox high-throughput experimentation capabilities. We also highlight AbbVie's academic-industry collaborations in this field that have been leveraged to develop new synthetic strategies, along with discussing the internal adoption of photoredox cross-coupling reactions. The work described herein has culminated in robust photocatalysis and cross-coupling capabilities which are viewed as key platforms for medicinal chemistry research at AbbVie.
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Affiliation(s)
- Nathan J Gesmundo
- Advanced Chemistry Technologies Group, Small Molecule Therapeutics & Platform Technologies, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alexander J Rago
- Advanced Chemistry Technologies Group, Small Molecule Therapeutics & Platform Technologies, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Jonathon M Young
- Advanced Chemistry Technologies Group, Small Molecule Therapeutics & Platform Technologies, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Sebastian Keess
- Global Medicinal Chemistry, Small Molecule Therapeutics & Platform Technologies, AbbVie Deutschland GmbH & Co. KG, 67061 Ludwigshafen, Germany
| | - Ying Wang
- Advanced Chemistry Technologies Group, Small Molecule Therapeutics & Platform Technologies, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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11
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Williams JD, Pu F, Sawicki JW, Elsen NL. Ultra-high-throughput mass spectrometry in drug discovery: fundamentals and recent advances. Expert Opin Drug Discov 2024; 19:291-301. [PMID: 38111363 DOI: 10.1080/17460441.2023.2293153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
INTRODUCTION Ultra-high-throughput mass spectrometry, uHT-MS, is a technology that utilizes ionization and sample delivery technologies optimized to enable sampling from well plates at > 1 sample per second. These technologies do not need a chromatographic separation step and can be utilized in a wide variety of assays to detect a broad range of analytes including small molecules, lipids, and proteins. AREAS COVERED This manuscript provides a brief historical review of high-throughput mass spectrometry and the recently developed technologies that have enabled uHT-MS. The report also provides examples and references on how uHT-MS has been used in biochemical and chemical assays, nuisance compound profiling, protein analysis and high throughput experimentation for chemical synthesis. EXPERT OPINION The fast analysis time provided by uHT-MS is transforming how biochemical and chemical assays are performed in drug discovery. The potential to associate phenotypic responses produced by 1000's of compound treatments with changes in endogenous metabolite and lipid signals is becoming feasible. With the augmentation of simple, fast, high-throughput sample preparation, the scope of uHT-MS usage will increase. However, it likely will not supplant LC-MS for analyses that require low detection limits from complex matrices or characterization of complex biotherapeutics such as antibody-drug conjugates.
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Affiliation(s)
| | - Fan Pu
- Abbvie Discovery Research, North Chicago, IL, USA
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12
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Niu KK, Cui J, Dong RZ, Yu S, Liu H, Xing LB. Visible-light-mediated direct C3 alkylation of quinoxalin-2(1 H)-ones using alkanes. Chem Commun (Camb) 2024; 60:2409-2412. [PMID: 38323602 DOI: 10.1039/d3cc06285f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Due to the high C-H bond dissociation energy of alkanes, the utilization of alkanes as alkyl radical precursors for C-H functionalization of heteroarenes is synthetically captivating but practically challenging, especially under metal- and photocatalyst-free conditions. We report herein a mild and practical visible-light-mediated method for C-H alkylation of quinoxalin-2(1H)-ones using trifluoroacetic acid as a hydrogen atom transfer reagent and air as an oxidant. This mild protocol was performed under metal- and photocatalyst-free circumstances and presented good functional-group tolerance as well as a broad substrate scope.
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Affiliation(s)
- Kai-Kai Niu
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
| | - Jing Cui
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
| | - Rui-Zhi Dong
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
| | - Shengsheng Yu
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
| | - Hui Liu
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
| | - Ling-Bao Xing
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China.
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13
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Brocklehurst CE, Altmann E, Bon C, Davis H, Dunstan D, Ertl P, Ginsburg-Moraff C, Grob J, Gosling DJ, Lapointe G, Marziale AN, Mues H, Palmieri M, Racine S, Robinson RI, Springer C, Tan K, Ulmer W, Wyler R. MicroCycle: An Integrated and Automated Platform to Accelerate Drug Discovery. J Med Chem 2024; 67:2118-2128. [PMID: 38270627 DOI: 10.1021/acs.jmedchem.3c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
We herein describe the development and application of a modular technology platform which incorporates recent advances in plate-based microscale chemistry, automated purification, in situ quantification, and robotic liquid handling to enable rapid access to high-quality chemical matter already formatted for assays. In using microscale chemistry and thus consuming minimal chemical matter, the platform is not only efficient but also follows green chemistry principles. By reorienting existing high-throughput assay technology, the platform can generate a full package of relevant data on each set of compounds in every learning cycle. The multiparameter exploration of chemical and property space is hereby driven by active learning models. The enhanced compound optimization process is generating knowledge for drug discovery projects in a time frame never before possible.
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Affiliation(s)
- Cara E Brocklehurst
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Eva Altmann
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Corentin Bon
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Holly Davis
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - David Dunstan
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Ertl
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Carol Ginsburg-Moraff
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jonathan Grob
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel J Gosling
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Guillaume Lapointe
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Alexander N Marziale
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Heinrich Mues
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Marco Palmieri
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Sophie Racine
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Richard I Robinson
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Clayton Springer
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Kian Tan
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - William Ulmer
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - René Wyler
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
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14
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Zhang R, Mahjour B, Outlaw A, McGrath A, Hopper T, Kelley B, Walters WP, Cernak T. Exploring the combinatorial explosion of amine-acid reaction space via graph editing. Commun Chem 2024; 7:22. [PMID: 38310120 PMCID: PMC10838272 DOI: 10.1038/s42004-024-01101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
Amines and carboxylic acids are abundant chemical feedstocks that are nearly exclusively united via the amide coupling reaction. The disproportionate use of the amide coupling leaves a large section of unexplored reaction space between amines and acids: two of the most common chemical building blocks. Herein we conduct a thorough exploration of amine-acid reaction space via systematic enumeration of reactions involving a simple amine-carboxylic acid pair. This approach to chemical space exploration investigates the coarse and fine modulation of physicochemical properties and molecular shapes. With the invention of reaction methods becoming increasingly automated and bringing conceptual reactions into reality, our map provides an entirely new axis of chemical space exploration for rational property design.
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Affiliation(s)
- Rui Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Babak Mahjour
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Outlaw
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Andrew McGrath
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Tim Cernak
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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15
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Nippa DF, Atz K, Hohler R, Müller AT, Marx A, Bartelmus C, Wuitschik G, Marzuoli I, Jost V, Wolfard J, Binder M, Stepan AF, Konrad DB, Grether U, Martin RE, Schneider G. Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning. Nat Chem 2024; 16:239-248. [PMID: 37996732 PMCID: PMC10849962 DOI: 10.1038/s41557-023-01360-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Late-stage functionalization is an economical approach to optimize the properties of drug candidates. However, the chemical complexity of drug molecules often makes late-stage diversification challenging. To address this problem, a late-stage functionalization platform based on geometric deep learning and high-throughput reaction screening was developed. Considering borylation as a critical step in late-stage functionalization, the computational model predicted reaction yields for diverse reaction conditions with a mean absolute error margin of 4-5%, while the reactivity of novel reactions with known and unknown substrates was classified with a balanced accuracy of 92% and 67%, respectively. The regioselectivity of the major products was accurately captured with a classifier F-score of 67%. When applied to 23 diverse commercial drug molecules, the platform successfully identified numerous opportunities for structural diversification. The influence of steric and electronic information on model performance was quantified, and a comprehensive simple user-friendly reaction format was introduced that proved to be a key enabler for seamlessly integrating deep learning and high-throughput experimentation for late-stage functionalization.
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Affiliation(s)
- David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kenneth Atz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Remo Hohler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Alex T Müller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andreas Marx
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Bartelmus
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Georg Wuitschik
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Irene Marzuoli
- Process Chemistry and Catalysis (PCC), F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Vera Jost
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Jens Wolfard
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Martin Binder
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Antonia F Stepan
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - David B Konrad
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- ETH Singapore SEC Ltd, Singapore, Singapore.
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16
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Hu H, Singh AN, Lehnherr D, Mdluli V, Chun SW, Makarewicz AM, Gouker JR, Ukaegbu O, Li S, Wen X, McLaren DG, Velasquez JE, Moore JC, Galanie S, Appiah-Amponsah E, Regalado EL. Accelerating Pharmaceutical Process Development with an Acoustic Droplet Ejection-Multiple Reaction Monitoring-Mass Spectrometry Workflow. Anal Chem 2024; 96:1138-1146. [PMID: 38165811 DOI: 10.1021/acs.analchem.3c04211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Fast-paced pharmaceutical process developments (e.g., high-throughput experimentation, directed evolution, and machine learning) involve the introduction of fast, sensitive, and accurate analytical assays using limited sample volumes. In recent years, acoustic droplet ejection (ADE) coupled with an open port interface has been invented as a sampling technology for mass spectrometry, providing high-throughput nanoliter analytical measurements directly from the standard microplates. Herein, we introduce an ADE-multiple reaction monitoring-mass spectrometry (ADE-MRM-MS) workflow to accelerate pharmaceutical process research and development (PR&D). This systematic workflow outlines the selection of MRM transitions and optimization of assay parameters in a data-driven manner using rapid measurements (1 sample/s). The synergy between ADE sampling and MRM analysis enables analytical assays with excellent sensitivity, selectivity, and speed for PR&D reaction screenings. This workflow was utilized to develop new ADE-MRM-MS assays guiding a variety of industrial processes, including (1) screening of Ni-based catalysts for C-N cross-coupling reaction at 1 Hz and (2) high-throughput regioisomer analysis-enabled enzyme library screening for peptide ligation reaction. ADE-MRM-MS assays were demonstrated to deliver accurate results that are comparable to conventional liquid chromatography (LC) experiments while providing >100-fold throughput enhancement.
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Affiliation(s)
- Hang Hu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew N Singh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dan Lehnherr
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Velabo Mdluli
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie W Chun
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Amanda M Makarewicz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joseph R Gouker
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ophelia Ukaegbu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiujuan Wen
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David G McLaren
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Juan E Velasquez
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie Galanie
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Erik L Regalado
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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17
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Samha MH, Karas LJ, Vogt DB, Odogwu EC, Elward J, Crawford JM, Steves JE, Sigman MS. Predicting success in Cu-catalyzed C-N coupling reactions using data science. SCIENCE ADVANCES 2024; 10:eadn3478. [PMID: 38232169 PMCID: PMC10793951 DOI: 10.1126/sciadv.adn3478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
Data science is assuming a pivotal role in guiding reaction optimization and streamlining experimental workloads in the evolving landscape of synthetic chemistry. A discipline-wide goal is the development of workflows that integrate computational chemistry and data science tools with high-throughput experimentation as it provides experimentalists the ability to maximize success in expensive synthetic campaigns. Here, we report an end-to-end data-driven process to effectively predict how structural features of coupling partners and ligands affect Cu-catalyzed C-N coupling reactions. The established workflow underscores the limitations posed by substrates and ligands while also providing a systematic ligand prediction tool that uses probability to assess when a ligand will be successful. This platform is strategically designed to confront the intrinsic unpredictability frequently encountered in synthetic reaction deployment.
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Affiliation(s)
- Mohammad H. Samha
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112, USA
| | - Lucas J. Karas
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112, USA
| | - David B. Vogt
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112, USA
| | - Emmanuel C. Odogwu
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112, USA
| | - Jennifer Elward
- Molecular Design, GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA
| | - Jennifer M. Crawford
- Drug Substance Development, GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA
| | - Janelle E. Steves
- Drug Substance Development, GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112, USA
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18
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Pipaón Fernández N, Cruise O, Easton SEF, Kaplan JM, Woodard JL, Hruszkewycz DP, Leitch DC. Direct Heterocycle C-H Alkenylation via Dual Catalysis Using a Palladacycle Precatalyst: Multifactor Optimization and Scope Exploration Enabled by High-Throughput Experimentation. J Org Chem 2024. [PMID: 38206166 DOI: 10.1021/acs.joc.3c02311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
One of the major challenges in developing catalytic methods for C-C bond formation is the identification of generally applicable reaction conditions, particularly if multiple substrate structural classes are involved. Pd-catalyzed direct arylation reactions are powerful transformations that enable direct functionalization of C-H bonds; however, the corresponding direct alkenylation reactions, using vinyl (pseudo) halide electrophiles, are less well developed. Inspired by process development efforts toward GSK3368715, an investigational active pharmaceutical ingredient, we report that a Pd(II) palladacycle derived from tri-tert-butylphosphine and Pd(OAc)2 is an effective single-component precatalyst for a variety of direct alkenylation reactions. High-throughput experimentation identified optimal solvent/base combinations for a variety of HetAr-H substrate classes undergoing C-H activation without the need for cocatalysts or stoichiometric silver bases (e.g., Ag2CO3). We propose this reaction proceeds via a dual cooperative catalytic mechanism, where in situ-generated Pd(0) supports a canonical Pd(0)/(II) cross-coupling cycle and the palladacycle effects C-H activation via CMD in a redox-neutral cycle. In all, 192 substrate combinations were tested with a hit rate of approximately 40% and 24 isolated examples. Importantly, this method was applied to prepare a key intermediate in the synthesis of GSK3368715 on multigram scale.
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Affiliation(s)
- Nahiane Pipaón Fernández
- Department of Chemistry, University of Victoria, 3800 Finnerty Road., Victoria, Briish Columbia V8P 5C2, Canada
| | - Odhran Cruise
- Department of Chemistry, University of Victoria, 3800 Finnerty Road., Victoria, Briish Columbia V8P 5C2, Canada
| | - Sarah E F Easton
- Department of Chemistry, University of Victoria, 3800 Finnerty Road., Victoria, Briish Columbia V8P 5C2, Canada
| | - Justin M Kaplan
- Chemical Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - John L Woodard
- Chemical Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Damian P Hruszkewycz
- Chemical Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - David C Leitch
- Department of Chemistry, University of Victoria, 3800 Finnerty Road., Victoria, Briish Columbia V8P 5C2, Canada
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19
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Voinarovska V, Kabeshov M, Dudenko D, Genheden S, Tetko IV. When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. J Chem Inf Model 2024; 64:42-56. [PMID: 38116926 PMCID: PMC10778086 DOI: 10.1021/acs.jcim.3c01524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Machine Learning (ML) techniques face significant challenges when predicting advanced chemical properties, such as yield, feasibility of chemical synthesis, and optimal reaction conditions. These challenges stem from the high-dimensional nature of the prediction task and the myriad essential variables involved, ranging from reactants and reagents to catalysts, temperature, and purification processes. Successfully developing a reliable predictive model not only holds the potential for optimizing high-throughput experiments but can also elevate existing retrosynthetic predictive approaches and bolster a plethora of applications within the field. In this review, we systematically evaluate the efficacy of current ML methodologies in chemoinformatics, shedding light on their milestones and inherent limitations. Additionally, a detailed examination of a representative case study provides insights into the prevailing issues related to data availability and transferability in the discipline.
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Affiliation(s)
- Varvara Voinarovska
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
- TUM
Graduate School, Faculty of Chemistry, Technical
University of Munich, 85748 Garching, Germany
| | - Mikhail Kabeshov
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Dmytro Dudenko
- Enamine
Ltd., 78 Chervonotkatska str., 02094 Kyiv, Ukraine
| | - Samuel Genheden
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Igor V. Tetko
- Molecular
Targets and Therapeutics Center, Helmholtz Munich − Deutsches
Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Structural Biology, 85764 Neuherberg, Germany
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20
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Townley C, Branduardi D, Chessari G, Cons BD, Griffiths-Jones C, Hall RJ, Johnson CN, Ochi Y, Whibley S, Grainger R. Enabling synthesis in fragment-based drug discovery (FBDD): microscale high-throughput optimisation of the medicinal chemist's toolbox reactions. RSC Med Chem 2023; 14:2699-2713. [PMID: 38107176 PMCID: PMC10718589 DOI: 10.1039/d3md00495c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 12/19/2023] Open
Abstract
Miniaturised high-throughput experimentation (HTE) is widely employed in industrial and academic laboratories for rapid reaction optimisation using material-limited, multifactorial reaction condition screening. In fragment-based drug discovery (FBDD), common toolbox reactions such as the Suzuki-Miyaura and Buchwald-Hartwig cross couplings can be hampered by the fragment's intrinsic heteroatom-rich pharmacophore which is required for ligand-protein binding. At Astex, we are using microscale HTE to speed up reaction optimisation and prevent target down-prioritisation. By identifying catalyst/base/solvent combinations which tolerate unprotected heteroatoms we can rapidly optimise key cross-couplings and expedite route design by avoiding superfluous protecting group manipulations. However, HTE requires extensive upfront training, and this modern automated synthesis technique largely differs to the way organic chemists are traditionally trained. To make HTE accessible to all our synthetic chemists we have developed a semi-automated workflow enabled by pre-made 96-well screening kits, rapid analytical methods and in-house software development, which is empowering chemists at Astex to run HTE screens independently with minimal training.
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Affiliation(s)
- Chloe Townley
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Davide Branduardi
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Gianni Chessari
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Benjamin D Cons
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Richard J Hall
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Yuji Ochi
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Stuart Whibley
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rachel Grainger
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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21
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Stevens R, Bendito-Moll E, Battersby DJ, Miah AH, Wellaway N, Law RP, Stacey P, Klimaszewska D, Macina JM, Burley GA, Harling JD. Integrated Direct-to-Biology Platform for the Nanoscale Synthesis and Biological Evaluation of PROTACs. J Med Chem 2023; 66:15437-15452. [PMID: 37933562 DOI: 10.1021/acs.jmedchem.3c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules that co-opt the cell's natural proteasomal degradation mechanisms to degrade undesired proteins. A challenge associated with PROTACs is the time and resource-intensive optimization; thus, the development of high-throughput platforms for their synthesis and biological evaluation is required. In this study, we establish an ultra-high-throughput experimentation (ultraHTE) platform for PROTAC synthesis, followed by direct addition of the crude reaction mixtures to cellular degradation assays without any purification. This 'direct-to-biology' (D2B) approach was validated and then exemplified in a medicinal chemistry campaign to identify novel BRD4 PROTACs. Using the D2B platform, the synthesis of 650 PROTACs was carried out in a 1536-well plate, and subsequent biological evaluation was performed by a single scientist in less than 1 month. Due to its ability to hugely accelerate the optimization of new degraders, we anticipate our platform will transform the synthesis and testing of PROTACs.
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Affiliation(s)
- Rebecca Stevens
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Enrique Bendito-Moll
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - David J Battersby
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Afjal H Miah
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Natalie Wellaway
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Robert P Law
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter Stacey
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Diana Klimaszewska
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Justyna M Macina
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John D Harling
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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22
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Makey DM, Diehl RC, Xin Y, Murray BE, Stoll DR, Ruotolo BT, Grinias JP, Narayan ARH, Lopez-Carillo V, Stark M, Johnen P, Kennedy RT. High-Throughput Liquid Chromatographic Analysis Using a Segmented Flow Injector with a 1 s Cycle Time. Anal Chem 2023; 95:17028-17036. [PMID: 37943345 PMCID: PMC11027085 DOI: 10.1021/acs.analchem.3c03719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
High-throughput screening (HTS) workflows are revolutionizing many fields, including drug discovery, reaction discovery and optimization, diagnostics, sensing, and enzyme engineering. Liquid chromatography (LC) is commonly deployed during HTS to reduce matrix effects, distinguish isomers, and preconcentrate prior to detection, but LC separation time often limits throughput. Although subsecond LC separations have been demonstrated, they are rarely utilized during HTS due to limitations associated with the speed of common autosamplers. In this work, these limits are overcome by utilizing droplet microfluidics for sample introduction. In the method, a train of samples segmented by air are continuously pumped into the inlet of an LC injection valve that is actuated once each sample fills the sample loop. Coupled with 2.1 mm diameter × 5 mm long columns packed with 2.7 μm superficially porous C18 particles operated at 5 mL/min, the injector enabled separation of 3 components at 1 s/sample and analysis of a 96-well plate in 1.6 min with <2% peak area relative standard deviation. Analyte-dependent carryover was minimized by including wash droplets composed of organic solvent in between sample droplets. High-throughput LC coupled with mass spectrometric detection using the segmented flow injector was applied to a screen of inhibitors of a cytochrome P450-catalyzed hydroxylation reaction. Measurements of the reaction substrate and product concentrations made using fast LC with the segmented flow injector correlated well with measurements made using a more conventional, 3 min LC method. These results demonstrate the potential for droplet microfluidics to be used for sample introduction during high-throughput LC analysis.
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Affiliation(s)
- Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Roger C Diehl
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yue Xin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bridget E Murray
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dwight R Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, Minnesota 56082, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Nippa DF, Atz K, Müller AT, Wolfard J, Isert C, Binder M, Scheidegger O, Konrad DB, Grether U, Martin RE, Schneider G. Identifying opportunities for late-stage C-H alkylation with high-throughput experimentation and in silico reaction screening. Commun Chem 2023; 6:256. [PMID: 37985850 PMCID: PMC10661846 DOI: 10.1038/s42004-023-01047-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Enhancing the properties of advanced drug candidates is aided by the direct incorporation of specific chemical groups, avoiding the need to construct the entire compound from the ground up. Nevertheless, their chemical intricacy often poses challenges in predicting reactivity for C-H activation reactions and planning their synthesis. We adopted a reaction screening approach that combines high-throughput experimentation (HTE) at a nanomolar scale with computational graph neural networks (GNNs). This approach aims to identify suitable substrates for late-stage C-H alkylation using Minisci-type chemistry. GNNs were trained using experimentally generated reactions derived from in-house HTE and literature data. These trained models were then used to predict, in a forward-looking manner, the coupling of 3180 advanced heterocyclic building blocks with a diverse set of sp3-rich carboxylic acids. This predictive approach aimed to explore the substrate landscape for Minisci-type alkylations. Promising candidates were chosen, their production was scaled up, and they were subsequently isolated and characterized. This process led to the creation of 30 novel, functionally modified molecules that hold potential for further refinement. These results positively advocate the application of HTE-based machine learning to virtual reaction screening.
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Affiliation(s)
- David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany
| | - Kenneth Atz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Alex T Müller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Jens Wolfard
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Clemens Isert
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Martin Binder
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Oliver Scheidegger
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - David B Konrad
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany.
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
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24
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Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, Aschenbrenner JC, Balcomb BH, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bilenko VA, Borden B, Boulet P, Bowman GR, Brewitz L, Brun J, Bvnbs S, Calmiano M, Carbery A, Carney DW, Cattermole E, Chang E, Chernyshenko E, Clyde A, Coffland JE, Cohen G, Cole JC, Contini A, Cox L, Croll TI, Cvitkovic M, De Jonghe S, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett LE, Eastman P, Erez N, Eyermann CJ, Fairhead M, Fate G, Fedorov O, Fernandes RS, Ferrins L, Foster R, Foster H, Fraisse L, Gabizon R, García-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen RC, Glinert I, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Haneef A, Hassell Hart S, Heer J, Henry M, Hill M, Horrell S, Huang QYJ, Huliak VD, Hurley MFD, Israely T, Jajack A, Jansen J, Jnoff E, Jochmans D, John T, Kaminow B, Kang L, Kantsadi AL, Kenny PW, Kiappes JL, Kinakh SO, Kovar B, Krojer T, La VNT, Laghnimi-Hahn S, Lefker BA, Levy H, Lithgo RM, Logvinenko IG, Lukacik P, Macdonald HB, MacLean EM, Makower LL, Malla TR, Marples PG, Matviiuk T, McCorkindale W, McGovern BL, Melamed S, Melnykov KP, Michurin O, Miesen P, Mikolajek H, Milne BF, Minh D, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Mowbray CE, Nakamura AM, Neto JB, Neyts J, Nguyen L, Noske GD, Oleinikovas V, Oliva G, Overheul GJ, Owen CD, Pai R, Pan J, Paran N, Payne AM, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Pšenák V, Pulido I, Puni R, Rangel VL, Reddi RN, Rees P, Reid SP, Reid L, Resnick E, Ripka EG, Robinson RP, Rodriguez-Guerra J, Rosales R, Rufa DA, Saar K, Saikatendu KS, Salah E, Schaller D, Scheen J, Schiffer CA, Schofield CJ, Shafeev M, Shaikh A, Shaqra AM, Shi J, Shurrush K, Singh S, Sittner A, Sjö P, Skyner R, Smalley A, Smeets B, Smilova MD, Solmesky LJ, Spencer J, Strain-Damerell C, Swamy V, Tamir H, Taylor JC, Tennant RE, Thompson W, Thompson A, Tomásio S, Tomlinson CWE, Tsurupa IS, Tumber A, Vakonakis I, van Rij RP, Vangeel L, Varghese FS, Vaschetto M, Vitner EB, Voelz V, Volkamer A, Walsh MA, Ward W, Weatherall C, Weiss S, White KM, Wild CF, Witt KD, Wittmann M, Wright N, Yahalom-Ronen Y, Yilmaz NK, Zaidmann D, Zhang I, Zidane H, Zitzmann N, Zvornicanin SN. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science 2023; 382:eabo7201. [PMID: 37943932 PMCID: PMC7615835 DOI: 10.1126/science.abo7201] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.
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Affiliation(s)
- Melissa L Boby
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Program in Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Matteo Ferla
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK
| | - Mihajlo Filep
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - John D Chodera
- Program in Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Annette von Delft
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Hagit Achdout
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Anthony Aimon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Dominic S Alonzi
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
| | - Robert Arbon
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Jasmin C Aschenbrenner
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Blake H Balcomb
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Elad Bar-David
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Haim Barr
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - Amir Ben-Shmuel
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - James Bennett
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
- University of Oxford, Nuffield Department of Medicine, Target Discovery Institute, Oxford, OX3 7FZ, UK
| | - Vitaliy A Bilenko
- Enamine Ltd, Kyiv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
| | | | - Pascale Boulet
- Drugs for Neglected Diseases Initiative (DNDi), Geneva, 1202, Switzerland
| | - Gregory R Bowman
- University of Pennsylvania, Departments of Biochemistry and Biophysics and Bioengineering, Philadelphia, PA 19083, USA
| | - Lennart Brewitz
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Juliane Brun
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
| | - Sarma Bvnbs
- Sai Life Sciences Limited, ICICI Knowledge Park, Shameerpet, Hyderabad 500 078, Telangana, India
| | | | - Anna Carbery
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- University of Oxford, Department of Statistics, Oxford OX1 3LB, UK
| | - Daniel W Carney
- Takeda Development Center Americas, Inc., San Diego, CA 92121, USA
| | - Emma Cattermole
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA 92121, USA
| | | | | | | | - Galit Cohen
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, Cambridge, CB2 1EZ, UK
| | - Alessandro Contini
- University of Milan, Department of General and Organic Chemistry, Milan, 20133, Italy
| | - Lisa Cox
- Life Compass Consulting Ltd, Macclesfield, SK10 5UE, UK
| | - Tristan Ian Croll
- The University of Cambridge, Cambridge Institute for Medical Research, Department of Haematology, Cambridge CB2 0XY, UK
- Present address: Altos Labs, BioML group, Great Abington, CB21 6GP
| | | | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Alex Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Kim Donckers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Shirly Duberstein
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - Tim Dudgeon
- Informatics Matters Ltd, Bicester, OX26 6JU, UK
| | - Louise E Dunnett
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter Eastman
- Stanford University, Department of Chemistry, Stanford, CA 94305, USA
| | - Noam Erez
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Charles J Eyermann
- Northeastern University, Department of Chemistry and Chemical Biology, Boston MA 02115, USA
| | - Michael Fairhead
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Gwen Fate
- Thames Pharma Partners LLC, Mystic, CT 06355, USA
| | - Oleg Fedorov
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
- University of Oxford, Nuffield Department of Medicine, Target Discovery Institute, Oxford, OX3 7FZ, UK
| | - Rafaela S Fernandes
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
| | - Lori Ferrins
- Northeastern University, Department of Chemistry and Chemical Biology, Boston MA 02115, USA
| | - Richard Foster
- University of Leeds, School of Chemistry, Leeds, LS2 9JT, UK
| | - Holly Foster
- University of Leeds, School of Chemistry, Leeds, LS2 9JT, UK
- Present address: Exscientia, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Laurent Fraisse
- Drugs for Neglected Diseases Initiative (DNDi), Geneva, 1202, Switzerland
| | - Ronen Gabizon
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, 7610001, Israel
| | - Adolfo García-Sastre
- Icahn School of Medicine at Mount Sinai, Department of Microbiology, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Division of Infectious Diseases, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Department of Pathology, Molecular and Cell-Based Medicine, New York, NY 10029, USA
| | - Victor O Gawriljuk
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
- Present address: University of Groningen, Groningen Research Institute of Pharmacy, Department of Drug Design, Groningen, 9700 AV, Netherlands
| | - Paul Gehrtz
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, 7610001, Israel
- Present address: Merck Healthcare KGaA, Darmstadt, 64293, Germany
| | - Carina Gileadi
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Charline Giroud
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
- University of Oxford, Nuffield Department of Medicine, Target Discovery Institute, Oxford, OX3 7FZ, UK
| | - William G Glass
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
- Present address: Exscientia, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Robert C Glen
- University of Cambridge, Department of Chemistry, Cambridge, CB2 1EW, UK
| | - Itai Glinert
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Andre S Godoy
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
| | - Marian Gorichko
- Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
| | - Tyler Gorrie-Stone
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ed J Griffen
- MedChemica Ltd, Macclesfield, Cheshire. SK11 6PU UK
| | - Amna Haneef
- Illinois Institute of Technology, Department of Biology, Chicago IL 60616 USA
| | - Storm Hassell Hart
- University of Sussex, Department of Chemistry, School of Life Sciences, Brighton, East Sussex, BN1 9QJ, UK
| | - Jag Heer
- Syngene International Limited, Headington, Oxford, OX3 7BZ, UK
| | - Michael Henry
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Michelle Hill
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
- Present address: Sir William Dunn School of Pathology, Oxford. OX1 3RE, UK
| | - Sam Horrell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Qiu Yu Judy Huang
- University of Massachusetts, Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester MA 01655, USA
| | | | | | - Tomer Israely
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | | | - Jitske Jansen
- RWTH Aachen University, Institute of Experimental Medicine and Systems Biology, Aachen, 52074, Germany
| | - Eric Jnoff
- UCB, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Tobias John
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
- Present address: AMSilk, Neuried, 82061, Germany
| | - Benjamin Kaminow
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Lulu Kang
- Illinois Institute of Technology, Department of Applied Mathematics, Chicago IL 60616 USA
| | - Anastassia L Kantsadi
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
- University of Thessaly, Department of Biochemistry and Biotechnology, Larissa, 415 00, Greece
| | - Peter W Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
| | - J L Kiappes
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
- Present address: University College of London, Department of Chemistry, London WC1H 0AJ, UK
| | | | - Boris Kovar
- M2M solutions s.r.o. Žilina, 010 01, Slovakia
| | - Tobias Krojer
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
- MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | - Van Ngoc Thuy La
- Illinois Institute of Technology, Department of Biology, Chicago IL 60616 USA
| | | | | | - Haim Levy
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Ryan M Lithgo
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | | | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Hannah Bruce Macdonald
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
- Present address: Charm Therapeutics, London, N1C 4AG, UK
| | - Elizabeth M MacLean
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Laetitia L Makower
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
| | - Tika R Malla
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Peter G Marples
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | | | - Willam McCorkindale
- Present address: Charm Therapeutics, London, N1C 4AG, UK
- University of Cambridge, Cavendish Laboratory, Cambridge, CB3 0HE UK
| | - Briana L McGovern
- Icahn School of Medicine at Mount Sinai, Department of Microbiology, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY 10029, USA
| | - Sharon Melamed
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Kostiantyn P Melnykov
- Enamine Ltd, Kyiv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
| | | | - Pascal Miesen
- Radboud University Medical Center, Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, 6525 GA, Netherlands
| | - Halina Mikolajek
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Bruce F Milne
- University of Aberdeen, Department of Chemistry, Old Aberdeen, AB24 3UE Scotland, UK
- University of Coimbra, CFisUC, Department of Physics, Coimbra, 3004-516, Portugal
| | - David Minh
- Illinois Institute of Technology, Department of Chemistry, Chicago IL 60616 USA
| | | | - Garrett M Morris
- University of Oxford, Department of Statistics, Oxford OX1 3LB, UK
| | - Melody Jane Morwitzer
- University of Nebraska Medical Centre, Dept of Pathology and Microbiology, Omaha, NE 68198-5900, USA
| | | | - Charles E Mowbray
- Drugs for Neglected Diseases Initiative (DNDi), Geneva, 1202, Switzerland
| | - Aline M Nakamura
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
- Present address: Instituto Butantan, Sao Paulo, 05503-900, Brazil
| | - Jose Brandao Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Gabriela D Noske
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
| | - Vladas Oleinikovas
- UCB, Slough, SL1 3WE, UK
- Present address: Monte Rosa Therapeutics, Basel, CH 4057, Switzerland
| | - Glaucius Oliva
- University of Sao Paulo, Sao Carlos Institute of Physics, Sao Carlos, 13563-120, Brazil
| | - Gijs J Overheul
- Radboud University Medical Center, Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, 6525 GA, Netherlands
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ruby Pai
- PostEra Inc., Cambridge, MA, 02142, USA
| | - Jin Pan
- PostEra Inc., Cambridge, MA, 02142, USA
| | - Nir Paran
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Alexander Matthew Payne
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Benjamin Perry
- Drugs for Neglected Diseases Initiative (DNDi), Geneva, 1202, Switzerland
- Present address: Medicxi, Geneva, 1204, Switzerland
| | - Maneesh Pingle
- Sai Life Sciences Limited, ICICI Knowledge Park, Shameerpet, Hyderabad 500 078, Telangana, India
| | - Jakir Pinjari
- Sai Life Sciences Limited, ICICI Knowledge Park, Shameerpet, Hyderabad 500 078, Telangana, India
- Present address: Sun Pharma Advanced Research Company (SPARC), Baroda, India
| | - Boaz Politi
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Ailsa Powell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | | | - Iván Pulido
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Reut Puni
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Victor L Rangel
- University of São Paulo, Ribeirão Preto School of Pharmaceutical Sciences, Ribeirão Preto - SP/CEP 14040-903, Brazil
- Present address: Evotec (UK) Ltd, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Rambabu N Reddi
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, 7610001, Israel
| | - Paul Rees
- Compass Bussiness Partners Ltd, Southcliffe, Bucks, SL9 0PD, UK
| | - St Patrick Reid
- University of Nebraska Medical Centre, Dept of Pathology and Microbiology, Omaha, NE 68198-5900, USA
| | - Lauren Reid
- MedChemica Ltd, Macclesfield, Cheshire. SK11 6PU UK
| | - Efrat Resnick
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, 7610001, Israel
| | | | | | - Jaime Rodriguez-Guerra
- Charité - Universitätsmedizin Berlin, In silico Toxicology and Structural Bioinformatics, Berlin, 10117, Germany
| | - Romel Rosales
- Icahn School of Medicine at Mount Sinai, Department of Microbiology, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY 10029, USA
| | - Dominic A Rufa
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Kadi Saar
- University of Cambridge, Cavendish Laboratory, Cambridge, CB3 0HE UK
| | | | - Eidarus Salah
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - David Schaller
- Charité - Universitätsmedizin Berlin, In silico Toxicology and Structural Bioinformatics, Berlin, 10117, Germany
| | - Jenke Scheen
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Celia A Schiffer
- University of Massachusetts, Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester MA 01655, USA
| | - Christopher J Schofield
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | | | - Aarif Shaikh
- Sai Life Sciences Limited, ICICI Knowledge Park, Shameerpet, Hyderabad 500 078, Telangana, India
| | - Ala M Shaqra
- University of Massachusetts, Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester MA 01655, USA
| | - Jiye Shi
- UCB, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium
- Present address: Eli Lilly and Company, San Diego, CA 92121, USA
| | - Khriesto Shurrush
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - Sukrit Singh
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Assa Sittner
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Peter Sjö
- Drugs for Neglected Diseases Initiative (DNDi), Geneva, 1202, Switzerland
| | - Rachael Skyner
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | | | - Bart Smeets
- Radboud University Medical Center, Department of pathology, Radboud Institute for Molecular Life Sciences, Nijmegen, 6525 GA, Netherlands
| | - Mihaela D Smilova
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Leonardo J Solmesky
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - John Spencer
- University of Sussex, Department of Chemistry, School of Life Sciences, Brighton, East Sussex, BN1 9QJ, UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Vishwanath Swamy
- Sai Life Sciences Limited, ICICI Knowledge Park, Shameerpet, Hyderabad 500 078, Telangana, India
- Present address: TCG Life Sciences, Pune, India
| | - Hadas Tamir
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Jenny C Taylor
- University of Oxford, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | | | - Warren Thompson
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Andrew Thompson
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
- Present address: Walter and Eliza Hall Institute, Parkville 3052, Victoria, Australia
| | | | - Charles W E Tomlinson
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | | | - Anthony Tumber
- University of Oxford, Department of Chemistry, Chemistry Research Laboratory, Oxford, OX1 3TA, UK
| | - Ioannis Vakonakis
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
- Present address: Lonza Biologics, Lonza Ltd, Lonzastrasse, CH-3930 Visp, Switzerland
| | - Ronald P van Rij
- Radboud University Medical Center, Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, 6525 GA, Netherlands
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Finny S Varghese
- Radboud University Medical Center, Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Nijmegen, 6525 GA, Netherlands
- Present address: uniQure Biopharma, Amsterdam, 1105 BP, Netherlands
| | | | - Einat B Vitner
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Vincent Voelz
- Temple University, Department of Chemistry, Philadelphia, PA 19122, USA
| | - Andrea Volkamer
- Charité - Universitätsmedizin Berlin, In silico Toxicology and Structural Bioinformatics, Berlin, 10117, Germany
- Present address: Saarland University, Data Driven Drug Design, Campus - E2.1, 66123 Saarbrücken, Germany
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Walter Ward
- Walter Ward Consultancy and Training, Derbyshire, SK22 4AA, UK
| | | | - Shay Weiss
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Kris M White
- Icahn School of Medicine at Mount Sinai, Department of Microbiology, New York, NY 10029, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, NY 10029, USA
| | - Conor Francis Wild
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Karolina D Witt
- University of Oxford, Nuffield Department of Medicine, Pandemic Sciences Institute, Oxford, Oxon, OX3 7DQ, UK
| | - Matthew Wittmann
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Nathan Wright
- University of Oxford, Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford, OX3 7DQ, UK
| | - Yfat Yahalom-Ronen
- Israel Institute for Biological Research, Department of Infectious Diseases, Ness-Ziona, Israel
| | - Nese Kurt Yilmaz
- University of Massachusetts, Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester MA 01655, USA
| | - Daniel Zaidmann
- The Weizmann Institute of Science, Department of Chemical and Structural Biology, Rehovot, 7610001, Israel
| | - Ivy Zhang
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, Computational and Systems Biology Program, New York, NY 10065, USA
| | - Hadeer Zidane
- The Weizmann Institute of Science, Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Rehovot, 7610001, Israel
| | - Nicole Zitzmann
- University of Oxford, Department of Biochemistry, Oxford Glycobiology Institute, South Parks Road, Oxford OX1 3QU, UK
| | - Sarah N Zvornicanin
- University of Massachusetts, Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester MA 01655, USA
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25
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Nie W, Wan Q, Sun J, Chen M, Gao M, Chen S. Ultra-high-throughput mapping of the chemical space of asymmetric catalysis enables accelerated reaction discovery. Nat Commun 2023; 14:6671. [PMID: 37865636 PMCID: PMC10590410 DOI: 10.1038/s41467-023-42446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
The discovery of highly enantioselective catalysts and elucidating their generality face great challenges due to the complex multidimensional chemical space of asymmetric catalysis and inefficient screening methods. Here, we develop a general strategy for ultra-high-throughput mapping of the chemical space of asymmetric catalysis by escaping the time-consuming chiral chromatography separation. The ultrafast ( ~ 1000 reactions/day) and accurate (median error < ±1%) analysis of enantiomeric excess are achieved through the ion mobility-mass spectrometry combines with the diastereoisomerization strategy. A workflow for accelerated asymmetric reaction screening is established and verified by mapping the large-scale chemical space of more than 1600 reactions of α-asymmetric alkylation of aldehyde with organocatalysis and photocatalysis. Importantly, a class of high-enantioselectivity primary amine organocatalysts of 1,2-diphenylethane-1,2-diamine-based sulfonamides is discovered by the accelerated screening, and the mechanism for high-selectivity is demonstrated by computational chemistry. This study provides a practical and robust solution for large-scale screening and discovery of asymmetric reactions.
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Affiliation(s)
- Wenjing Nie
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jian Sun
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Moran Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ming Gao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei, 430072, China.
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26
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Rinehart NI, Saunthwal RK, Wellauer J, Zahrt AF, Schlemper L, Shved AS, Bigler R, Fantasia S, Denmark SE. A machine-learning tool to predict substrate-adaptive conditions for Pd-catalyzed C-N couplings. Science 2023; 381:965-972. [PMID: 37651532 DOI: 10.1126/science.adg2114] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Machine-learning methods have great potential to accelerate the identification of reaction conditions for chemical transformations. A tool that gives substrate-adaptive conditions for palladium (Pd)-catalyzed carbon-nitrogen (C-N) couplings is presented. The design and construction of this tool required the generation of an experimental dataset that explores a diverse network of reactant pairings across a set of reaction conditions. A large scope of C-N couplings was actively learned by neural network models by using a systematic process to design experiments. The models showed good performance in experimental validation: Ten products were isolated in more than 85% yield from a range of couplings with out-of-sample reactants designed to challenge the models. Importantly, the developed workflow continually improves the prediction capability of the tool as the corpus of data grows.
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Affiliation(s)
- N Ian Rinehart
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rakesh K Saunthwal
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joël Wellauer
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., Basel, Switzerland
| | - Andrew F Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lukas Schlemper
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., Basel, Switzerland
| | - Alexander S Shved
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Raphael Bigler
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., Basel, Switzerland
| | - Serena Fantasia
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry and Catalysis, F. Hoffmann-La Roche, Ltd., Basel, Switzerland
| | - Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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27
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Eyke NS, Schneider TN, Jin B, Hart T, Monfette S, Hawkins JM, Morse PD, Howard RM, Pfisterer DM, Nandiwale KY, Jensen KF. Parallel multi-droplet platform for reaction kinetics and optimization. Chem Sci 2023; 14:8798-8809. [PMID: 37621435 PMCID: PMC10445457 DOI: 10.1039/d3sc02082g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware operations and ensures droplet integrity as well as overall efficiency. We design and incorporate all of the necessary hardware and software to enable the platform to be used to study both thermal and photochemical reactions. We incorporate a Bayesian optimization algorithm into the control software to enable reaction optimization over both categorical and continuous variables. We demonstrate the capabilities of both the preliminary single-channel and parallelized versions of the platform using a series of model thermal and photochemical reactions. We conduct a series of reaction optimization campaigns and demonstrate rapid acquisition of the data necessary to determine reaction kinetics. The platform is flexible in terms of use case: it can be used either to investigate reaction kinetics or to perform reaction optimization over a wide range of chemical domains.
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Affiliation(s)
- Natalie S Eyke
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Timo N Schneider
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Brooke Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Travis Hart
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Sebastien Monfette
- Pfizer Worldwide Research and Development 445 Eastern Point Rd Groton CT 06340 USA
| | - Joel M Hawkins
- Pfizer Worldwide Research and Development 445 Eastern Point Rd Groton CT 06340 USA
| | - Peter D Morse
- Pfizer Worldwide Research and Development 445 Eastern Point Rd Groton CT 06340 USA
| | - Roger M Howard
- Pfizer Worldwide Research and Development 445 Eastern Point Rd Groton CT 06340 USA
| | - David M Pfisterer
- Pfizer Worldwide Research and Development 445 Eastern Point Rd Groton CT 06340 USA
| | | | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
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28
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Mikhael M, Alektiar SN, Yeung CS, Wickens ZK. Translating Planar Heterocycles into Three-Dimensional Analogs by Photoinduced Hydrocarboxylation. Angew Chem Int Ed Engl 2023; 62:e202303264. [PMID: 37199340 PMCID: PMC10524292 DOI: 10.1002/anie.202303264] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023]
Abstract
The rapid preparation of complex three-dimensional (3D) heterocyclic scaffolds is a key challenge in modern medicinal chemistry. Despite the increased probability of clinical success for small molecule therapeutic candidates with increased 3D complexity, new drug targets remain dominated by flat molecules due to the abundance of coupling reactions available for their construction. In principle, heteroarene hydrofunctionalization reactions offer an opportunity to transform readily accessible planar molecules into more three-dimensionally complex analogs through the introduction of a single molecular vector. Unfortunately, dearomative hydrofunctionalization reactions remain limited. Herein, we report a new strategy to enable the dearomative hydrocarboxylation of indoles and related heterocycles. This reaction represents a rare example of a heteroarene hydrofunctionalization that meets the numerous requirements for broad implementation in drug discovery. The transformation is highly chemoselective, broad in scope, operationally simple, and readily amenable to high-throughput experimentation (HTE). Accordingly, this process will allow existing libraries of heteroaromatic compounds to be translated into diverse 3D analogs and enable exploration of new classes of medicinally relevant molecules.
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Affiliation(s)
- Myriam Mikhael
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Sara N. Alektiar
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
| | - Charles S. Yeung
- Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, United States
| | - Zachary K. Wickens
- Department of Chemistry, University of Wisconsin-Madison; Madison, Wisconsin, 53706, United States
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29
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Wu J, Zhang J, Hu M, Reiser P, Torresi L, Friederich P, Lahn L, Kasian O, Guldi DM, Pérez-Ojeda ME, Barabash A, Rocha-Ortiz JS, Zhao Y, Xie Z, Luo J, Wang Y, Seok SI, Hauch JA, Brabec CJ. Integrated System Built for Small-Molecule Semiconductors via High-Throughput Approaches. J Am Chem Soc 2023. [PMID: 37467341 PMCID: PMC10401720 DOI: 10.1021/jacs.3c03271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
High-throughput synthesis of solution-processable structurally variable small-molecule semiconductors is both an opportunity and a challenge. A large number of diverse molecules provide a possibility for quick material discovery and machine learning based on experimental data. However, the diversity of the molecular structure leads to the complexity of molecular properties, such as solubility, polarity, and crystallinity, which poses great challenges to solution processing and purification. Here, we first report an integrated system for the high-throughput synthesis, purification, and characterization of molecules with a large variety. Based on the principle "Like dissolves like," we combine theoretical calculations and a robotic platform to accelerate the purification of those molecules. With this platform, a material library containing 125 molecules and their optical-electronic properties was built within a timeframe of weeks. More importantly, the high repeatability of recrystallization we design is a reliable approach to further upgrading and industrial production.
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Affiliation(s)
- Jianchang Wu
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Jiyun Zhang
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Manman Hu
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Korea
| | - Patrick Reiser
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Luca Torresi
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Pascal Friederich
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Ham Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Leopold Lahn
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
- Helmholtz-Zentrum Berlin GmbH, Helmholtz Institut Erlangen-Nürnberg, Cauerstraße 1, 91058 Erlangen, Germany
| | - Olga Kasian
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
- Helmholtz-Zentrum Berlin GmbH, Helmholtz Institut Erlangen-Nürnberg, Cauerstraße 1, 91058 Erlangen, Germany
| | - Dirk M Guldi
- Department of Chemistry and Pharmacy & Interdisciplinary Center of Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - M Eugenia Pérez-Ojeda
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Anastasia Barabash
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Juan S Rocha-Ortiz
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Yicheng Zhao
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
- University of Electronic Science and Technology of China, School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Films and Integrated Devices, 611731 Chengdu, P. R. China
| | - Zhiqiang Xie
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Junsheng Luo
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
- University of Electronic Science and Technology of China, School of Electronic Science and Engineering, State Key Laboratory of Electronic Thin Films and Integrated Devices, 611731 Chengdu, P. R. China
| | - Yunuo Wang
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Sang Il Seok
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Korea
| | - Jens A Hauch
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
| | - Christoph J Brabec
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Immerwahrstraße 2, 91058 Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstrasse 7, 91058 Erlangen, Germany
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30
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Ahmad BIZ, Keasler KT, Stacy EE, Meng S, Hicks TJ, Milner PJ. MOFganic Chemistry: Challenges and Opportunities for Metal-Organic Frameworks in Synthetic Organic Chemistry. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:4883-4896. [PMID: 38222037 PMCID: PMC10785605 DOI: 10.1021/acs.chemmater.3c00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Metal-organic frameworks (MOFs) are porous, crystalline solids constructed from organic linkers and inorganic nodes that have been widely studied for applications in gas storage, chemical separations, and drug delivery. Owing to their highly modular structures and tunable pore environments, we propose that MOFs have significant untapped potential as catalysts and reagents relevant to the synthesis of next-generation therapeutics. Herein, we outline the properties of MOFs that make them promising for applications in synthetic organic chemistry, including new reactivity and selectivity, enhanced robustness, and user-friendly preparation. In addition, we outline the challenges facing the field and propose new directions to maximize the utility of MOFs for drug synthesis. This perspective aims to bring together the organic and MOF communities to develop new heterogeneous platforms capable of achieving synthetic transformations that cannot be replicated by homogeneous systems.
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Affiliation(s)
- Bayu I. Z. Ahmad
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Kaitlyn T. Keasler
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Emily E. Stacy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Sijing Meng
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Thomas J. Hicks
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
| | - Phillip J. Milner
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, United States
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31
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Mahjour B, Zhang R, Shen Y, McGrath A, Zhao R, Mohamed OG, Lin Y, Zhang Z, Douthwaite JL, Tripathi A, Cernak T. Rapid planning and analysis of high-throughput experiment arrays for reaction discovery. Nat Commun 2023; 14:3924. [PMID: 37400469 DOI: 10.1038/s41467-023-39531-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
High-throughput experimentation (HTE) is an increasingly important tool in reaction discovery. While the hardware for running HTE in the chemical laboratory has evolved significantly in recent years, there remains a need for software solutions to navigate data-rich experiments. Here we have developed phactor™, a software that facilitates the performance and analysis of HTE in a chemical laboratory. phactor™ allows experimentalists to rapidly design arrays of chemical reactions or direct-to-biology experiments in 24, 96, 384, or 1,536 wellplates. Users can access online reagent data, such as a chemical inventory, to virtually populate wells with experiments and produce instructions to perform the reaction array manually, or with the assistance of a liquid handling robot. After completion of the reaction array, analytical results can be uploaded for facile evaluation, and to guide the next series of experiments. All chemical data, metadata, and results are stored in machine-readable formats that are readily translatable to various software. We also demonstrate the use of phactor™ in the discovery of several chemistries, including the identification of a low micromolar inhibitor of the SARS-CoV-2 main protease. Furthermore, phactor™ has been made available for free academic use in 24- and 96-well formats via an online interface.
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Affiliation(s)
- Babak Mahjour
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Rui Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Yuning Shen
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Andrew McGrath
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ruheng Zhao
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Osama G Mohamed
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Yingfu Lin
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Zirong Zhang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - James L Douthwaite
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ashootosh Tripathi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tim Cernak
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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32
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Shim E, Tewari A, Cernak T, Zimmerman PM. Machine Learning Strategies for Reaction Development: Toward the Low-Data Limit. J Chem Inf Model 2023; 63:3659-3668. [PMID: 37312524 PMCID: PMC11163943 DOI: 10.1021/acs.jcim.3c00577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Machine learning models are increasingly being utilized to predict outcomes of organic chemical reactions. A large amount of reaction data is used to train these models, which is in stark contrast to how expert chemists discover and develop new reactions by leveraging information from a small number of relevant transformations. Transfer learning and active learning are two strategies that can operate in low-data situations, which may help fill this gap and promote the use of machine learning for tackling real-world challenges in organic synthesis. This Perspective introduces active and transfer learning and connects these to potential opportunities and directions for further research, especially in the area of prospective development of chemical transformations.
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Affiliation(s)
- Eunjae Shim
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ambuj Tewari
- Department of Statistics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tim Cernak
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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33
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Murray BE, Penabad LI, Kennedy RT. Advances in coupling droplet microfluidics to mass spectrometry. Curr Opin Biotechnol 2023; 82:102962. [PMID: 37336080 DOI: 10.1016/j.copbio.2023.102962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Droplet microfluidics enables development of workflows with low sample consumption and high throughput. Fluorescence-based assays are most used with droplet microfluidics; however, the requirement of a fluorescent reporter restricts applicability of this approach. The coupling of droplets to mass spectrometry (MS) has enabled selective assays on complex mixtures to broaden the analyte scope. Droplet microfluidics has been interfaced to MS via electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). The works reviewed herein outline the development of this nascent field as well as initial exploration of its application in biotechnology and bioanalysis, including synthetic biology, reaction development, and in vivo sensing.
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Affiliation(s)
- Bridget E Murray
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Laura I Penabad
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA.
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34
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Talaty NN, Johnson RW, Sawicki J, Nacham O, Djuric SW. Recent Developments in Mass Spectrometry to Support Next-Generation Synthesis and Screening. ACS Med Chem Lett 2023; 14:711-718. [PMID: 37312853 PMCID: PMC10258828 DOI: 10.1021/acsmedchemlett.3c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
The complexity of new therapeutics continues to increase and the timeline for the discovery of these therapeutics continues to shrink. This creates demand for new analytical techniques to facilitate quicker discovery and development of novel drugs. Mass spectrometry is one of the most prolific analytical techniques that has been applied across the entire drug discovery pipeline. New mass spectrometers and the associated methods for sampling have been introduced at a rate that keeps pace with new chemistries, therapeutic types, and screening practices used by modern drug hunters. This microperspective covers application and implementation of new mass spectrometry workflows that enable current and future efforts in screening and synthesis for drug discovery.
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Affiliation(s)
- Nari N. Talaty
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Robert W. Johnson
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James Sawicki
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stevan W. Djuric
- Discovery
Chemistry and Technology Consulting LLC, New Bern, North Carolina 28562, United States
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35
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Taylor CJ, Felton KC, Wigh D, Jeraal MI, Grainger R, Chessari G, Johnson CN, Lapkin AA. Accelerated Chemical Reaction Optimization Using Multi-Task Learning. ACS CENTRAL SCIENCE 2023; 9:957-968. [PMID: 37252348 PMCID: PMC10214532 DOI: 10.1021/acscentsci.3c00050] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/31/2023]
Abstract
Functionalization of C-H bonds is a key challenge in medicinal chemistry, particularly for fragment-based drug discovery (FBDD) where such transformations require execution in the presence of polar functionality necessary for protein binding. Recent work has shown the effectiveness of Bayesian optimization (BO) for the self-optimization of chemical reactions; however, in all previous cases these algorithmic procedures have started with no prior information about the reaction of interest. In this work, we explore the use of multitask Bayesian optimization (MTBO) in several in silico case studies by leveraging reaction data collected from historical optimization campaigns to accelerate the optimization of new reactions. This methodology was then translated to real-world, medicinal chemistry applications in the yield optimization of several pharmaceutical intermediates using an autonomous flow-based reactor platform. The use of the MTBO algorithm was shown to be successful in determining optimal conditions of unseen experimental C-H activation reactions with differing substrates, demonstrating an efficient optimization strategy with large potential cost reductions when compared to industry-standard process optimization techniques. Our findings highlight the effectiveness of the methodology as an enabling tool in medicinal chemistry workflows, representing a step-change in the utilization of data and machine learning with the goal of accelerated reaction optimization.
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Affiliation(s)
- Connor J. Taylor
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Kobi C. Felton
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Daniel Wigh
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Mohammed I. Jeraal
- Cambridge
Centre for Advanced Research and Education in Singapore Ltd., 1 Create Way, CREATE Tower #05-05, 138602, Singapore
| | - Rachel Grainger
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Christopher N. Johnson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Alexei A. Lapkin
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore Ltd., 1 Create Way, CREATE Tower #05-05, 138602, Singapore
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36
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Huang KH, Morato NM, Feng Y, Cooks RG. High-Throughput Diversification of Complex Bioactive Molecules by Accelerated Synthesis in Microdroplets. Angew Chem Int Ed Engl 2023; 62:e202300956. [PMID: 36941213 PMCID: PMC10182919 DOI: 10.1002/anie.202300956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Late-stage diversification of drug molecules is an important strategy in drug discovery that can be facilitated by reaction screening using high-throughput experimentation. Here we present a rapid method for functionalizing bioactive molecules based on accelerated reactions in microdroplets. Reaction mixtures are nebulized at throughputs better than 1 reaction/second and the accelerated reactions occurring in the microdroplets are followed by desorption electrospray ionization mass spectrometry (DESI-MS). Because the accelerated reactions occur on the millisecond timescale, they allow an overall screening throughput of 1 Hz working at the low nanogram scale. Using this approach, an opioid agonist (PZM21) and an antagonist (naloxone) were diversified using three reactions important in medicinal chemistry: sulfur fluoride exchange (SuFEx) click reactions, imine formation reactions, and ene-type click reactions. Some 269 functionalized analogs of naloxone and PZM21 were generated and characterized by tandem mass spectrometry (MS/MS) after screening over 500 reactions.
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Affiliation(s)
- Kai-Hung Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yunfei Feng
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
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37
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Toupalas G, Ribadeau-Dumas L, Morandi B. Ni-catalyzed mild hydrogenolysis and oxidations of C-O bonds via carbonate redox tags. Nat Commun 2023; 14:2604. [PMID: 37147279 PMCID: PMC10163265 DOI: 10.1038/s41467-023-38305-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Oxygenated molecules are omnipresent in natural as well as artificial settings making the redox transformation of the present C-O bonds a central tool for their processing. However, the required (super)stoichiometric redox agents which traditionally include highly reactive and hazardous reagents pose multiple practical challenges including process safety hazards or special waste management requirements. Here, we report a mild Ni-catalyzed fragmentation strategy based on carbonate redox tags for redox transformations of oxygenated hydrocarbons in the absence of any external redox equivalents or other additives. The purely catalytic process enables the hydrogenolysis of strong C(sp2)-O bonds including that of enol carbonates as well as the catalytic oxidation of C-O bonds under mild conditions down to room temperature. Additionally, we investigated the underlying mechanism and showcased the benefits of carbonate redox tags in multiple applications. More broadly, the work herein demonstrates the potential of redox tags for organic synthesis.
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Affiliation(s)
- Georgios Toupalas
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Loélie Ribadeau-Dumas
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Bill Morandi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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38
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Capaldo L, Wen Z, Noël T. A field guide to flow chemistry for synthetic organic chemists. Chem Sci 2023; 14:4230-4247. [PMID: 37123197 PMCID: PMC10132167 DOI: 10.1039/d3sc00992k] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/15/2023] [Indexed: 03/17/2023] Open
Abstract
Flow chemistry has unlocked a world of possibilities for the synthetic community, but the idea that it is a mysterious "black box" needs to go. In this review, we show that several of the benefits of microreactor technology can be exploited to push the boundaries in organic synthesis and to unleash unique reactivity and selectivity. By "lifting the veil" on some of the governing principles behind the observed trends, we hope that this review will serve as a useful field guide for those interested in diving into flow chemistry.
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Affiliation(s)
- Luca Capaldo
- Flow Chemistry Group, Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam 1098 XH Amsterdam The Netherlands
| | - Zhenghui Wen
- Flow Chemistry Group, Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam 1098 XH Amsterdam The Netherlands
| | - Timothy Noël
- Flow Chemistry Group, Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam 1098 XH Amsterdam The Netherlands
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39
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Gesmundo NJ, Tu NP, Sarris KA, Wang Y. ChemBeads-Enabled Photoredox High-Throughput Experimentation Platform to Improve C(sp 2)-C(sp 3) Decarboxylative Couplings. ACS Med Chem Lett 2023; 14:521-529. [PMID: 37077401 PMCID: PMC10108395 DOI: 10.1021/acsmedchemlett.2c00538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
Enthusiasm surrounding nickel/photoredox C(sp2)-C(sp3) cross-couplings is very high; however, these methods are sometimes challenged by complex drug-like substrates in discovery chemistry. In our hands this has been especially true of the decarboxylative coupling, which has lagged behind other photoredox couplings in internal adoption and success. Herein, the development of a photoredox high-throughput experimentation platform to optimize challenging C(sp2)-C(sp3) decarboxylative couplings is described. Chemical-coated glass beads (ChemBeads) and a novel parallel bead dispenser are used to expedite the high-throughput experimentation process and identify improved coupling conditions. In this report, photoredox high-throughput experimentation is utilized to dramatically improve low-yielding decarboxylative C(sp2)-C(sp3) couplings, and libraries, using conditions not previously identified in the literature.
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Affiliation(s)
- Nathan J. Gesmundo
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Noah P. Tu
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Kathy A. Sarris
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Ying Wang
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
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40
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Lee Z, Lin PC, Yang T. Inverse design of ligands using a deep generative model semi‐supervised by a data‐driven ligand field strength metric. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202300066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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41
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Taylor CJ, Pomberger A, Felton KC, Grainger R, Barecka M, Chamberlain TW, Bourne RA, Johnson CN, Lapkin AA. A Brief Introduction to Chemical Reaction Optimization. Chem Rev 2023; 123:3089-3126. [PMID: 36820880 PMCID: PMC10037254 DOI: 10.1021/acs.chemrev.2c00798] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
From the start of a synthetic chemist's training, experiments are conducted based on recipes from textbooks and manuscripts that achieve clean reaction outcomes, allowing the scientist to develop practical skills and some chemical intuition. This procedure is often kept long into a researcher's career, as new recipes are developed based on similar reaction protocols, and intuition-guided deviations are conducted through learning from failed experiments. However, when attempting to understand chemical systems of interest, it has been shown that model-based, algorithm-based, and miniaturized high-throughput techniques outperform human chemical intuition and achieve reaction optimization in a much more time- and material-efficient manner; this is covered in detail in this paper. As many synthetic chemists are not exposed to these techniques in undergraduate teaching, this leads to a disproportionate number of scientists that wish to optimize their reactions but are unable to use these methodologies or are simply unaware of their existence. This review highlights the basics, and the cutting-edge, of modern chemical reaction optimization as well as its relation to process scale-up and can thereby serve as a reference for inspired scientists for each of these techniques, detailing several of their respective applications.
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Affiliation(s)
- Connor J Taylor
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alexander Pomberger
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kobi C Felton
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Rachel Grainger
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Magda Barecka
- Chemical Engineering Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Chemistry and Chemical Biology Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, 138602 Singapore
| | - Thomas W Chamberlain
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Richard A Bourne
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alexei A Lapkin
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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42
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Twitty JC, Hong Y, Garcia B, Tsang S, Liao J, Schultz DM, Hanisak J, Zultanski SL, Dion A, Kalyani D, Watson MP. Diversifying Amino Acids and Peptides via Deaminative Reductive Cross-Couplings Leveraging High-Throughput Experimentation. J Am Chem Soc 2023; 145:5684-5695. [PMID: 36853652 PMCID: PMC10117303 DOI: 10.1021/jacs.2c11451] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A deaminative reductive coupling of amino acid pyridinium salts with aryl bromides has been developed to enable efficient synthesis of noncanonical amino acids and diversification of peptides. This method transforms natural, commercially available lysine, ornithine, diaminobutanoic acid, and diaminopropanoic acid to aryl alanines and homologated derivatives with varying chain lengths. Attractive features include ability to transverse scales, tolerance of pharma-relevant (hetero)aryls and biorthogonal functional groups, and the applicability beyond monomeric amino acids to short and macrocyclic peptide substrates. The success of this work relied on high-throughput experimentation to identify complementary reaction conditions that proved critical for achieving the coupling of a broad scope of aryl bromides with a range of amino acid and peptide substrates including macrocyclic peptides.
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Affiliation(s)
- J. Cameron Twitty
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Yun Hong
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Bria Garcia
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Stephanie Tsang
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jennie Liao
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Danielle M. Schultz
- Department of Process Research & Development, Merck & Co., Inc., MRL, Rahway, NJ 07065, United States
| | - Jennifer Hanisak
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L. Zultanski
- Department of Process Research & Development, Merck & Co., Inc., MRL, Rahway, NJ 07065, United States
| | - Amelie Dion
- Department of Process Research & Development, Merck & Co., Inc., MRL, Rahway, NJ 07065, United States
| | - Dipannita Kalyani
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mary P. Watson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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43
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Wiedmann JJ, Demirdögen YN, Schmidt S, Kuzina MA, Wu Y, Wang F, Nestler B, Hopf C, Levkin PA. Nanoliter Scale Parallel Liquid-Liquid Extraction for High-Throughput Purification on a Droplet Microarray. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204512. [PMID: 36538723 DOI: 10.1002/smll.202204512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
In the current drug discovery process, the synthesis of compound libraries is separated from biological screenings both conceptually and technologically. One of the reasons is that parallel on-chip high-throughput purification of synthesized compounds is still a major challenge. Here, on-chip miniaturized high-throughput liquid-liquid extraction in volumes down to 150 nL with efficiency comparable to or better than large-scale extraction utilizing separation funnels is demonstrated. The method is based on automated and programmable merging of arrays of aqueous nanoliter droplets with organic droplets. Multi-step extraction performed simultaneously or with changing conditions as well as handling of femtomoles of compounds are demonstrated. In addition, the extraction efficiency is analyzed with a fast optical readout as well as matrix-assisted laser desorption ionization-mass spectrometry on-chip detection. The new massively parallel and miniaturized purification method adds another important tool to the chemBIOS concept combining chemical combinatorial synthesis with biological screenings on the same miniaturized droplet microarray platform, which will be essential to accelerate drug discovery.
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Affiliation(s)
- Janne J Wiedmann
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yelda N Demirdögen
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Mariia A Kuzina
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yanchen Wu
- Institute for Applied Materials - Microstructure Modelling and Simulation, Karlsruhe Institute of Technology (KIT), Strasse am Forum 7, 76131, Karlsruhe, Germany
| | - Fei Wang
- Institute for Applied Materials - Microstructure Modelling and Simulation, Karlsruhe Institute of Technology (KIT), Strasse am Forum 7, 76131, Karlsruhe, Germany
| | - Britta Nestler
- Institute for Applied Materials - Microstructure Modelling and Simulation, Karlsruhe Institute of Technology (KIT), Strasse am Forum 7, 76131, Karlsruhe, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
- Medical Faculty, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Theodor Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Kaiserstraße 12, 76131, Karlsruhe, Germany
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44
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Mass spectrometry in materials synthesis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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45
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Haas C, Lübbesmeyer M, Jin EH, McDonald MA, Koscher BA, Guimond N, Di Rocco L, Kayser H, Leweke S, Niedenführ S, Nicholls R, Greeves E, Barber DM, Hillenbrand J, Volpin G, Jensen KF. Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening. ACS CENTRAL SCIENCE 2023; 9:307-317. [PMID: 36844498 PMCID: PMC9951288 DOI: 10.1021/acscentsci.2c01042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 06/18/2023]
Abstract
Automation and digitalization solutions in the field of small molecule synthesis face new challenges for chemical reaction analysis, especially in the field of high-performance liquid chromatography (HPLC). Chromatographic data remains locked in vendors' hardware and software components, limiting their potential in automated workflows and data science applications. In this work, we present an open-source Python project called MOCCA for the analysis of HPLC-DAD (photodiode array detector) raw data. MOCCA provides a comprehensive set of data analysis features, including an automated peak deconvolution routine of known signals, even if overlapped with signals of unexpected impurities or side products. We highlight the broad applicability of MOCCA in four studies: (i) a simulation study to validate MOCCA's data analysis features; (ii) a reaction kinetics study on a Knoevenagel condensation reaction demonstrating MOCCA's peak deconvolution feature; (iii) a closed-loop optimization study for the alkylation of 2-pyridone without human control during data analysis; (iv) a well plate screening of categorical reaction parameters for a novel palladium-catalyzed cyanation of aryl halides employing O-protected cyanohydrins. By publishing MOCCA as a Python package with this work, we envision an open-source community project for chromatographic data analysis with the potential of further advancing its scope and capabilities.
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Affiliation(s)
- Christian
P. Haas
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Maximilian Lübbesmeyer
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Edward H. Jin
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthew A. McDonald
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brent A. Koscher
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nicolas Guimond
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Alfred-Nobel-Straße 50, 40789 Monheim am Rhein, Germany
| | - Laura Di Rocco
- Chemical
& Pharmaceutical Development, Bayer
AG, Pharmaceuticals Division, Müllerstraße 178, 13353 Berlin, Germany
| | - Henning Kayser
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Alfred-Nobel-Straße 50, 40789 Monheim am Rhein, Germany
| | - Samuel Leweke
- Applied
Mathematics, Bayer AG, Enabling Functions
Division, Kaiser-Wilhelm-Allee
1, 51368 Leverkusen, Germany
| | - Sebastian Niedenführ
- Research
and Development, Computational Life Science, Bayer AG, Crop Science Division, Alfred-Nobel-Straße 50, 40789 Monheim am Rhein, Germany
| | - Rachel Nicholls
- Research
and Development, Computational Life Science, Bayer AG, Crop Science Division, Alfred-Nobel-Straße 50, 40789 Monheim am Rhein, Germany
| | - Emily Greeves
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - David M. Barber
- Research
and Development, Weed Control Chemistry, Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Julius Hillenbrand
- Chemical
& Pharmaceutical Development, Bayer
AG, Pharmaceuticals Division, Friedrich-Ebert-Straße 475, 42117 Wuppertal, Germany
| | - Giulio Volpin
- Research
and Development, Small Molecules Technologies, Bayer AG, Crop Science Division, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Klavs F. Jensen
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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46
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Tan B, Zhang J, Xiao C, Liu Y, Yang X, Wang W, Li Y, Liu N. Progress of Artificial Intelligence in Drug Synthesis and Prospect of Its Application in Nitrification of Energetic Materials. Molecules 2023; 28:1900. [PMID: 36838887 PMCID: PMC9963094 DOI: 10.3390/molecules28041900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Artificial intelligence technology shows the advantages of improving efficiency, reducing costs, shortening time, reducing the number of staff on site and achieving precise operations, making impressive research progress in the fields of drug discovery and development, but there are few reports on application in energetic materials. This paper addresses the high safety risks in the current nitrification process of energetic materials, comprehensively analyses and summarizes the main safety risks and their control elements in the nitrification process, proposes possibilities and suggestions for using artificial intelligence technology to enhance the "essential safety" of the nitrification process in energetic materials, reviews the research progress of artificial intelligence in the field of drug synthesis, looks forward to the application prospects of artificial intelligence technology in the nitrification of energetic materials and provides support and guidance for the safe processing of nitrification in the propellants and explosives industry.
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Affiliation(s)
- Bojun Tan
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Jing Zhang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Chuan Xiao
- Academy of Ordnance Science, Beijing 100089, China
| | - Yingzhe Liu
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Xiong Yang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Wei Wang
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Yanan Li
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
| | - Ning Liu
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, China
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47
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Ruan Y, Lin S, Mo Y. AROPS: A Framework of Automated Reaction Optimization with Parallelized Scheduling. J Chem Inf Model 2023; 63:770-781. [PMID: 36653913 DOI: 10.1021/acs.jcim.2c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
With the development of automated experimental platforms and optimization algorithms, chemists can easily optimize chemical reactions in an automated and high-throughput fashion. However, the modules in existing automated experimental platforms are operated in a linear fashion without orchestrating with the optimization algorithm, thus leaving room for further efficiency improvement. Here, we introduced a framework of automated reaction optimization with parallelized scheduling (AROPS) to realize the integration of the optimization algorithm and module scheduling. AROPS relies on a customized Bayesian optimizer to solve multi-reactor/analyzer reaction optimization problems with three different scheduling modes to arrange tasks for various experimental modules. In addition, a mechanism based on probability of improvement (PI) for discarding unpromising ongoing experiments was developed to facilitate freeing up valuable experimental resources in parallelized optimization. We tested the performance of AROPS using a hardware emulator on three representative benchmark reactions encountered in organic synthesis, illustrating that AROPS can trade off optimization time and cost according to the chemists' preference.
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Affiliation(s)
- Yixiang Ruan
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou311215, China
| | - Sen Lin
- Shanghai ChemLex Technology Co., Ltd., Shanghai201210, China
| | - Yiming Mo
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou311215, China
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48
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Martinek N, Morrison KM, Field JM, Fisher SA, Stradiotto M. Comparative Screening of DalPhos/Ni Catalysts in C-N Cross-couplings of (Hetero)aryl Chlorides Enables Development of Aminopyrazole Cross-couplings with Amine Base. Chemistry 2023; 29:e202203394. [PMID: 36331074 DOI: 10.1002/chem.202203394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022]
Abstract
A systematic competitive evaluation of the DalPhos ligand family in nickel-catalyzed N-arylation chemistry is reported, involving primary (linear and branched) and secondary alkylamines, as well as a primary five-membered heteroarylamine (aminopyrazole), in combination with a diverse set of test electrophiles and bases (NaOtBu, K2 CO3 , DBU/NaTFA). In addition to providing optimal ligand/catalyst identification, and bringing to light methodology limitations (e. g., unwanted C-O cross-coupling with NaOtBu), our survey enabled the development of the first efficient catalyst system for heteroatom-dense C-N cross-coupling of aminopyrazoles and related nucleophiles with (hetero)aryl chlorides by use of an amine 'dual-base' system.
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Affiliation(s)
- Nicole Martinek
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Kathleen M Morrison
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Justin M Field
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Samuel A Fisher
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Mark Stradiotto
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
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49
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Abdiaj I, Cañellas S, Dieguez A, Linares ML, Pijper B, Fontana A, Rodriguez R, Trabanco A, Palao E, Alcázar J. End-to-End Automated Synthesis of C(sp 3)-Enriched Drug-like Molecules via Negishi Coupling and Novel, Automated Liquid-Liquid Extraction. J Med Chem 2023; 66:716-732. [PMID: 36520521 PMCID: PMC9841985 DOI: 10.1021/acs.jmedchem.2c01646] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Indexed: 12/23/2022]
Abstract
Herein, we report an end-to-end process including synthesis, work-up, purification, and post-purification with minimal human intervention using Negishi coupling as a key transformation to increase Fsp3 in bioactive molecules. The main advantages of this protocol are twofold. First, the automated sequential generation of organozinc reagents from readily available alkyl halides offers a large diversity of alkyl groups to functionalize (hetero)aryl halide scaffolds via Pd-catalyzed Negishi coupling in continuous flow. Second, a fully automated liquid-liquid extraction has been developed and successfully applied for unattended operations. The workflow was completed with mass-triggered preparative high-performance liquid chromatography HPLC, providing an efficient production line of compounds with enriched sp3 character and better drug-like properties. The modular nature allows a smooth adaptation to a wide variety of synthetic methods and protocols and makes it applicable to any medchem laboratory.
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Affiliation(s)
- Irini Abdiaj
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Santiago Cañellas
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Alejandro Dieguez
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Maria Lourdes Linares
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Brenda Pijper
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Alberto Fontana
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Raquel Rodriguez
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Andres Trabanco
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Eduardo Palao
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Jesus Alcázar
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
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50
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Ruck RT, Strotman NA, Krska SW. The Catalysis Laboratory at Merck: 20 Years of Catalyzing Innovation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Rebecca T. Ruck
- Department of Process Research & Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Neil A. Strotman
- Department of Pharmaceutical Sciences & Clinical Supplies, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Shane W. Krska
- Chemistry Capabilities Accelerating Therapeutics, Merck & Co., Inc., Kenilworth, New Jersey07033, United States
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