1
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Dinh LP, Starbuck HF, Hamby TB, LaLama MJ, He CQ, Kalyani D, Sevov CS. Persistent organonickel complexes as general platforms for Csp 2-Csp 3 coupling reactions. Nat Chem 2024; 16:1515-1522. [PMID: 38684816 PMCID: PMC11374490 DOI: 10.1038/s41557-024-01528-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
The importance of constructing Csp2-Csp3 bonds has motivated the development of electrochemical, photochemical and thermal activation methods to reductively couple abundant aryl and alkyl electrophiles. However, these methodologies are limited to couplings of very specific substrate classes and require specialized sets of catalysts and reaction set-ups. Here we show a consolidation of these myriad strategies into a single set of conditions that enable reliable alkyl-aryl couplings, including those that were previously unknown. These reactions rely on the discovery of unusually persistent organonickel complexes that serve as stoichiometric platforms for C(sp2)-C(sp3) coupling. Aryl, heteroaryl or vinyl complexes of Ni can be inexpensively prepared on a multigram scale by mild electroreduction from the corresponding C(sp2) electrophile. Organonickel complexes can be isolated and stored or telescoped directly to reliably diversify drug-like molecules. Finally, the procedure was miniaturized to micromole scales by integrating soluble battery chemistries as redox initiators, enabling a high-throughput exploration of substrate diversity.
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Affiliation(s)
- Long P Dinh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hunter F Starbuck
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Taylor B Hamby
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Matthew J LaLama
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Cyndi Q He
- Modelling & Informatics, Merck & Co., Inc., Rahway, NJ, USA
| | | | - Christo S Sevov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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2
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Buettner C, Stavagna C, Tilby MJ, Górski B, Douglas JJ, Yasukawa N, Leonori D. Synthesis and Suzuki-Miyaura Cross-Coupling of Alkyl Amine-Boranes. A Boryl Radical-Enabled Strategy. J Am Chem Soc 2024; 146:24042-24052. [PMID: 39137918 PMCID: PMC11363021 DOI: 10.1021/jacs.4c07767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Alkyl organoborons are powerful materials for the construction of C(sp3)-C(sp2) bonds, predominantly via Suzuki-Miyaura cross-coupling. These species are generally assembled using 2-electron processes that harness the ability of boron reagents to act as both electrophiles and nucleophiles. Herein, we demonstrate an alternative borylation strategy based on the reactivity of amine-ligated boryl radicals. This process features the use of a carboxylic acid containing amine-ligated borane that acts as boryl radical precursor for photoredox oxidation and decarboxylation. The resulting amine-ligated boryl radical undergoes facile addition to styrenes and imines through radical-polar crossover manifolds. This delivers a new class of sp3-organoborons that are stable solids and do not undergo protodeboronation. These novel materials include unprotected α-amino derivatives that are generally unstable. Crucially, these aliphatic organoboron species can be directly engaged in Suzuki-Miyaura cross-couplings with structurally complex aryl halides. Preliminary studies suggest that they enable slow-release of the corresponding and often difficult to handle alkyl boronic acids.
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Affiliation(s)
- Cornelia
S. Buettner
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Chiara Stavagna
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Michael J. Tilby
- Department
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
| | - Bartosz Górski
- Department
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
| | - James J. Douglas
- Early
Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, United Kingdom
| | - Naoki Yasukawa
- Department
of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Daniele Leonori
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
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3
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Singh S, Hernández-Lobato JM. Data-Driven Insights into the Transition-Metal-Catalyzed Asymmetric Hydrogenation of Olefins. J Org Chem 2024. [PMID: 39149801 DOI: 10.1021/acs.joc.4c01396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The transition-metal-catalyzed asymmetric hydrogenation of olefins is one of the key transformations with great utility in various industrial applications. The field has been dominated by the use of noble metal catalysts, such as iridium and rhodium. The reactions with the earth-abundant cobalt metal have increased only in recent years. In this work, we analyze the large amount of literature data available on iridium- and rhodium-catalyzed asymmetric hydrogenation. The limited data on reactions using Co catalysts are then examined in the context of Ir and Rh to obtain a better understanding of the reactivity pattern. A detailed data-driven study of the types of olefins, ligands, and reaction conditions such as solvent, temperature, and pressure is carried out. Our analysis provides an understanding of the literature trends and demonstrates that only a few olefin-ligand combinations or reaction conditions are frequently used. The knowledge of this bias in the literature data toward a certain group of substrates or reaction conditions can be useful for practitioners to design new reaction data sets that are suitable to obtain meaningful predictions from machine-learning models.
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Affiliation(s)
- Sukriti Singh
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, U.K
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4
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Hu C, Tsien J, Chen SJ, Kong M, Merchant RR, Kanda Y, Qin T. A General Three-Component Alkyl Petasis Boron-Mannich Reaction. J Am Chem Soc 2024; 146:21769-21777. [PMID: 39072677 DOI: 10.1021/jacs.4c05940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Aryl amines are one of the most common moieties in biologically active molecules, and approximately 37% of drug candidates contain aromatic amines. Recent advancements in medicinal chemistry, coined "escaping from flatland", have led to a greater focus on accessing highly functionalized C (sp3)-rich amines to improve the physicochemical and pharmacokinetic properties of compounds. This article presents a modular and operationally straightforward three-component alkyl Petasis boron-Mannich (APBM) reaction that utilizes ubiquitous starting materials, including amines, aldehydes, and alkyl boronates. By adaptation of this transformation to high-throughput experimentation (HTE), it offers rapid access to an array of diverse C(sp3)-rich complex amines, amenable for rapid identification of drug candidates.
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Affiliation(s)
- Chao Hu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Si-Jie Chen
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - May Kong
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Rohan R Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Yuzuru Kanda
- Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
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5
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Charboneau DJ, Huang H, Barth EL, Deziel AP, Germe CC, Hazari N, Jia X, Kim S, Nahiyan S, Birriel-Rodriguez L, Uehling MR. Homogeneous Organic Reductant Based on 4,4'- tBu 2-2,2'-Bipyridine for Cross-Electrophile Coupling. Tetrahedron Lett 2024; 145:155159. [PMID: 39036418 PMCID: PMC11258959 DOI: 10.1016/j.tetlet.2024.155159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
The synthesis of a new homogeneous reductant based on 4,4'-tBu2-2,2'-bipyridine, tBu-OED4, is reported. tBu-OED4 was prepared on a multigram scale in two steps from inexpensive and commercially available starting materials, with no chromatography required for purification. tBu-OED4 has a reduction potential of -1.33 V (vs Ferrocenium/Ferrocene) and is soluble in a range of common organic solvents. We demonstrate that tBu-OED4 can facilitate Ni/Co dual-catalyzed C(sp2)-C(sp3) cross-electrophile coupling reactions and is highly functional group tolerant. tBu-OED4 is expected to be a valuable addition to the set of homogeneous reductants available for organic transformations.
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Affiliation(s)
- David J Charboneau
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Haotian Huang
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Emily L Barth
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Anthony P Deziel
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Cameron C Germe
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Nilay Hazari
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Xiaofan Jia
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Seoyeon Kim
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Sheikh Nahiyan
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | | | - Mycah R Uehling
- Merck & Co., Inc., Discovery Chemistry, HTE and Lead Discovery Capabilities, Rahway, New Jersey, 07065, USA
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6
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Huang H, Alvarez-Hernandez JL, Hazari N, Mercado BQ, Uehling MR. Effect of 6,6'-Substituents on Bipyridine-Ligated Ni Catalysts for Cross-Electrophile Coupling. ACS Catal 2024; 14:6897-6914. [PMID: 38737398 PMCID: PMC11087080 DOI: 10.1021/acscatal.4c00827] [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] [Indexed: 05/14/2024]
Abstract
A family of 4,4'-tBu2-2,2'-bipyridine (tBubpy) ligands with substituents in either the 6-position, 4,4'-tBu2-6-Me-bpy (tBubpyMe), or 6 and 6'-positions, 4,4'-tBu2-6,6'-R2-bpy (tBubpyR2; R = Me, iPr, sBu, Ph, or Mes), was synthesized. These ligands were used to prepare Ni complexes in the 0, I, and II oxidation states. We observed that the substituents in the 6 and 6'-positions of the tBubpy ligand impact the properties of the Ni complexes. For example, bulkier substituents in the 6,6'-positions of tBubpy better stabilized (tBubpyR2)NiICl species and resulted in cleaner reduction from (tBubpyR2)NiIICl2. However, bulkier substituents hindered or prevented coordination of tBubpyR2 ligands to Ni0(cod)2. In addition, by using complexes of the type (tBubpyMe)NiCl2 and (tBubpyR2)NiCl2 as precatalysts for different XEC reactions, we demonstrated that the 6 or 6,6' substituents lead to major differences in catalytic performance. Specifically, while (tBubpyMe)NiIICl2 is one of the most active catalysts reported to date for XEC and can facilitate XEC reactions at room temperature, lower turnover frequencies were observed for catalysts containing tBubpyR2 ligands. A detailed study on the catalytic intermediates (tBubpy)Ni(Ar)I and (tBubpyMe2)Ni(Ar)I revealed several factors that likely contributed to the differences in catalytic activity. For example, whereas complexes of the type (tBubpy)Ni(Ar)I are low spin and relatively stable, complexes of the type (tBubpyMe2)Ni(Ar)I are high-spin and less stable. Further, (tBubpyMe2)Ni(Ar)I captures primary and benzylic alkyl radicals more slowly than (tBubpy)Ni(Ar)I, consistent with the lower activity of the former in catalysis. Our findings will assist in the design of tailor-made ligands for Ni-catalyzed transformations.
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Affiliation(s)
- Haotian Huang
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | | | - Nilay Hazari
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Brandon Q Mercado
- Department of Chemistry, Yale University, P. O. Box 208107, New Haven, Connecticut, 06520, USA
| | - Mycah R Uehling
- Merck & Co., Inc., Discovery Chemistry, HTE and Lead Discovery Capabilities, Rahway, New Jersey, 07065, USA
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7
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Li J, Chandgude AL, Zheng Q, Dömling A. Innovative synthesis of drug-like molecules using tetrazole as core building blocks. Beilstein J Org Chem 2024; 20:950-958. [PMID: 38711589 PMCID: PMC11070966 DOI: 10.3762/bjoc.20.85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
Tetrazole is widely utilized as a bioisostere for carboxylic acid in the field of medicinal chemistry and drug development, enhancing the drug-like characteristics of various molecules. Typically, tetrazoles are introduced from their nitrile precursors through late-stage functionalization. In this work, we propose a novel strategy involving the use of diversely protected, unprecedented tetrazole aldehydes as building blocks. This approach facilitates the incorporation of the tetrazole group into multicomponent reactions or other chemistries, aiding in the creation of a variety of complex, drug-like molecules. These innovative tetrazole building blocks are efficiently and directly synthesized using a Passerini three-component reaction (PT-3CR), employing cost-effective and readily available materials. We further showcase the versatility of these new tetrazole building blocks by integrating the tetrazole moiety into various multicomponent reactions (MCRs), which are already significantly employed in drug discovery. This technique represents a unique and complementary method to existing tetrazole synthesis processes. It aims to meet the growing demand for tetrazole-based compound libraries and novel scaffolds, which are challenging to synthesize through other methods.
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Affiliation(s)
- Jingyao Li
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ajay L Chandgude
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qiang Zheng
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic
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8
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Rana D, Pflüger PM, Hölter NP, Tan G, Glorius F. Standardizing Substrate Selection: A Strategy toward Unbiased Evaluation of Reaction Generality. ACS CENTRAL SCIENCE 2024; 10:899-906. [PMID: 38680564 PMCID: PMC11046462 DOI: 10.1021/acscentsci.3c01638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
With over 10,000 new reaction protocols arising every year, only a handful of these procedures transition from academia to application. A major reason for this gap stems from the lack of comprehensive knowledge about a reaction's scope, i.e., to which substrates the protocol can or cannot be applied. Even though chemists invest substantial effort to assess the scope of new protocols, the resulting scope tables involve significant biases, reducing their expressiveness. Herein we report a standardized substrate selection strategy designed to mitigate these biases and evaluate the applicability, as well as the limits, of any chemical reaction. Unsupervised learning is utilized to map the chemical space of industrially relevant molecules. Subsequently, potential substrate candidates are projected onto this universal map, enabling the selection of a structurally diverse set of substrates with optimal relevance and coverage. By testing our methodology on different chemical reactions, we were able to demonstrate its effectiveness in finding general reactivity trends by using a few highly representative examples. The developed methodology empowers chemists to showcase the unbiased applicability of novel methodologies, facilitating their practical applications. We hope that this work will trigger interdisciplinary discussions about biases in synthetic chemistry, leading to improved data quality.
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Affiliation(s)
- Debanjan Rana
- Universität Münster,
Organisch-Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
| | - Philipp M. Pflüger
- Universität Münster,
Organisch-Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
| | - Niklas P. Hölter
- Universität Münster,
Organisch-Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
| | - Guangying Tan
- Universität Münster,
Organisch-Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
| | - Frank Glorius
- Universität Münster,
Organisch-Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
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9
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Webb EW, Cheng K, Winton WP, Klein BJ, Bowden GD, Horikawa M, Liu SW, Wright JS, Verhoog S, Kalyani D, Wismer M, Krska SW, Sanford MS, Scott PJ. Development of High-Throughput Experimentation Approaches for Rapid Radiochemical Exploration. J Am Chem Soc 2024; 146:10581-10590. [PMID: 38580459 PMCID: PMC11099536 DOI: 10.1021/jacs.3c14822] [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: 04/07/2024]
Abstract
Positron emission tomography is a widely used imaging platform for studying physiological processes. Despite the proliferation of modern synthetic methodologies for radiolabeling, the optimization of these reactions still primarily relies on inefficient one-factor-at-a-time approaches. High-throughput experimentation (HTE) has proven to be a powerful approach for optimizing reactions in many areas of chemical synthesis. However, to date, HTE has rarely been applied to radiochemistry. This is largely because of the short lifetime of common radioisotopes, which presents major challenges for efficient parallel reaction setup and analysis using standard equipment and workflows. Herein, we demonstrate an effective HTE workflow and apply it to the optimization of copper-mediated radiofluorination of pharmaceutically relevant boronate ester substrates. The workflow utilizes commercial equipment and allows for rapid analysis of reactions for optimizing reactions, exploring chemical space using pharmaceutically relevant aryl boronates for radiofluorinations, and constructing large radiochemistry data sets.
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Affiliation(s)
- E. William Webb
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Kevin Cheng
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Wade P. Winton
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Brandon J.C. Klein
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Gregory D. Bowden
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, Tuebingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, Tuebingen 72074, Germany
| | - Mami Horikawa
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - S. Wendy Liu
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Jay S. Wright
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Stefan Verhoog
- Translational Imaging, Merck and Co., Inc., West Point, PA 19486, United States
| | - Dipannita Kalyani
- Discovery Chemistry, Merck Research Laboratories, Merck and Co., Inc., Rahway, NJ 07065, United States
| | - Michael Wismer
- Discovery Chemistry, Merck Research Laboratories, Merck and Co., Inc., Rahway, NJ 07065, United States
| | - Shane W. Krska
- Discovery Chemistry, Merck Research Laboratories, Merck and Co., Inc., Rahway, NJ 07065, United States
| | - Melanie S. Sanford
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Peter J.H. Scott
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 North University Avenue, Ann Arbor, Michigan 48109, United States
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10
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Schrader ML, Schäfer FR, Schäfers F, Glorius F. Bridging the information gap in organic chemical reactions. Nat Chem 2024; 16:491-498. [PMID: 38548884 DOI: 10.1038/s41557-024-01470-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 02/02/2024] [Indexed: 04/07/2024]
Abstract
The varying quality of scientific reports is a well-recognized problem and often results from a lack of standardization and transparency in scientific publications. This situation ultimately leads to prominent complications such as reproducibility issues and the slow uptake of newly developed synthetic methods for pharmaceutical and agrochemical applications. In recent years, various impactful approaches have been advocated to bridge information gaps and to improve the quality of experimental protocols in synthetic organic publications. Here we provide a critical overview of these strategies and present the reader with a versatile set of tools to augment their standard procedures. We formulate eight principles to improve data management in scientific publications relating to data standardization, reproducibility and evaluation, and encourage scientists to go beyond current publication standards. We are aware that this is a substantial effort, but we are convinced that the resulting improved data situation will greatly benefit the progress of chemistry.
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Affiliation(s)
- Malte L Schrader
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany
| | - Felix R Schäfer
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany
| | - Felix Schäfers
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany.
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11
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King-Smith E, Berritt S, Bernier L, Hou X, Klug-McLeod JL, Mustakis J, Sach NW, Tucker JW, Yang Q, Howard RM, Lee AA. Probing the chemical 'reactome' with high-throughput experimentation data. Nat Chem 2024; 16:633-643. [PMID: 38168924 PMCID: PMC10997498 DOI: 10.1038/s41557-023-01393-w] [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: 11/11/2022] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
High-throughput experimentation (HTE) has the potential to improve our understanding of organic chemistry by systematically interrogating reactivity across diverse chemical spaces. Notable bottlenecks include few publicly available large-scale datasets and the need for facile interpretation of these data's hidden chemical insights. Here we report the development of a high-throughput experimentation analyser, a robust and statistically rigorous framework, which is applicable to any HTE dataset regardless of size, scope or target reaction outcome, which yields interpretable correlations between starting material(s), reagents and outcomes. We improve the HTE data landscape with the disclosure of 39,000+ previously proprietary HTE reactions that cover a breadth of chemistry, including cross-coupling reactions and chiral salt resolutions. The high-throughput experimentation analyser was validated on cross-coupling and hydrogenation datasets, showcasing the elucidation of statistically significant hidden relationships between reaction components and outcomes, as well as highlighting areas of dataset bias and the specific reaction spaces that necessitate further investigation.
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Affiliation(s)
- Emma King-Smith
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | | | - Xinjun Hou
- Pfizer Research and Development, Cambridge, MA, USA
| | | | | | - Neal W Sach
- Pfizer Research and Development, La Jolla, CA, USA
| | | | - Qingyi Yang
- Pfizer Research and Development, Cambridge, MA, USA
| | | | - Alpha A Lee
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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12
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Iyer K, Kavthe RD, Lammert RM, Yirak JR, Lipshutz BH. Ligated Pd-Catalyzed Aminations of Aryl/Heteroaryl Halides with Aliphatic Amines under Sustainable Aqueous Micellar Conditions. JACS AU 2024; 4:680-689. [PMID: 38425930 PMCID: PMC10900223 DOI: 10.1021/jacsau.3c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/02/2024]
Abstract
Sustainable technology for constructing Pd-catalyzed C-N bonds involving aliphatic amines is reported. A catalytic system that relies on low levels of recyclable precious metal, a known and commercially available ligand, and a recyclable aqueous medium are combined, leading to a newly developed procedure. This new technology can be used in ocean water with equal effectiveness. Applications involving highly challenging reaction partners constituting late-stage functionalization are documented, as is a short but efficient synthesis of the drug naftopidil. Comparisons with existing aminations highlight the many advances being offered.
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Affiliation(s)
| | | | - Robert M. Lammert
- Department of Chemistry and
Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Jordan R. Yirak
- Department of Chemistry and
Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bruce H. Lipshutz
- Department of Chemistry and
Biochemistry, University of California, Santa Barbara, California 93106, United States
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13
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Iyer K, Kavthe R, Hu Y, Lipshutz BH. Nanoparticles as Heterogeneous Catalysts for ppm Pd-Catalyzed Aminations in Water. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:1997-2008. [PMID: 38333203 PMCID: PMC10848299 DOI: 10.1021/acssuschemeng.3c06527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 02/10/2024]
Abstract
A general protocol employing heterogeneous catalysis has been developed that enables ppm of Pd-catalyzed C-N cross-coupling reactions under aqueous micellar catalysis. A new nanoparticle catalyst containing specifically ligated Pd, in combination with nanoreactors composed of the designer surfactant Savie, a biodegradable amphiphile, catalyzes C-N bond formations in recyclable water. A variety of coupling partners, ranging from highly functionalized pharmaceutically relevant APIs to educts from the Merck Informer Library, readily participate under these environmentally responsible, sustainable reaction conditions. Other key features associated with this report include the low levels of residual Pd found in the products, the recyclability of the aqueous reaction medium, the use of ocean water as an alternative source of reaction medium, options for the use of pseudohalides as alternative reaction partners, and associated low E factors. In addition, an unprecedented 5-step, one-pot sequence is presented, featuring several of the most widely used transformations in the pharmaceutical industry, suggesting potential industrial applications.
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Affiliation(s)
| | | | - Yuting Hu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bruce H. Lipshutz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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14
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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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15
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Michel NWM, Gabbey AL, Edjoc RK, Fagbola E, Hughes JME, Campeau LC, Rousseaux SAL. Nickel-Catalyzed Reductive Arylation of Redox Active Esters for the Synthesis of α-Aryl Nitriles: Investigation of a Chlorosilane Additive. J Org Chem 2024. [PMID: 38197128 DOI: 10.1021/acs.joc.3c02354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
A nickel-catalyzed reductive cross-coupling of redox active N-hydroxyphthalimide (NHP) esters and iodoarenes for the synthesis of α-aryl nitriles is described. The NHP ester substrate is derived from cyanoacetic acid, which allows for a modular synthesis of substituted α-aryl nitriles, an important scaffold in the pharmaceutical sciences. The reaction exhibits a broad scope, and many functional groups are compatible under the reaction conditions, including complex highly functionalized medicinal agents. Mechanistic studies reveal that reduction and decarboxylation of the NHP ester to the reactive radical intermediate are accomplished by a combination of a chlorosilane additive and Zn dust. We demonstrate that stoichiometric chlorosilane is essential for product formation and that chlorosilane plays a role beyond activation of the metal reductant.
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Affiliation(s)
- Nicholas W M Michel
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Alexis L Gabbey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Racquel K Edjoc
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Emmanuel Fagbola
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jonathan M E Hughes
- Department of Process Research and Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Louis-Charles Campeau
- Department of Process Research and Development, Merck & Company Inc., Rahway, New Jersey 07065, United States
| | - Sophie A L Rousseaux
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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16
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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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17
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Raghavan P, Haas BC, Ruos ME, Schleinitz J, Doyle AG, Reisman SE, Sigman MS, Coley CW. Dataset Design for Building Models of Chemical Reactivity. ACS CENTRAL SCIENCE 2023; 9:2196-2204. [PMID: 38161380 PMCID: PMC10755851 DOI: 10.1021/acscentsci.3c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024]
Abstract
Models can codify our understanding of chemical reactivity and serve a useful purpose in the development of new synthetic processes via, for example, evaluating hypothetical reaction conditions or in silico substrate tolerance. Perhaps the most determining factor is the composition of the training data and whether it is sufficient to train a model that can make accurate predictions over the full domain of interest. Here, we discuss the design of reaction datasets in ways that are conducive to data-driven modeling, emphasizing the idea that training set diversity and model generalizability rely on the choice of molecular or reaction representation. We additionally discuss the experimental constraints associated with generating common types of chemistry datasets and how these considerations should influence dataset design and model building.
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Affiliation(s)
- Priyanka Raghavan
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Brittany C. Haas
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Madeline E. Ruos
- Department
of Chemistry & Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jules Schleinitz
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Abigail G. Doyle
- Department
of Chemistry & Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Sarah E. Reisman
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Matthew S. Sigman
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Connor W. Coley
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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18
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Matador E, Tilby MJ, Saridakis I, Pedrón M, Tomczak D, Llaveria J, Atodiresei I, Merino P, Ruffoni A, Leonori D. A Photochemical Strategy for the Conversion of Nitroarenes into Rigidified Pyrrolidine Analogues. J Am Chem Soc 2023; 145:27810-27820. [PMID: 38059920 DOI: 10.1021/jacs.3c10863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Bicyclic amines are important motifs for the preparation of bioactive materials. These species have well-defined exit vectors that enable accurate disposition of substituents toward specific areas of chemical space. Of all possible skeletons, the 2-azabicyclo[3.2.0]heptane framework is virtually absent from MedChem libraries due to a paucity of synthetic methods for its preparation. Here, we report a modular synthetic strategy that utilizes nitroarenes as flat and easy-to-functionalize feedstocks for the assembly of these sp3-rich materials. Mechanistically, this approach exploits two concomitant photochemical processes that sequentially ring-expand the nitroarene into an azepine and then fold it into a rigid bicycle pyrroline by means of singlet nitrene-mediated nitrogen insertion and excited-state-4π electrocyclization. A following hydrogenolysis provides, with full diastereocontrol, the desired bicyclic amine derivatives whereby the aromatic substitution pattern has been translated into the one of the three-dimensional heterocycle. These molecules can be considered rigid pyrrolidine analogues with a well-defined orientation of their substituents. Furthermore, unsupervised clustering of an expansive virtual database of saturated N-heterocycles revealed these derivatives as effective isosteres of rigidified piperidines. Overall, this platform enables the conversion of nitroarene feedstocks into complex sp3-rich heterocycles of potential interest to drug development.
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Affiliation(s)
- Esteban Matador
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
- Departamento de Química Orgánica, Universidad de Sevilla and Centro de Innovación en Química Avanzada (ORFEO-CINQA), C/Prof. García González 1, 41012 Sevilla, Spain
| | - Michael J Tilby
- Department of Chemistry, University of Manchester, M13 9PL Manchester, U.K
| | - Iakovos Saridakis
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Manuel Pedrón
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50009 Zaragoza, Spain
| | - Dawid Tomczak
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Josep Llaveria
- Global Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, Janssen Research & Development, Janssen-Cilag S.A., Jarama 75A, 45007 Toledo, Spain
| | - Iuliana Atodiresei
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Pedro Merino
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50009 Zaragoza, Spain
| | - Alessandro Ruffoni
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Daniele Leonori
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
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19
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Thomas RM, Obbard DB, Lipshutz BH. Challenging cross couplings, in water, aided by in situ iodination of (hetero)aromatic bromides. Chem Sci 2023; 14:13503-13507. [PMID: 38033910 PMCID: PMC10686040 DOI: 10.1039/d3sc04199a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
Palladium-catalyzed reactions that involve functionalized substrates are oftentimes problematic. Those involving aryl or heteroaryl bromides that are either resistant to, or inefficient in such couplings present challenges that are difficult to overcome and may require development of an entirely new route, or worse, no opportunity to install the desired group using a standard coupling strategy. In this report, we describe a solution that allows for the in situ conversion of such bromo educts to transient iodide derivatives that can be made and used under environmentally responsible conditions, for subsequent reactions to highly functionalized, complex targets.
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Affiliation(s)
- Rohan M Thomas
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106 USA
| | - David B Obbard
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106 USA
| | - Bruce H Lipshutz
- Department of Chemistry and Biochemistry, University of California Santa Barbara CA 93106 USA
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20
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Garcia B, Sampson J, Watson MP, Kalyani D. Primary vs. secondary alkylpyridinium salts: a comparison under electrochemical and chemical reduction conditions. Faraday Discuss 2023; 247:324-332. [PMID: 37477413 PMCID: PMC10799965 DOI: 10.1039/d3fd00120b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
This report details a systematic comparison of the scope of aryl bromides in nickel-catalyzed, reductive cross-electrophile couplings of primary vs. secondary alkylpyridinium salts using both electrochemical and chemical reductants. Facilitated by the use of high-throughput experimentation (HTE) techniques, 37 aryl bromides, including 13 complex, drug-like examples, were investigated. By using primary and secondary substrates differing only by one methylene, we observed that the trends in ArBr scope are similar between the primary and secondary alkylpyridinium salts, although distinctions were observed in isolated cases. In addition, the electrochemical conditions compared favorably to those using chemical reductants, especially among the more complex, drug-like aryl halides.
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Affiliation(s)
- Bria Garcia
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Jessica Sampson
- High Throughput Experimentation Facility, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Mary P Watson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Dipannita Kalyani
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, USA.
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21
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Götz J, Jackl MK, Jindakun C, Marziale AN, André J, Gosling DJ, Springer C, Palmieri M, Reck M, Luneau A, Brocklehurst CE, Bode JW. High-throughput synthesis provides data for predicting molecular properties and reaction success. SCIENCE ADVANCES 2023; 9:eadj2314. [PMID: 37889964 PMCID: PMC10610918 DOI: 10.1126/sciadv.adj2314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
The generation of attractive scaffolds for drug discovery efforts requires the expeditious synthesis of diverse analogues from readily available building blocks. This endeavor necessitates a trade-off between diversity and ease of access and is further complicated by uncertainty about the synthesizability and pharmacokinetic properties of the resulting compounds. Here, we document a platform that leverages photocatalytic N-heterocycle synthesis, high-throughput experimentation, automated purification, and physicochemical assays on 1152 discrete reactions. Together, the data generated allow rational predictions of the synthesizability of stereochemically diverse C-substituted N-saturated heterocycles with deep learning and reveal unexpected trends on the relationship between structure and properties. This study exemplifies how organic chemists can exploit state-of-the-art technologies to markedly increase throughput and confidence in the preparation of drug-like molecules.
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Affiliation(s)
- Julian Götz
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Moritz K. Jackl
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Chalupat Jindakun
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexander N. Marziale
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Jérôme André
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Daniel J. Gosling
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Clayton Springer
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA 02139, USA
| | - Marco Palmieri
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Marcel Reck
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Alexandre Luneau
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Cara E. Brocklehurst
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4056 Basel, Switzerland
| | - Jeffrey W. Bode
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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22
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Chen SJ, He CQ, Kong M, Wang J, Lin S, Krska SW, Stahl SS. Accessing three-dimensional molecular diversity through benzylic C-H cross-coupling. NATURE SYNTHESIS 2023; 2:998-1008. [PMID: 38463240 PMCID: PMC10923599 DOI: 10.1038/s44160-023-00332-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 04/25/2023] [Indexed: 03/12/2024]
Abstract
Pharmaceutical and agrochemical discovery efforts rely on robust methods for chemical synthesis that rapidly access diverse molecules1,2. Cross-coupling reactions are the most widely used synthetic methods3, but these methods typically form bonds to C(sp2)-hybridized carbon atoms (e.g., amide coupling, biaryl coupling) and lead to a prevalence of "flat" molecular structures with suboptimal physicochemical and topological properties4. Benzylic C(sp3)-H cross-coupling methods offer an appealing strategy to address this limitation by directly forming bonds to C(sp3)-hybridized carbon atoms, and emerging methods exhibit synthetic versatility that rivals conventional cross-coupling methods to access products with drug-like properties. Here, we use a virtual library of >350,000 benzylic ethers and ureas derived from benzylic C-H cross-coupling to test the widely held view that coupling at C(sp3)-hybridized carbon atoms affords products with improved three-dimensionality. The results show that the conformational rigidity of the benzylic scaffold strongly influences the product dimensionality. Products derived from flexible scaffolds often exhibit little or no improvement in three-dimensionality, unless they adopt higher energy conformations. This outcome introduces an important consideration when designing routes to topologically diverse molecular libraries. The concepts elaborated herein are validated experimentally through an informatics-guided synthesis of selected targets and the use of high-throughput experimentation to prepare a library of three-dimensional products that are broadly distributed across drug-like chemical space.
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Affiliation(s)
- Si-Jie Chen
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI, USA
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Cyndi Qixin He
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - May Kong
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Jun Wang
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Shishi Lin
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Shane W. Krska
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Shannon S. Stahl
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI, USA
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23
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Eckart-Frank IK, Wilkerson-Hill SM. Palladium-Catalyzed Trans-Selective Synthesis of Spirocyclic Cyclobutanes Using α,α-Dialkylcrotyl- and Allylhydrazones. J Am Chem Soc 2023; 145:18591-18597. [PMID: 37552631 DOI: 10.1021/jacs.3c05699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Herein, we demonstrate the use of E/Z mixtures of α,α-disubstituted crotylhydrazones to obtain spirocyclic vinylcyclobutanes in a diastereoselective fashion. We show 24 examples of a 1,1-insertion/4-exo-trig tandem process to produce these motifs. Additionally, spirocyclic alkylidene cyclobutanes can be obtained by using α,α-disubstituted allylated hydrazones (11 examples). In this study, we show that the aryl migrating group has a dramatic impact on the course of the reaction. Specifically, allylic C-H insertion products can be obtained in good yields using bromoenones as reaction partners. When Pd(0) is used with no aryl or alkenyl bromide, an intramolecular cyclopropanation reaction takes place to afford [2.1.0]-bicycles.
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Affiliation(s)
- Isaiah K Eckart-Frank
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sidney M Wilkerson-Hill
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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24
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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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25
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Fu J, Lundy W, Chowdhury R, Twitty JC, Dinh LP, Sampson J, Lam YH, Sevov CS, Watson MP, Kalyani D. Nickel-Catalyzed Electroreductive Coupling of Alkylpyridinium Salts and Aryl Halides. ACS Catal 2023; 13:9336-9345. [PMID: 38188282 PMCID: PMC10769313 DOI: 10.1021/acscatal.3c01939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
An electrochemical, nickel-catalyzed reductive coupling of alkylpyridinium salts and aryl halides is reported. High-throughput experimentation (HTE) was employed for rapid reaction optimization and evaluation of a broad scope of pharmaceutically relevant structurally diverse aryl halides, including complex drug-like substrates. In addition, the transformation is compatible with both primary and secondary alkylpyridinium salts with distinct conditions. Mechanistic insights were critical to enhance the efficiency of coupling using secondary alkylpyridinium salts. Systematic comparisons of the electrochemical and non-electrochemical methods revealed the complementary scope and efficiency of the two approaches.
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Affiliation(s)
- Jiantao Fu
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Windsor Lundy
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Rajdip Chowdhury
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - J. Cameron Twitty
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Long P. Dinh
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica Sampson
- High Throughput Experimentation Facility, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Yu-hong Lam
- Modeling & Informatics, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Christo S. Sevov
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mary P. Watson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Dipannita Kalyani
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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26
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Fogel M, Koide K. Recent Progress on One-Pot Multisubstrate Screening. Org Process Res Dev 2023; 27:1235-1247. [PMID: 37529075 PMCID: PMC10389808 DOI: 10.1021/acs.oprd.3c00128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 08/03/2023]
Abstract
Traditionally, new synthetic reactions have been developed using a model substrate to screen reaction conditions before testing the optimized conditions with a range of more complex substrates. In 1998, Gao and Kagan pooled multiple substrates in one pot to study the generality of an enantioselective method. Although such one-pot multisubstrate screenings may be powerful, few applications have appeared in the literature. With the advancement of various chromatography techniques, it may be time to revisit this underutilized platform. This review article discusses the applications of one-pot multisubstrate screenings as a method for developing new synthetic methods.
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27
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Chambers RK, Weaver JD, Kim J, Hoar JL, Krska SW, White MC. A preparative small-molecule mimic of liver CYP450 enzymes in the aliphatic C-H oxidation of carbocyclic N-heterocycles. Proc Natl Acad Sci U S A 2023; 120:e2300315120. [PMID: 37428920 PMCID: PMC10629554 DOI: 10.1073/pnas.2300315120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/15/2023] [Indexed: 07/12/2023] Open
Abstract
An emerging trend in small-molecule pharmaceuticals, generally composed of nitrogen heterocycles (N-heterocycles), is the incorporation of aliphatic fragments. Derivatization of the aliphatic fragments to improve drug properties or identify metabolites often requires lengthy de novo syntheses. Cytochrome P450 (CYP450) enzymes are capable of direct site- and chemo-selective oxidation of a broad range of substrates but are not preparative. A chemoinformatic analysis underscored limited structural diversity of N-heterocyclic substrates oxidized using chemical methods relative to pharmaceutical chemical space. Here, we describe a preparative chemical method for direct aliphatic oxidation that tolerates a wide range of nitrogen functionality (chemoselective) and matches the site of oxidation (site-selective) of liver CYP450 enzymes. Commercial small-molecule catalyst Mn(CF3-PDP) selectively effects direct methylene oxidation in compounds bearing 25 distinct heterocycles including 14 out of 27 of the most frequent N-heterocycles found in U.S. Food and Drug Administration (FDA)-approved drugs. Mn(CF3-PDP) oxidations of carbocyclic bioisostere drug candidates (for example, HCV NS5B and COX-2 inhibitors including valdecoxib and celecoxib derivatives) and precursors of antipsychotic drugs blonanserin, buspirone, and tiospirone and the fungicide penconazole are demonstrated to match the major site of aliphatic metabolism obtained with liver microsomes. Oxidations are demonstrated at low Mn(CF3-PDP) loadings (2.5 to 5 mol%) on gram scales of substrate to furnish preparative amounts of oxidized products. A chemoinformatic analysis supports that Mn(CF3-PDP) significantly expands the pharmaceutical chemical space accessible to small-molecule C-H oxidation catalysis.
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Affiliation(s)
- Rachel K. Chambers
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL61801
| | - Jacob D. Weaver
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL61801
| | - Jinho Kim
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL61801
| | - Jason L. Hoar
- Department of Discovery Chemistry, Merck & Co., Inc., Rahway, NJ07065
| | - Shane W. Krska
- Department of Discovery Chemistry, Merck & Co., Inc., Rahway, NJ07065
| | - M. Christina White
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, IL61801
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28
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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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29
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Abstract
Azines, such as pyridines, quinolines, pyrimidines, and pyridazines, are widespread components of pharmaceuticals. Their occurrence derives from a suite of physiochemical properties that match key criteria in drug design and is tunable by varying their substituents. Developments in synthetic chemistry, therefore, directly impact these efforts, and methods that can install various groups from azine C-H bonds are particularly valuable. Furthermore, there is a growing interest in late-stage functionalization (LSF) reactions that focus on advanced candidate compounds that are often complex structures with multiple heterocycles, functional groups, and reactive sites. Because of factors such as their electron-deficient nature and the effects of the Lewis basic N atom, azine C-H functionalization reactions are often distinct from their arene counterparts, and the application of these reactions in LSF contexts is difficult. However, there have been many significant advances in azine LSF reactions, and this review will describe this progress, much of which has occurred over the past decade. It is possible to categorize these reactions as radical addition processes, metal-catalyzed C-H activation reactions, and transformations occurring via dearomatized intermediates. Substantial variation in reaction design within each category indicates both the rich reactivity of these heterocycles and the creativity of the approaches involved.
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Affiliation(s)
- Celena M Josephitis
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Hillary M H Nguyen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Andrew McNally
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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30
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Li SW, Xu LC, Zhang C, Zhang SQ, Hong X. Reaction performance prediction with an extrapolative and interpretable graph model based on chemical knowledge. Nat Commun 2023; 14:3569. [PMID: 37322041 DOI: 10.1038/s41467-023-39283-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Accurate prediction of reactivity and selectivity provides the desired guideline for synthetic development. Due to the high-dimensional relationship between molecular structure and synthetic function, it is challenging to achieve the predictive modelling of synthetic transformation with the required extrapolative ability and chemical interpretability. To meet the gap between the rich domain knowledge of chemistry and the advanced molecular graph model, herein we report a knowledge-based graph model that embeds the digitalized steric and electronic information. In addition, a molecular interaction module is developed to enable the learning of the synergistic influence of reaction components. In this study, we demonstrate that this knowledge-based graph model achieves excellent predictions of reaction yield and stereoselectivity, whose extrapolative ability is corroborated by additional scaffold-based data splittings and experimental verifications with new catalysts. Because of the embedding of local environment, the model allows the atomic level of interpretation of the steric and electronic influence on the overall synthetic performance, which serves as a useful guide for the molecular engineering towards the target synthetic function. This model offers an extrapolative and interpretable approach for reaction performance prediction, pointing out the importance of chemical knowledge-constrained reaction modelling for synthetic purpose.
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Affiliation(s)
- Shu-Wen Li
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Li-Cheng Xu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Cheng Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Shuo-Qing Zhang
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China.
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China.
- Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street No. 2, Beijing, 100190, PR China.
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
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31
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Liu W, Mulhearn J, Hao B, Cañellas S, Last S, Gómez JE, Jones A, De Vera A, Kumar K, Rodríguez R, Van Eynde L, Strambeanu II, Wolkenberg SE. Enabling Deoxygenative C(sp 2)-C(sp 3) Cross-Coupling for Parallel Medicinal Chemistry. ACS Med Chem Lett 2023; 14:853-859. [PMID: 37312855 PMCID: PMC10258906 DOI: 10.1021/acsmedchemlett.3c00118] [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: 03/31/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Herein we report the development of an automated deoxygenative C(sp2)-C(sp3) coupling of aryl bromide with alcohols to enable parallel medicinal chemistry. Alcohols are among the most diverse and abundant building blocks, but their usage as alkyl precursors has been limited. Although metallaphotoredox deoxygenative coupling is becoming a promising strategy to form C(sp2)-C(sp3) bond, the reaction setup limits its widespread application in library synthesis. To achieve high throughput and consistency, an automated workflow involving solid-dosing and liquid-handling robots has been developed. We have successfully demonstrated this high-throughput protocol is robust and consistent across three automation platforms. Furthermore, guided by cheminformatic analysis, we examined alcohols with comprehensive chemical space coverage and established a meaningful scope for medicinal chemistry applications. By accessing the rich diversity of alcohols, this automated protocol has the potential to substantially increase the impact of C(sp2)-C(sp3) cross-coupling in drug discovery.
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Affiliation(s)
- Wei Liu
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - James Mulhearn
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Bo Hao
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Santiago Cañellas
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Stefaan Last
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - José Enrique Gómez
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Alexander Jones
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - Alexander De Vera
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Kiran Kumar
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Raquel Rodríguez
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Lars Van Eynde
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - Iulia I. Strambeanu
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Scott E. Wolkenberg
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
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32
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Lutovsky GA, Gockel SN, Bundesmann MW, Bagley SW, Yoon TP. Iron-mediated modular decarboxylative cross-nucleophile coupling. Chem 2023; 9:1610-1621. [PMID: 37637494 PMCID: PMC10449378 DOI: 10.1016/j.chempr.2023.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Carboxylic acids are valuable building blocks for pharmaceutical discovery because of their chemical stability, commercial availability, and structural diversity. Decarboxylative coupling reactions enable versatile functionalization of these feedstock chemicals, but many of the most general methods require prefunctionalization of carboxylic acids with redox-active moieties. These internal oxidants can be costly, their installation impedes rapid library synthesis, and their use results in environmentally problematic organic byproducts. We report herein a method for the direct decarboxylative cross-coupling of native carboxylic acids with nucleophilic coupling partners mediated by inexpensive, terrestrially abundant, and nontoxic Fe(III) salts. This method involves an initial photochemical decarboxylation followed by radical-polar crossover, which enables the construction of diverse carbon-carbon, carbon-oxygen, and carbon-nitrogen bonds with remarkable generality.
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Affiliation(s)
- Grace A. Lutovsky
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706, USA
- These authors contributed equally
| | - Samuel N. Gockel
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706, USA
- Department of Chemistry, Colorado State University Pueblo, 2200 Bonforte Boulevard, Pueblo, CO 81001, USA
| | | | - Scott W. Bagley
- Medicine Design, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Tehshik P. Yoon
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706, USA
- Lead contact
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33
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Kim ST, Strauss MJ, Cabré A, Buchwald SL. Room-Temperature Cu-Catalyzed Amination of Aryl Bromides Enabled by DFT-Guided Ligand Design. J Am Chem Soc 2023; 145:6966-6975. [PMID: 36926889 PMCID: PMC10415864 DOI: 10.1021/jacs.3c00500] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Ullmann-type C-N coupling reactions represent an important alternative to well-established Pd-catalyzed approaches due to the differing reactivity and the lower cost of Cu. While the design of anionic Cu ligands, particularly those by Ma, has enabled the coupling of various classes of aryl halides and alkyl amines, most methods require conditions that can limit their utility on complex substrates. Herein, we disclose the development of anionic N1,N2-diarylbenzene-1,2-diamine ligands that promote the Cu-catalyzed amination of aryl bromides under mild conditions. Guided by DFT calculations, these ligands were designed to (1) increase the electron density on Cu, thereby increasing the rate of oxidative addition of aryl bromides, and (2) stabilize the active anionic CuI complex via a π-interaction. Under optimized conditions, structurally diverse aryl and heteroaryl bromides and a broad range of alkyl amine nucleophiles, including pharmaceuticals bearing multiple functional groups, were efficiently coupled at room temperature. Combined computational and experimental studies support a mechanism of C-N bond formation that follows a catalytic cycle akin to the well-explored Pd-catalyzed variants. Modification of the ligand structure to include a naphthyl residue resulted in a lower energy barrier to oxidative addition, providing a 30-fold rate increase relative to what is seen with other ligands. Collectively, these results establish a new class of anionic ligands for Cu-catalyzed C-N couplings, which we anticipate may be extended to other Cu-catalyzed C-heteroatom and C-C bond-forming reactions.
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Affiliation(s)
- Seoung-Tae Kim
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Michael J Strauss
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Albert Cabré
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
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34
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Dotson JJ, van Dijk L, Timmerman JC, Grosslight S, Walroth RC, Gosselin F, Püntener K, Mack KA, Sigman MS. Data-Driven Multi-Objective Optimization Tactics for Catalytic Asymmetric Reactions Using Bisphosphine Ligands. J Am Chem Soc 2023; 145:110-121. [PMID: 36574729 DOI: 10.1021/jacs.2c08513] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Optimization of the catalyst structure to simultaneously improve multiple reaction objectives (e.g., yield, enantioselectivity, and regioselectivity) remains a formidable challenge. Herein, we describe a machine learning workflow for the multi-objective optimization of catalytic reactions that employ chiral bisphosphine ligands. This was demonstrated through the optimization of two sequential reactions required in the asymmetric synthesis of an active pharmaceutical ingredient. To accomplish this, a density functional theory-derived database of >550 bisphosphine ligands was constructed, and a designer chemical space mapping technique was established. The protocol used classification methods to identify active catalysts, followed by linear regression to model reaction selectivity. This led to the prediction and validation of significantly improved ligands for all reaction outputs, suggesting a general strategy that can be readily implemented for reaction optimizations where performance is controlled by bisphosphine ligands.
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Affiliation(s)
- Jordan J Dotson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Lucy van Dijk
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jacob C Timmerman
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Samantha Grosslight
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Richard C Walroth
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Kurt Püntener
- Synthetic Molecules Technical Development, Process Chemistry & Catalysis, F. Hoffmann-La Roche Limited, CH-4070 Basel, Switzerland
| | - Kyle A Mack
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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35
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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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36
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Rago AJ, Vasilopoulos A, Dombrowski AW, Wang Y. Di(2-picolyl)amines as Modular and Robust Ligands for Nickel-Catalyzed C(sp 2)–C(sp 3) Cross-Electrophile Coupling. Org Lett 2022; 24:8487-8492. [DOI: 10.1021/acs.orglett.2c03346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Alexander J. Rago
- Advanced Chemistry Technologies Group, AbbVie, Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Aristidis Vasilopoulos
- Advanced Chemistry Technologies Group, AbbVie, Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Amanda W. Dombrowski
- Advanced Chemistry Technologies Group, AbbVie, Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Ying Wang
- Advanced Chemistry Technologies Group, AbbVie, Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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37
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Palkowitz MD, Laudadio G, Kolb S, Choi J, Oderinde MS, Ewing TEH, Bolduc PN, Chen T, Zhang H, Cheng PTW, Zhang B, Mandler MD, Blasczak VD, Richter JM, Collins MR, Schioldager RL, Bravo M, Dhar TGM, Vokits B, Zhu Y, Echeverria PG, Poss MA, Shaw SA, Clementson S, Petersen NN, Mykhailiuk PK, Baran PS. Overcoming Limitations in Decarboxylative Arylation via Ag-Ni Electrocatalysis. J Am Chem Soc 2022; 144:17709-17720. [PMID: 36106767 PMCID: PMC9805175 DOI: 10.1021/jacs.2c08006] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A useful protocol for achieving decarboxylative cross-coupling (DCC) of redox-active esters (RAE, isolated or generated in situ) and halo(hetero)arenes is reported. This pragmatically focused study employs a unique Ag-Ni electrocatalytic platform to overcome numerous limitations that have plagued this strategically powerful transformation. In its optimized form, coupling partners can be combined in a surprisingly simple way: open to the air, using technical-grade solvents, an inexpensive ligand and Ni source, and substoichiometric AgNO3, proceeding at room temperature with a simple commercial potentiostat. Most importantly, all of the results are placed into context by benchmarking with state-of-the-art methods. Applications are presented that simplify synthesis and rapidly enable access to challenging chemical space. Finally, adaptation to multiple scale regimes, ranging from parallel milligram-based synthesis to decagram recirculating flow is presented.
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Affiliation(s)
- Maximilian D Palkowitz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gabriele Laudadio
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Simon Kolb
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jin Choi
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Martins S Oderinde
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Tamara El-Hayek Ewing
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philippe N Bolduc
- Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hao Zhang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Peter T W Cheng
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Benxiang Zhang
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Mandler
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Vanna D Blasczak
- Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jeremy M Richter
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Michael R Collins
- Oncology Medicinal Chemistry Department, Pfizer Pharmaceuticals, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Ryan L Schioldager
- Oncology Medicinal Chemistry Department, Pfizer Pharmaceuticals, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Martin Bravo
- Oncology Medicinal Chemistry Department, Pfizer Pharmaceuticals, 10770 Science Center Drive, San Diego, California 92121, United States
| | - T G Murali Dhar
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Benjamin Vokits
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Yeheng Zhu
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | | | - Michael A Poss
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | - Scott A Shaw
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08534, United States
| | | | | | | | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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38
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When machine learning meets molecular synthesis. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Singh S, Sunoj RB. A Transfer Learning Approach for Reaction Discovery in Small Data Situations Using Generative Model. iScience 2022; 25:104661. [PMID: 35832891 PMCID: PMC9272387 DOI: 10.1016/j.isci.2022.104661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/01/2022] Open
Abstract
Sustainable practices in chemical sciences can be better realized by adopting interdisciplinary approaches that combine the advantages of machine learning (ML) on the initially acquired small data in reaction discovery. Developing new reactions generally remains heuristic and even time and resource intensive. For instance, synthesis of fluorine-containing compounds, which constitute ∼20% of the marketed drugs, relies on deoxyfluorination of abundantly available alcohols. Herein, we demonstrate the use of a recurrent neural network-based deep generative model built on a library of just 37 alcohols for effective learning and exploration of the chemical space. The proof-of-concept ML model is able to generate good quality, synthetically accessible, higher-yielding novel alcohol molecules. This protocol would have superior utility for deployment into a practical reaction discovery pipeline. Dual pronged transfer learning, both to generate and predict yields of new molecules Demonstrated the utility for an important family of deoxyfluorination of alcohols Applicable for practically more likely situations with relatively smaller data Extendable to other reaction manifolds to facilitate expedited reaction discovery
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40
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Chen TQ, Pedersen PS, Dow NW, Fayad R, Hauke CE, Rosko MC, Danilov EO, Blakemore DC, Dechert-Schmitt AM, Knauber T, Castellano FN, MacMillan DWC. A Unified Approach to Decarboxylative Halogenation of (Hetero)aryl Carboxylic Acids. J Am Chem Soc 2022; 144:8296-8305. [PMID: 35486956 DOI: 10.1021/jacs.2c02392] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aryl halides are a fundamental motif in synthetic chemistry, playing a critical role in metal-mediated cross-coupling reactions and serving as important scaffolds in drug discovery. Although thermal decarboxylative functionalization of aryl carboxylic acids has been extensively explored, the scope of existing halodecarboxylation methods remains limited, and there currently exists no unified strategy that provides access to any type of aryl halide from an aryl carboxylic acid precursor. Herein, we report a general catalytic method for direct decarboxylative halogenation of (hetero)aryl carboxylic acids via ligand-to-metal charge transfer. This strategy accommodates an exceptionally broad scope of substrates. We leverage an aryl radical intermediate toward divergent functionalization pathways: (1) atom transfer to access bromo- or iodo(hetero)arenes or (2) radical capture by copper and subsequent reductive elimination to generate chloro- or fluoro(hetero)arenes. The proposed ligand-to-metal charge transfer mechanism is supported through an array of spectroscopic studies.
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Affiliation(s)
- Tiffany Q Chen
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - P Scott Pedersen
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan W Dow
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Remi Fayad
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Cory E Hauke
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael C Rosko
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Evgeny O Danilov
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - David C Blakemore
- Worldwide Research and Development, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anne-Marie Dechert-Schmitt
- Worldwide Research and Development, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Thomas Knauber
- Worldwide Research and Development, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Felix N Castellano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
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41
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Weis E, Johansson M, Korsgren P, Martín-Matute B, Johansson MJ. Merging Directed C-H Activations with High-Throughput Experimentation: Development of Iridium-Catalyzed C-H Aminations Applicable to Late-Stage Functionalization. JACS AU 2022; 2:906-916. [PMID: 35557751 PMCID: PMC9088304 DOI: 10.1021/jacsau.2c00039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 05/14/2023]
Abstract
Herein, we report an iridium-catalyzed directed C-H amination methodology developed using a high-throughput experimentation (HTE)-based strategy, applicable for the needs of automated modern drug discovery. The informer library approach for investigating the accessible directing group chemical space, in combination with functional group tolerance screening and substrate scope investigations, allowed for the generation of reaction application guidelines to aid future users. Applicability to late-stage functionalization of complex drugs and natural products, in combination with multiple deprotection protocols leading to the desirable aniline matched pairs, serve to demonstrate the utility of the method for drug discovery. Finally, reaction miniaturization to a nanomolar range highlights the opportunities for more sustainable screening with decreased material consumption.
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Affiliation(s)
- Erik Weis
- Department
of Organic Chemistry, Stockholm University, Stockholm, SE 106 91, Sweden
- Medicinal
Chemistry, Research and Early Development; Cardiovascular, Renal and
Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden
1, Mölndal, 431 50 Gothenburg, Sweden
| | - Maria Johansson
- Compound
Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431
50 Gothenburg, Sweden
| | - Pernilla Korsgren
- Compound
Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431
50 Gothenburg, Sweden
| | - Belén Martín-Matute
- Department
of Organic Chemistry, Stockholm University, Stockholm, SE 106 91, Sweden
| | - Magnus J. Johansson
- Department
of Organic Chemistry, Stockholm University, Stockholm, SE 106 91, Sweden
- Medicinal
Chemistry, Research and Early Development; Cardiovascular, Renal and
Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden
1, Mölndal, 431 50 Gothenburg, Sweden
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42
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Xu G, Gao P, Colacot TJ. Tunable Unsymmetrical Ferrocene Ligands Bearing a Bulky Di-1-adamantylphosphino Motif for Many Kinds of C sp2–C sp3 Couplings. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00352] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Guolin Xu
- Research and Development, Life Science Chemistry, MilliporeSigma, 6000 N. Teutonia Avenue, Milwaukee, Wisconsin 53209, United States
| | - Peng Gao
- Research and Development, Life Science Chemistry, MilliporeSigma, 6000 N. Teutonia Avenue, Milwaukee, Wisconsin 53209, United States
| | - Thomas J. Colacot
- Research and Development, Life Science Chemistry, MilliporeSigma, 6000 N. Teutonia Avenue, Milwaukee, Wisconsin 53209, United States
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43
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Konno S, Kobayashi K, Senda M, Funai Y, Seki Y, Tamai I, Schäkel L, Sakata K, Pillaiyar T, Taguchi A, Taniguchi A, Gütschow M, Müller CE, Takeuchi K, Hirohama M, Kawaguchi A, Kojima M, Senda T, Shirasaka Y, Kamitani W, Hayashi Y. 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J Med Chem 2022; 65:2926-2939. [PMID: 34313428 PMCID: PMC8340582 DOI: 10.1021/acs.jmedchem.1c00665] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 02/08/2023]
Abstract
The novel coronavirus, SARS-CoV-2, has been identified as the causative agent for the current coronavirus disease (COVID-19) pandemic. 3CL protease (3CLpro) plays a pivotal role in the processing of viral polyproteins. We report peptidomimetic compounds with a unique benzothiazolyl ketone as a warhead group, which display potent activity against SARS-CoV-2 3CLpro. The most potent inhibitor YH-53 can strongly block the SARS-CoV-2 replication. X-ray structural analysis revealed that YH-53 establishes multiple hydrogen bond interactions with backbone amino acids and a covalent bond with the active site of 3CLpro. Further results from computational and experimental studies, including an in vitro absorption, distribution, metabolism, and excretion profile, in vivo pharmacokinetics, and metabolic analysis of YH-53 suggest that it has a high potential as a lead candidate to compete with COVID-19.
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Affiliation(s)
- Sho Konno
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Kiyotaka Kobayashi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of
Materials Structure Science, High Energy Accelerator Research Organization
(KEK), Tsukuba 305-0801, Japan
| | - Yuta Funai
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Yuta Seki
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Ikumi Tamai
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Laura Schäkel
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Kyousuke Sakata
- School of Life Sciences, Tokyo University
of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392,
Japan
| | - Thanigaimalai Pillaiyar
- Pharmaceutical Institute, Pharmaceutical/Medicinal Chemistry,
University of Tübingen, Tübingen 72076,
Germany
| | - Akihiro Taguchi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Atsuhiko Taniguchi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Christa E. Müller
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research
Institute, National Institute of Advanced Industrial Science and
Technology, Koto, Tokyo 135-0064, Japan
| | - Mikako Hirohama
- Faculty of Medicine, Transborder Medical Research
Center, University of Tsukuba, Tsukuba 305-8575,
Japan
| | - Atsushi Kawaguchi
- Faculty of Medicine, Transborder Medical Research
Center, University of Tsukuba, Tsukuba 305-8575,
Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University
of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392,
Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of
Materials Structure Science, High Energy Accelerator Research Organization
(KEK), Tsukuba 305-0801, Japan
| | - Yoshiyuki Shirasaka
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense,
Gunma University Graduate School of Medicine, Maebashi
371-8511, Japan
| | - Yoshio Hayashi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
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44
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Li S, Pissarnitski D, Nowak T, Wleklinski M, Krska SW. Merging Late-Stage Diversification with Solid-Phase Peptide Synthesis Enabled by High-Throughput On-Resin Reaction Screening. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shasha Li
- Department of Analytical R&D, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dmitri Pissarnitski
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Timothy Nowak
- Department of Analytical R&D, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Michael Wleklinski
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Shane W. Krska
- Department of Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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45
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Dong J, Peng L, Yang X, Zhang Z, Zhang P. XGBoost-based intelligence yield prediction and reaction factors analysis of amination reaction. J Comput Chem 2022; 43:289-302. [PMID: 34862652 DOI: 10.1002/jcc.26791] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 11/10/2022]
Abstract
Buchwald-Hartwig amination reaction catalyzed by palladium plays an important role in drug synthesis. In the last few years, machine learning-assisted strategies emerged and quickly gained attention. In this article, an importance and relevance-based integrated feature screening method is proposed to effectively filter high-dimensional feature descriptor data. Then, a regularized machine learning boosting tree model, eXtreme Gradient Boosting, is introduced to intelligently predict reaction performance in multidimensional chemistry space. Furthermore, convergence, interpretability, generalization, and the internal association between reaction conditions and yields are excavated, which provides intelligent assistance for the optimal design of coupling reaction system and evaluating the reaction conditions. Compared with recently published results, the proposed method requires fewer feature descriptors, takes less time, and achieves more accurate prediction accuracy.
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Affiliation(s)
- Jing Dong
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, China
| | - Lichao Peng
- National & Local Joint Engineering Research Center for Applied Technology of Hybrid Nanomaterials, Henan University, Kaifeng, China
| | - Xiaohui Yang
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, China
| | - Zelin Zhang
- School of Computer and Information Engineering, Henan University, Kaifeng, China
| | - Puyu Zhang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, China
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46
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Kariofillis SK, Jiang S, Żurański AM, Gandhi SS, Martinez Alvarado JI, Doyle AG. Using Data Science To Guide Aryl Bromide Substrate Scope Analysis in a Ni/Photoredox-Catalyzed Cross-Coupling with Acetals as Alcohol-Derived Radical Sources. J Am Chem Soc 2022; 144:1045-1055. [PMID: 34985904 PMCID: PMC8810294 DOI: 10.1021/jacs.1c12203] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ni/photoredox catalysis has emerged as a powerful platform for C(sp2)-C(sp3) bond formation. While many of these methods typically employ aryl bromides as the C(sp2) coupling partner, a variety of aliphatic radical sources have been investigated. In principle, these reactions enable access to the same product scaffolds, but it can be hard to discern which method to employ because nonstandardized sets of aryl bromides are used in scope evaluation. Herein, we report a Ni/photoredox-catalyzed (deutero)methylation and alkylation of aryl halides where benzaldehyde di(alkyl) acetals serve as alcohol-derived radical sources. Reaction development, mechanistic studies, and late-stage derivatization of a biologically relevant aryl chloride, fenofibrate, are presented. Then, we describe the integration of data science techniques, including DFT featurization, dimensionality reduction, and hierarchical clustering, to delineate a diverse and succinct collection of aryl bromides that is representative of the chemical space of the substrate class. By superimposing scope examples from published Ni/photoredox methods on this same chemical space, we identify areas of sparse coverage and high versus low average yields, enabling comparisons between prior art and this new method. Additionally, we demonstrate that the systematically selected scope of aryl bromides can be used to quantify population-wide reactivity trends and reveal sources of possible functional group incompatibility with supervised machine learning.
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Affiliation(s)
- Stavros K. Kariofillis
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Shutian Jiang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andrzej M. Żurański
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Shivaani S. Gandhi
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | | | - Abigail G. Doyle
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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47
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Lu J, Donnecke S, Paci I, Leitch DC. A reactivity model for oxidative addition to palladium enables quantitative predictions for catalytic cross-coupling reactions. Chem Sci 2022; 13:3477-3488. [PMID: 35432873 PMCID: PMC8943861 DOI: 10.1039/d2sc00174h] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Making accurate, quantitative predictions of chemical reactivity based on molecular structure is an unsolved problem in chemical synthesis, particularly for complex molecules. We report an approach to reactivity prediction for...
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Affiliation(s)
- Jingru Lu
- Department of Chemistry, University of Victoria 3800 Finnerty Rd Victoria BC V8P 5C2 Canada
| | - Sofia Donnecke
- Department of Chemistry, University of Victoria 3800 Finnerty Rd Victoria BC V8P 5C2 Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria 3800 Finnerty Rd Victoria BC V8P 5C2 Canada
| | - David C Leitch
- Department of Chemistry, University of Victoria 3800 Finnerty Rd Victoria BC V8P 5C2 Canada
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48
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Qi N, Wismer MK, Conway DV, Krska SW, Dreher SD, Lin S. Development of a high intensity parallel photoreactor for high throughput screening. REACT CHEM ENG 2022. [DOI: 10.1039/d1re00317h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enhanced reactivity of decarboxylative cross-coupling using a new parallel photoreactor.
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Affiliation(s)
- Ning Qi
- HTE and Lead Discovery Capabilities, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Michael K. Wismer
- Scientific Design and Engineering, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Donald V. Conway
- Scientific Design and Engineering, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Shane W. Krska
- HTE and Lead Discovery Capabilities, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Spencer D. Dreher
- HTE and Lead Discovery Capabilities, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Shishi Lin
- HTE and Lead Discovery Capabilities, 2000 Galloping Hill Rd, Merck & Co., Inc., Kenilworth, NJ 07033, USA
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49
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Charboneau DJ, Huang H, Barth EL, Germe CC, Hazari N, Mercado BQ, Uehling MR, Zultanski SL. Tunable and Practical Homogeneous Organic Reductants for Cross-Electrophile Coupling. J Am Chem Soc 2021; 143:21024-21036. [PMID: 34846142 DOI: 10.1021/jacs.1c10932] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The syntheses of four new tunable homogeneous organic reductants based on a tetraaminoethylene scaffold are reported. The new reductants have enhanced air stability compared to current homogeneous reductants for metal-mediated reductive transformations, such as cross-electrophile coupling (XEC), and are solids at room temperature. In particular, the weakest reductant is indefinitely stable in air and has a reduction potential of -0.85 V versus ferrocene, which is significantly milder than conventional reductants used in XEC. All of the new reductants can facilitate C(sp2)-C(sp3) Ni-catalyzed XEC reactions and are compatible with complex substrates that are relevant to medicinal chemistry. The reductants span a range of nearly 0.5 V in reduction potential, which allows for control over the rate of electron transfer events in XEC. Specifically, we report a new strategy for controlled alkyl radical generation in Ni-catalyzed C(sp2)-C(sp3) XEC. The key to our approach is to tune the rate of alkyl radical generation from Katritzky salts, which liberate alkyl radicals upon single electron reduction, by varying the redox potentials of the reductant and Katritzky salt utilized in catalysis. Using our method, we perform XEC reactions between benzylic Katritzky salts and aryl halides. The method tolerates a variety of functional groups, some of which are particularly challenging for most XEC transformations. Overall, we expect that our new reductants will both replace conventional homogeneous reductants in current reductive transformations due to their stability and relatively facile synthesis and lead to the development of novel synthetic methods due to their tunability.
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Affiliation(s)
- David J Charboneau
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Haotian Huang
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Emily L Barth
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Cameron C Germe
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Nilay Hazari
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Brandon Q Mercado
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mycah R Uehling
- Discovery Chemistry, HTE and Lead Discovery Capabilities, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L Zultanski
- Department of Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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50
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Wang Y, Haight I, Gupta R, Vasudevan A. What is in Our Kit? An Analysis of Building Blocks Used in Medicinal Chemistry Parallel Libraries. J Med Chem 2021; 64:17115-17122. [PMID: 34807604 DOI: 10.1021/acs.jmedchem.1c01139] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Building blocks are the molecular foundations for drug molecule design. The building block is one of the determining factors of final compound qualities in any given medicinal chemistry campaign. Herein, we describe our analysis of the building blocks used in parallel library synthesis at AbbVie. The results gave insights into the synthetic tractability and accessibilities of building blocks used in medicinal chemistry. Furthermore, our analysis showed that opportunities still exist for the identification and future incorporation of underrepresented building blocks, even for commonly used reactions, to obtain intellectual and competitive advantages in drug discovery.
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Affiliation(s)
- Ying Wang
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Isabella Haight
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rishi Gupta
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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