1
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Dey J, Kaltenberger S, van Gemmeren M. Palladium(II)-Catalyzed Nondirected Late-Stage C(sp 2)-H Deuteration of Heteroarenes Enabled Through a Multi-Substrate Screening Approach. Angew Chem Int Ed Engl 2024; 63:e202404421. [PMID: 38512005 DOI: 10.1002/anie.202404421] [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: 03/04/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
The importance of deuterium labelling in a variety of applications, ranging from mechanistic studies to drug-discovery, has spurred immense interest in the development of new methods for its efficient incorporation in organic, and especially in bioactive molecules. The five-membered heteroarenes at the center of this work are ubiquitous motifs in bioactive molecules and efficient methods for the deuterium labelling of these compounds are therefore highly desirable. However, the profound differences in chemical properties encountered between different heteroarenes hamper the development of a single set of broadly applicable reaction conditions, often necessitating a separate optimization campaign for a given type of heteroarene. In this study we describe the use of a multi-substrate screening approach to identify optimal reaction conditions for different classes of heteroarenes from a minimal number of screening reactions. Using this approach, four sets of complementary reaction conditions derived from our dual ligand-based palladium catalysts for nondirected C(sp2)-H activation were identified, that together enable the deuteration of structurally diverse heteroarenes, including bioactive molecules.
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Affiliation(s)
- Jyotirmoy Dey
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Otto-Hahn-Platz 4, 24098, Kiel, Germany
| | - Simon Kaltenberger
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Otto-Hahn-Platz 4, 24098, Kiel, Germany
| | - Manuel van Gemmeren
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Otto-Hahn-Platz 4, 24098, Kiel, Germany
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2
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Wang Y, Bi C, Kawamata Y, Grant LN, Samp L, Richardson PF, Zhang S, Harper KC, Palkowitz MD, Vasilopoulos A, Collins MR, Oderinde MS, Tyrol CC, Chen D, LaChapelle EA, Bailey JB, Qiao JX, Baran PS. Discovery of N-X anomeric amides as electrophilic halogenation reagents. Nat Chem 2024:10.1038/s41557-024-01539-4. [PMID: 38769366 DOI: 10.1038/s41557-024-01539-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Electrophilic halogenation is a widely used tool employed by medicinal chemists to either pre-functionalize molecules for further diversity or incorporate a halogen atom into drugs or drug-like compounds to solve metabolic problems or modulate off-target effects. Current methods to increase the power of halogenation rely on either the invention of new reagents or activating commercially available reagents with various additives such as Lewis or Brønsted acids, Lewis bases and hydrogen-bonding activators. There is a high demand for new reagents that can halogenate otherwise unreactive compounds under mild conditions. Here we report the invention of a class of halogenating reagents based on anomeric amides, taking advantage of the energy stored in the pyramidalized nitrogen of N-X anomeric amides as a driving force. These robust halogenating methods are compatible with a variety of functional groups and heterocycles, as exemplified on over 50 compounds (including 13 gram-scale examples and 1 flow chemistry scale-up).
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Affiliation(s)
- Yu Wang
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Cheng Bi
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Yu Kawamata
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Lauren N Grant
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Lacey Samp
- Chemical Research and Development, Pfizer Inc., Groton, CT, USA
| | - Paul F Richardson
- Oncology Medicinal Chemistry Department, Pfizer Medicine Design, San Diego, CA, USA
| | - Shasha Zhang
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Kaid C Harper
- AbbVie Process Research and Development, North Chicago, IL, USA
| | | | | | - Michael R Collins
- Oncology Medicinal Chemistry Department, Pfizer Medicine Design, San Diego, CA, USA
| | - Martins S Oderinde
- Small Molecule Discovery Chemistry, Bristol Myers Squibb Research and Early Development, Princeton, NJ, USA
| | | | - Doris Chen
- Oncology Medicinal Chemistry Department, Pfizer Medicine Design, San Diego, CA, USA
| | | | - Jake B Bailey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer X Qiao
- Small Molecule Drug Discovery, Bristol Myers Squibb, Cambridge, MA, USA
| | - Phil S Baran
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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3
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Kriegelstein M, Nováková G, Marek A. Synthesis of [ 3 H]Org24598 using in-house prepared [ 3 H]MeI. J Labelled Comp Radiopharm 2024; 67:91-103. [PMID: 38221662 DOI: 10.1002/jlcr.4084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
The synthesis of tritium-labelled glycine transporter 1 inhibitor Org24598 is reported. Because of the instability of the Org24598 skeleton under hydrogenation conditions, a synthetic approach using an in-house prepared tritium-labelled alkylating agent ([3 H]MeI, SA = 26.2 Ci/mmol) was employed. Alternative methods of labelling are discussed.
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Affiliation(s)
- Michal Kriegelstein
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
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4
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King-Smith E, Faber FA, Reilly U, Sinitskiy AV, Yang Q, Liu B, Hyek D, Lee AA. Predictive Minisci late stage functionalization with transfer learning. Nat Commun 2024; 15:426. [PMID: 38225239 PMCID: PMC10789750 DOI: 10.1038/s41467-023-42145-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/01/2023] [Indexed: 01/17/2024] Open
Abstract
Structural diversification of lead molecules is a key component of drug discovery to explore chemical space. Late-stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity of LSF is still an open challenge in the field. Numerous efforts from chemoinformatics and machine learning (ML) groups have made strides in this area. However, it is arduous to isolate and characterize the multitude of LSF products generated, limiting available data and hindering pure ML approaches. We report the development of an approach that combines a message passing neural network and 13C NMR-based transfer learning to predict the atom-wise probabilities of functionalization for Minisci and P450-based functionalizations. We validated our model both retrospectively and with a series of prospective experiments, showing that it accurately predicts the outcomes of Minisci-type and P450 transformations and outperforms the well-established Fukui-based reactivity indices and other machine learning reactivity-based algorithms.
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Affiliation(s)
- Emma King-Smith
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Felix A Faber
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Usa Reilly
- Development & Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Anton V Sinitskiy
- Machine Learning Computational Sciences, Pfizer Worldwide Research, Cambridge, MA, USA
| | - Qingyi Yang
- Development & Medical, Pfizer Worldwide Research, Cambridge, MA, USA
| | - Bo Liu
- Spectrix Analytic Services, LLC., North Haven, CT, USA
| | - Dennis Hyek
- Spectrix Analytic Services, LLC., North Haven, CT, USA
| | - Alpha A Lee
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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5
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Chiodi D, Ishihara Y. "Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery. J Med Chem 2023; 66:5305-5331. [PMID: 37014977 DOI: 10.1021/acs.jmedchem.2c02015] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, California 92121, United States
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6
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Mahía A, Peña-Díaz S, Navarro S, José Galano-Frutos J, Pallarés I, Pujols J, Díaz-de-Villegas MD, Gálvez JA, Ventura S, Sancho J. Design, synthesis and structure-activity evaluation of novel 2-pyridone-based inhibitors of α-synuclein aggregation with potentially improved BBB permeability. Bioorg Chem 2021; 117:105472. [PMID: 34775206 DOI: 10.1016/j.bioorg.2021.105472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/20/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023]
Abstract
The treatment of Parkinson's disease (PD), the second most common neurodegenerative human disorder, continues to be symptomatic. Development of drugs able to stop or at least slowdown PD progression would benefit several million people worldwide. SynuClean-D is a low molecular weight 2-pyridone-based promising drug candidate that inhibits the aggregation of α-synuclein in human cultured cells and prevents degeneration of dopaminergic neurons in a Caenorhabditis elegans model of PD. Improving SynuClean-D pharmacokinetic/pharmacodynamic properties, performing structure/activity studies and testing its efficacy in mammalian models of PD requires the use of gr-amounts of the compound. However, not enough compound is on sale, and no synthetic route has been reported until now, which hampers the molecule progress towards clinical trials. To circumvent those problems, we describe here an efficient and economical route that enables the synthesis of SynuClean-D with good yields as well as the synthesis of SynuClean-D derivatives. Structure-activity comparison of the new compounds with SynuClean-D reveals the functional groups of the molecule that can be disposed of without activity loss and those that are crucial to interfere with α-synuclein aggregation. Several of the derivatives obtained retain the parent's compound excellent in vitro anti-aggregative activity, without compromising its low toxicity. Computational predictions and preliminary testing indicate that the blood brain barrier (BBB) permeability of SynuClean-D is low. Importantly, several of the newly designed and obtained active derivatives are predicted to display good BBB permeability. The synthetic route developed here will facilitate their synthesis for BBB permeability determination and for efficacy testing in mammalian models of PD.
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Affiliation(s)
- Alejandro Mahía
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Samuel Peña-Díaz
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Susanna Navarro
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Juan José Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain
| | - Irantzu Pallarés
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi Pujols
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - María D Díaz-de-Villegas
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-University of Zaragoza, 50009 Zaragoza, Spain
| | - José A Gálvez
- Departamento de Química Orgánica, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-University of Zaragoza, 50009 Zaragoza, Spain.
| | - Salvador Ventura
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; ICREA, 08010 Barcelona, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, 50009 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain.
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7
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Menard T, Laverny A, Denmark SE. Synthesis of Enantioenriched 3,4-Disubstituted Chromans through Lewis Base Catalyzed Carbosulfenylation. J Org Chem 2021; 86:14290-14310. [PMID: 34672591 DOI: 10.1021/acs.joc.1c02290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method for the catalytic, enantioselective, carbosulfenylation of alkenes to construct 3,4-disubstituted chromans is described. Alkene activation proceeds through the intermediacy of enantioenriched, configurationally stable thiiranium ions generated from catalytic, Lewis base activation of an electrophilic sulfenylating agent. The transformation affords difficult-to-generate, enantioenriched, 3,4-disubstituted chromans in moderate to high yields and excellent enantioselectivities. A variety of substituents are compatible including electronically diverse functional groups as well as several functional handles such as aryl halides, esters, anilines, and phenols. The resulting thioether moiety is amenable to a number of functional group manipulations and transformations. Notably, the pendant sulfide was successfully cleaved to furnish a free thiol which readily provides access to most sulfur-containing functional groups which are present in natural products and pharmaceuticals.
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Affiliation(s)
- Travis Menard
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Aragorn Laverny
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
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8
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Ree N, Göller AH, Jensen JH. RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions. J Cheminform 2021; 13:10. [PMID: 33579374 PMCID: PMC7881568 DOI: 10.1186/s13321-021-00490-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/27/2021] [Indexed: 01/01/2023] Open
Abstract
We present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. The following improvements have been made: The open source semiempirical tight binding program xtb is used instead of the closed source MOPAC program. Any low energy tautomeric forms of the input molecule are identified and regioselectivity predictions are made for each form. Finally, RegioSQM20 offers a qualitative prediction of the reactivity of each tautomer (low, medium, or high) based on the reaction center with the highest proton affinity. The inclusion of tautomers increases the success rate from 90.7 to 92.7%. RegioSQM20 is compared to two machine learning based models: one developed by Struble et al. (React Chem Eng 5:896, 2020) specifically for regioselectivity predictions of EAS reactions (WLN) and a more generally applicable reactivity predictor (IBM RXN) developed by Schwaller et al. (ACS Cent Sci 5:1572, 2019). RegioSQM20 and WLN offers roughly the same success rates for the entire data sets (without considering tautomers), while WLN is many orders of magnitude faster. The accuracy of the more general IBM RXN approach is somewhat lower: 76.3-85.0%, depending on the data set. The code is freely available under the MIT open source license and will be made available as a webservice (regiosqm.org) in the near future.
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Affiliation(s)
- Nicolai Ree
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Andreas H Göller
- Bayer AG, Pharmaceuticals, R&D, Computational Molecular Design, 42096, Wuppertal, Germany.
| | - Jan H Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
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9
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Struble TJ, Coley CW, Jensen KF. Multitask prediction of site selectivity in aromatic C–H functionalization reactions. REACT CHEM ENG 2020. [DOI: 10.1039/d0re00071j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aromatic C–H functionalization reactions are an important part of the synthetic chemistry toolbox.
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Affiliation(s)
- Thomas J. Struble
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- USA
| | - Connor W. Coley
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- USA
| | - Klavs F. Jensen
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- USA
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10
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Secrieru A, O’Neill PM, Cristiano MLS. Revisiting the Structure and Chemistry of 3(5)-Substituted Pyrazoles. Molecules 2019; 25:molecules25010042. [PMID: 31877672 PMCID: PMC6982847 DOI: 10.3390/molecules25010042] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
Pyrazoles are known as versatile scaffolds in organic synthesis and medicinal chemistry, often used as starting materials for the preparation of more complex heterocyclic systems with relevance in the pharmaceutical field. Pyrazoles are also interesting compounds from a structural viewpoint, mainly because they exhibit tautomerism. This phenomenon may influence their reactivity, with possible impact on the synthetic strategies where pyrazoles take part, as well as on the biological activities of targets bearing a pyrazole moiety, since a change in structure translates into changes in properties. Investigations of the structure of pyrazoles that unravel the tautomeric and conformational preferences are therefore of upmost relevance. 3(5)-Aminopyrazoles are largely explored as precursors in the synthesis of condensed heterocyclic systems, namely pyrazolo[1,5-a]pyrimidines. However, the information available in the literature concerning the structure and chemistry of 3(5)-aminopyrazoles is scarce and disperse. We provide a revision of data on the present subject, based on investigations using theoretical and experimental methods, together with the applications of the compounds in synthesis. It is expected that the combined information will contribute to a deeper understanding of structure/reactivity relationships in this class of heterocycles, with a positive impact in the design of synthetic methods, where they take part.
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Affiliation(s)
- Alina Secrieru
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal;
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK;
- Department of Chemistry and Pharmacy, Faculty of Sciences and Technology, FCT, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal
| | | | - Maria Lurdes Santos Cristiano
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal;
- Department of Chemistry and Pharmacy, Faculty of Sciences and Technology, FCT, Gambelas Campus, University of Algarve, UAlg, 8005-139 Faro, Portugal
- Correspondence: ; Tel.: +351-289-800-953
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11
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Li Q, Li C, Kim J, Ishida M, Li X, Gu T, Liang X, Zhu W, Ågren H, Kim D, Furuta H, Xie Y. Regioselectively Halogenated Expanded Porphyrinoids as Building Blocks for Constructing Porphyrin–Porphyrinoid Heterodyads with Tunable Energy Transfer. J Am Chem Soc 2019; 141:5294-5302. [DOI: 10.1021/jacs.8b13148] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qizhao Li
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Chengjie Li
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jinseok Kim
- Department of Chemistry and Spectroscopy Laboratory for Functional π-Electronic Systems, Yonsei University, Seoul 03722, Korea
| | - Masatoshi Ishida
- Department of Chemistry and Biochemistry, Graduate School of Engineering and Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Xin Li
- School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Tingting Gu
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xu Liang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Weihua Zhu
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Hans Ågren
- School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Dongho Kim
- Department of Chemistry and Spectroscopy Laboratory for Functional π-Electronic Systems, Yonsei University, Seoul 03722, Korea
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry, Graduate School of Engineering and Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
| | - Yongshu Xie
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
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12
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Zhao K, Niu W, Wang Y, Zhang S. Electrophilic substitution reaction as a facile and general approach for reactive removal of native ligands from nanocrystals surface. NANOTECHNOLOGY 2019; 30:015701. [PMID: 30359328 DOI: 10.1088/1361-6528/aae682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface property that strongly affects physical and chemical performances of inorganic nanocrystals (NCs) is a key enabler for NCs applications. Here, we report a facile, versatile and general strategy for reactive removal of NCs surface ligands based on electrophilic substitution reaction, in which an electrophile directly reacts with the electron-rich coordinating headgroup of surface-tethered ligands to form a non-coordinating product. This process leads to the break of NC-ligand bond, thereby achieving reactive removal of surface ligands. Based on this strategy, various hydrophobic NCs with different compositions and morphologies can be transferred into polar and hydrophilic media while preserving their size and shape. More importantly, the treated NCs present a great improvement in catalytic and biological performances in comparison with the untreated counterparts. This work not only provides a versatile ligand removal strategy for NCs surface modification but also opens up more opportunities for applications in the fields of electronics, catalysis and biotechnology.
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Affiliation(s)
- Kai Zhao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, People's Republic of China
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13
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Mirzaei S, Khosravi H. Predicting the regioselectivity of arynes: a simple model based on orbital electronegativity. NEW J CHEM 2019. [DOI: 10.1039/c8nj04027c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple model based on orbital electronegativity to predict the regioselectivity of arynes is reported; the nucleophiles attack the terminus possessing lower OE.
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Affiliation(s)
- Saber Mirzaei
- Department of Chemistry
- Marquette University
- Milwaukee
- USA
| | - Hormoz Khosravi
- Faculty of Chemistry
- K. N. Toosi University of Technology
- Tehran
- Iran
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14
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Tomberg A, Johansson MJ, Norrby PO. A Predictive Tool for Electrophilic Aromatic Substitutions Using Machine Learning. J Org Chem 2018; 84:4695-4703. [PMID: 30336024 DOI: 10.1021/acs.joc.8b02270] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At the early stages of the drug development process, thousands of compounds are synthesized in order to attain the best possible potency and pharmacokinetic properties. Once successful scaffolds are identified, large libraries of analogues are made, which is a challenging and time-consuming task. Recently, late stage functionalization (LSF) has become increasingly prominent since these reactions selectively functionalize C-H bonds, allowing to quickly produce analogues. Classical electrophilic aromatic halogenations are a powerful type of reaction in the LSF toolkit. However, the introduction of an electrophile in a regioselective manner on a drug-like molecule is a challenging task. Herein we present a machine learning model able to predict the reactive site of an electrophilic aromatic substitution with an accuracy of 93% (internal validation set). The model takes as input a SMILES of a compound and uses six quantum mechanics descriptors to identify its reactive site(s). On an external validation set, 90% of all molecules were correctly predicted.
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Smith JM, Dixon JA, deGruyter JN, Baran PS. Alkyl Sulfinates: Radical Precursors Enabling Drug Discovery. J Med Chem 2018; 62:2256-2264. [DOI: 10.1021/acs.jmedchem.8b01303] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Joel M. Smith
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 93037, United States
| | - Janice A. Dixon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 93037, United States
| | - Justine N. deGruyter
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 93037, United States
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 93037, United States
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Kromann JC, Jensen JH, Kruszyk M, Jessing M, Jørgensen M. Fast and accurate prediction of the regioselectivity of electrophilic aromatic substitution reactions. Chem Sci 2018; 9:660-665. [PMID: 29629133 PMCID: PMC5869546 DOI: 10.1039/c7sc04156j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
While computational prediction of chemical reactivity is possible it usually requires expert knowledge and there are relatively few computational tools that can be used by a bench chemist to help guide synthesis. The RegioSQM method for predicting the regioselectivity of electrophilic aromatic substitution reactions of heteroaromatic systems is presented in this paper. RegioSQM protonates all aromatic C-H carbon atoms and identifies those with the lowest free energies in chloroform using the PM3 semiempirical method as the most nucleophilic center. These positions are found to correlate qualitatively with the regiochemical outcome in a retrospective analysis of 96% of more than 525 literature examples of electrophilic aromatic halogenation reactions. The method is automated and requires only a SMILES string of the molecule of interest, which can easily be generated using chemical drawing programs such as ChemDraw. The computational cost is 1-10 minutes per molecule depending on size, using relatively modest computational resources and the method is freely available via a web server at ; http://www.regiosqm.org. RegioSQM should therefore be of practical use in the planning of organic synthesis.
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Affiliation(s)
- Jimmy C Kromann
- Department of Chemistry , University of Copenhagen , Copenhagen , Denmark . ; http://www.twitter.com/janhjensen
| | - Jan H Jensen
- Department of Chemistry , University of Copenhagen , Copenhagen , Denmark . ; http://www.twitter.com/janhjensen
| | - Monika Kruszyk
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
- Department of Drug Design and Pharmacology , University of Copenhagen , Copenhagen , Denmark
| | - Mikkel Jessing
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
| | - Morten Jørgensen
- Discovery Chemistry , DMPK , Neuroscience Drug Discovery , H. Lundbeck A/S, Valby , Denmark .
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Fan Z, Li J, Lu H, Wang DY, Wang C, Uchiyama M, Zhang A. Monomeric Octahedral Ruthenium(II) Complex Enabled meta-C–H Nitration of Arenes with Removable Auxiliaries. Org Lett 2017; 19:3199-3202. [DOI: 10.1021/acs.orglett.7b01297] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhoulong Fan
- CAS
Key Laboratory of Receptor Research and the State Key Laboratory of
Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- ShanghaiTech University, Shanghai 201210, China
| | - Heng Lu
- ShanghaiTech University, Shanghai 201210, China
| | - Dong-Yu Wang
- CAS
Key Laboratory of Receptor Research and the State Key Laboratory of
Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China
| | - Chao Wang
- Graduate
School of Pharmaceutical Sciences, University of Tokyo, Tokyo-to 113-0033, Japan
- Advanced
Elements Chemistry Research Team, RIKEN Center for Sustainable Resource Science and Elements Chemistry Laboratory, Saitama-ken 351-0198, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, University of Tokyo, Tokyo-to 113-0033, Japan
- Advanced
Elements Chemistry Research Team, RIKEN Center for Sustainable Resource Science and Elements Chemistry Laboratory, Saitama-ken 351-0198, Japan
| | - Ao Zhang
- CAS
Key Laboratory of Receptor Research and the State Key Laboratory of
Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- ShanghaiTech University, Shanghai 201210, China
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