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Yuen J, Chai J, Ding Y. Condensation of DNA-Conjugated Imines with Homophthalic Anhydride for the Synthesis of Isoquinolones On-DNA. Methods Mol Biol 2022; 2541:75-79. [PMID: 36083547 DOI: 10.1007/978-1-0716-2545-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Condensation of imines with anhydrides has been proven to be a valuable method for the synthesis of tetrahydroisoquinolines. Herein, we describe the application of this chemistry with DNA-conjugated imines. It is proven to be an efficient way to deliver isoquinolone chemotypes for DNA-encoded library.
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Affiliation(s)
- Josephine Yuen
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
| | - Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
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Lenci E, Baldini L, Trabocchi A. Diversity-oriented synthesis as a tool to expand the chemical space of DNA-encoded libraries. Bioorg Med Chem 2021; 41:116218. [PMID: 34030087 DOI: 10.1016/j.bmc.2021.116218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022]
Abstract
DNA-encoded libraries (DEL) represent a powerful technology for generating compound collections for drug discovery campaigns, that have allowed for the selection of many hit compounds over last three decades. However, the application of split-and-pool combinatorial methodologies, as well as the limitation imposed by DNA-compatible chemistry, has often brought to a limited exploration of the chemical space, with an over-representation of flat aromatic or peptide-like structures, whereas a higher scaffold complexity is generally associated with a more successful biological activity of the library. In this context, the application of Diversity-Oriented Synthesis, capable of creating sp3-rich molecular entities even starting from simple flat building blocks, can represent an efficient strategy to significantly broaden the chemical space explored by DELs. In this review, we present selected examples of DNA-compatible complexity-generating reactions that can be applied for the generation of DNA-encoded DOS libraries, including: (i) multicomponent reactions; (ii) C-H/C-X functionalization; (iii) tandem approaches; (iv) cycloadditions; (v) reactions introducing privileged elements. Also, selected case studies on the generation of DELs with high scaffold diversity are discussed, reporting their application in drug discovery programs.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Baldini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy; Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM), University of Florence, Viale Morgagni 85, 50134 Florence, Italy.
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Yuen J, Chai J, Ding Y. Condensation of DNA-Conjugated Imines with Homophthalic Anhydride for the Synthesis of Isoquinolones on DNA. Bioconjug Chem 2020; 31:2712-2718. [DOI: 10.1021/acs.bioconjchem.0c00508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Josephine Yuen
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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Floyd DM, Stein P, Wang Z, Liu J, Castro S, Clark JA, Connelly M, Zhu F, Holbrook G, Matheny A, Sigal MS, Min J, Dhinakaran R, Krishnan S, Bashyum S, Knapp S, Guy RK. Hit-to-Lead Studies for the Antimalarial Tetrahydroisoquinolone Carboxanilides. J Med Chem 2016; 59:7950-62. [PMID: 27505686 DOI: 10.1021/acs.jmedchem.6b00752] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenotypic whole-cell screening in erythrocytic cocultures of Plasmodium falciparum identified a series of dihydroisoquinolones that possessed potent antimalarial activity against multiple resistant strains of P. falciparum in vitro and show no cytotoxicity to mammalian cells. Systematic structure-activity studies revealed relationships between potency and modifications at N-2, C-3, and C-4. Careful structure-property relationship studies, coupled with studies of metabolism, addressed the poor aqueous solubility and metabolic vulnerability, as well as potential toxicological effects, inherent in the more potent primary screening hits such as 10b. Analogues 13h and 13i, with structural modifications at each site, were shown to possess excellent antimalarial activity in vivo. The (+)-(3S,4S) enantiomer of 13i and similar analogues were identified as the more potent. On the basis of these studies, we have selected (+)-13i for further study as a preclinical candidate.
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Affiliation(s)
- David M Floyd
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - Philip Stein
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - Zheng Wang
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - Jian Liu
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - Steve Castro
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - Julie A Clark
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Michele Connelly
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Fangyi Zhu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Gloria Holbrook
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Amy Matheny
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Martina S Sigal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
| | - Rajkumar Dhinakaran
- Syngene International Ltd. , Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India 560 099
| | - Senthil Krishnan
- Syngene International Ltd. , Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India 560 099
| | - Sridevi Bashyum
- Syngene International Ltd. , Plot No. 2 & 3, Bommasandra IV Phase, Jigani Link Road, Bangalore, India 560 099
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey , 610 Taylor Road, Piscataway, New Jersey 08854 United States
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105 United States
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