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Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
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Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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Gruber F, McDonagh AW, Rose V, Hunter J, Guasch L, Martin RE, Geigle SN, Britton R. sp 3 -Rich Heterocycle Synthesis on DNA: Application to DNA-Encoded Library Production. Angew Chem Int Ed Engl 2024; 63:e202319836. [PMID: 38330151 DOI: 10.1002/anie.202319836] [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: 12/21/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
DNA encoded library (DEL) synthesis represents a convenient means to produce, annotate and store large collections of compounds in a small volume. While DELs are well suited for drug discovery campaigns, the chemistry used in their production must be compatible with the DNA tag, which can limit compound class accessibility. As a result, most DELs are heavily populated with peptidomimetic and sp2 -rich molecules. Herein, we show that sp3 -rich mono- and bicyclic heterocycles can be made on DNA from ketochlorohydrin aldol products through a reductive amination and cyclization process. The resulting hydroxypyrrolidines possess structural features that are desirable for DELs and target a distinct region of pharmaceutically relevant chemical space.
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Affiliation(s)
- Felix Gruber
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Anthony W McDonagh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Victoria Rose
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - James Hunter
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Laura Guasch
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Stefanie N Geigle
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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Willems S, Detta E, Baldini L, Tietz D, Trabocchi A, Brunschweiger A. Diversifying DNA-Tagged Amines by Isocyanide Multicomponent Reactions for DNA-Encoded Library Synthesis. ACS OMEGA 2024; 9:7719-7724. [PMID: 38405463 PMCID: PMC10882610 DOI: 10.1021/acsomega.3c07136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 02/27/2024]
Abstract
In DNA-encoded library synthesis, amine-substituted building blocks are prevalent. We explored isocyanide multicomponent reactions to diversify DNA-tagged amines and reported the Ugi-azide reaction with high yields and a good substrate scope. In addition, the Ugi-aza-Wittig reaction and the Ugi-4-center-3-component reaction, which used bifunctional carboxylic acids to provide lactams, were explored. Five-, six-, and seven-membered lactams were synthesized from solid support-coupled DNA-tagged amines and bifunctional building blocks, providing access to structurally diverse scaffolds.
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Affiliation(s)
- Suzanne Willems
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Elena Detta
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Lorenzo Baldini
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Deniz Tietz
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Andreas Brunschweiger
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
- Institute
of Pharmacy and Food Chemistry, Julius Maximilian
University Würzburg, Am Hubland, 97074 Würzburg, Germany
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An Y, Lee J, Seo H, Bae S, Kang J, Lee J, Kim J, Nam MH, Song M, Hwang GT. Groebke-Blackburn-Bienaymé Reaction for DNA-Encoded Library Technology. Org Lett 2023; 25:4445-4450. [PMID: 37310879 DOI: 10.1021/acs.orglett.3c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study presents a DNA-compatible synthesis of diverse 5-arylimidazo[1,2-a]pyridin-3-amine derivatives using the Suzuki-Miyaura reaction, followed by a Groebke-Blackburn-Bienaymé (GBB) reaction. The GBB reaction demonstrates a wide substrate scope, mild one-pot reaction conditions, and compatibility with subsequent enzymatic ligation, highlighting its potential in DNA-encoded library technology.
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Affiliation(s)
- Yujin An
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Juyeon Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyewon Seo
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Seri Bae
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jihee Kang
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jieon Lee
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jinwoo Kim
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
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Wang Y, Fang X, Liao H, Zhang G, Li Y, Li Y. DNA-Compatible Synthesis of Thiazolidione Derivatives via Three-Component Annulation and Knoevenagel Condensation. Org Lett 2023; 25:4473-4477. [PMID: 37306473 DOI: 10.1021/acs.orglett.3c01482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Thiazolidione, conferring drug-like properties, is an important heterocycle that widely exists in medicinally relevant molecules. In this work, by efficiently assembling various DNA-tagged primary amines, abundant aryl isothiocyanates, and ethyl bromoacetate, we present a DNA-compatible three-component annulation to generate a 2-iminothiazolidin-4-one scaffold, which was further decorated via Knoevenagel condensation by employing (hetero)aryl and alkyl aldehydes. These thiazolidione derivatives should find broad use in focused DNA-encoded library construction.
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Affiliation(s)
- Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Huilin Liao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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