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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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Tan Y, Fu S, Yang T, Xie Y, Shen G, Yan J, Zhao Y, Ni F. Evaluation of Site-Diversified, Fully Functionalized Diazirine Probes for Chemical Proteomic Applications. Chem Commun (Camb) 2022; 58:9532-9535. [DOI: 10.1039/d2cc03868d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of site-diversified, fully functionalized diazirine probes are constructed based on a scaffold shared by several marketed EGFR-targeted drugs. The integrated analysis of protein targets of site-diversified probe toolkit...
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Korovesis D, Beard HA, Mérillat C, Verhelst SHL. Probes for Photoaffinity Labelling of Kinases. Chembiochem 2021; 22:2206-2218. [PMID: 33544409 DOI: 10.1002/cbic.202000874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/05/2021] [Indexed: 11/06/2022]
Abstract
Protein kinases, one of the largest enzyme superfamilies, regulate many physiological and pathological processes. They are drug targets for multiple human diseases, including various cancer types. Probes for the photoaffinity labelling of kinases are important research tools for the study of members of this enzyme superfamily. In this review, we discuss the design principles of these probes, which are mainly derived from inhibitors targeting the ATP pocket. Overall, insights from crystal structures guide the placement of photoreactive groups and detection tags. This has resulted in a wide variety of probes, of which we provide a comprehensive overview. We also discuss several areas of application of these probes, including the identification of targets and off-targets of kinase inhibitors, mapping of their binding sites, the development of inhibitor screening assays, the imaging of kinases, and identification of protein binding partners.
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Affiliation(s)
- Dimitris Korovesis
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology KU Leuven, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Hester A Beard
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology KU Leuven, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Christel Mérillat
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology KU Leuven, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology KU Leuven, Herestraat 49 box 802, 3000, Leuven, Belgium.,AG Chemical Proteomics, Leibniz Institute for Analytical Sciences ISAS, Otto-Hahn-Strasse 6b, 44227, Dortmund, Germany
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Guo X, Chen X, Cheng Y, Chang X, Li X, Li P. Organocatalytic enantioselective [2 + 4]-annulation of γ-substituted allenoates with N-acyldiazenes for the synthesis of optically active 1,3,4-oxadiazines. Org Biomol Chem 2021; 19:1727-1731. [PMID: 33538742 DOI: 10.1039/d0ob02508a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enantioselective [2 + 4]-annulation of γ-substituted allenoates with N-acyldiazenes has been developed for the first time. In the presence of an l-proline-derived DMAP analogue, the annulation proceeded smoothly to afford a broad range of 1,3,4-oxadiazine derivatives in good to excellent yields with high stereoselectivities.
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Affiliation(s)
- Xing Guo
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China. and Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Xuling Chen
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yuyu Cheng
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Xiaoyong Chang
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Pengfei Li
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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