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Al-Amin RA, Johansson L, Abdurakhmanov E, Landegren N, Löf L, Arngården L, Blokzijl A, Svensson R, Hammond M, Lönn P, Haybaeck J, Kamali-Moghaddam M, Jensen A, Danielson U, Artursson P, Lundbäck T, Landegren U. Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ. Nucleic Acids Res 2022; 50:e129. [PMID: 36189884 PMCID: PMC9825164 DOI: 10.1093/nar/gkac842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/29/2023] Open
Abstract
Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and in tissues.
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Affiliation(s)
- Rasel A Al-Amin
- To whom correspondence should be addressed. Tel: +46 70 0535324;
| | - Lars Johansson
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nils Landegren
- Center for Molecular Medicine, Department of Medicine (Solna), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Liza Löf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andries Blokzijl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annika Jenmalm Jensen
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Lundbäck
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Ulf Landegren
- Correspondence may also be addressed to Ulf Landegren. Tel: +46 18 4714910; Fax: +46 18 4714808;
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