| Project/Area Number |
22KF0096
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| Project/Area Number (Other) |
22F22743 (2022)
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| Research Category |
Grant-in-Aid for JSPS Fellows
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| Allocation Type | Multi-year Fund (2023)
Single-year Grants (2022) |
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| Section | 外国 |
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| Review Section |
Basic Section 37030:Chemical biology-related
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| Research Institution | The University of Tokyo |
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Principal Investigator |
菅 裕明 東京大学, 大学院理学系研究科(理学部), 教授 (00361668)
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| Co-Investigator(Kenkyū-buntansha) |
BINDL DANIEL 東京大学, 大学院理学系研究科(理学部), 外国人特別研究員
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| Project Period (FY) |
2023-03-08 – 2025-03-31
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| Project Status |
Granted (Fiscal Year 2023)
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| Budget Amount *help |
¥2,300,000 (Direct Cost: ¥2,300,000)
Fiscal Year 2024: ¥200,000 (Direct Cost: ¥200,000)
Fiscal Year 2023: ¥900,000 (Direct Cost: ¥900,000)
Fiscal Year 2022: ¥1,200,000 (Direct Cost: ¥1,200,000)
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| Keywords | Bioorthogonal chemistry / Cross-coupling chemistry |
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| Outline of Research at the Start |
Model peptide compounds containing suitable functional side chain groups will be synthesized and tested for their bioorthogonal reactivity towards intramolecular amide alkylation. Afterwards, flexizyme catalyzed loading of amino acid analogs bearing these groups onto tRNA and ribosomal in vitro translation will be optimized to enable their usage in RaPID screening for the discovery of novel protein binders.
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| Outline of Annual Research Achievements |
I have been working towards developing a new bioorthogonal intramolecular amide alkylation method for the past year. The goal is to have a reactive amino acid side chain moiety that, upon activation with light or reactants/catalysts, can cyclize onto the neighboring amide nitrogen. Reaction conditions must be bioorthogonal and compatible to be used in in vitro peptide translation and the mRNA display screening platform RaPID. However, despite our extensive efforts, none of the proposed methods have proven successful so far.
Several different approaches were investigated, including photochemical activation of diazirine and fluorenol containing compounds. Furthermore, metal-catalyzed cross-couplings, particularly utilizing Pd0 as well as CuI and CuII containing catalysts, in aqueous conditions were tested. Unfortunately, despite the initial promise and many iterations of these reaction methods, we have not achieved the desired outcome of a bioorthogonal amide alkylation.
Despite these setbacks, I remain hopeful that continued exploration of new reaction mechanisms and synthetic strategies will eventually lead to success in this area. Furthermore, I believe that the knowledge gained from these failed attempts will prove valuable in the development of future chemical biology techniques and applications. Overall, while the search for a new bioorthogonal amide alkylation method has been challenging, I remain committed to advancing the field and developing innovative solutions to this problem.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
In my work on developing a new bioorthogonal intramolecular amide alkylation method, I initially focused on photochemical approaches. However, after discovery unfavorable reactivities, I deemed these methods synthetically and technically too difficult for efficient further investigation and optimization.
As a result, I shifted my attention to metal-catalyzed cross-coupling reactions using different peptides as model compounds. While some progress has been made, achieving selectivity in these reactions is challenging due to the multiple reactive functional groups on peptides.
In some cases, I have observed a small conversion of starting materials to a product with the correct mass of the desired product. However, further investigation and confirmation are necessary to determine whether these products are truly the desired bioorthogonal amide alkylation products or related byproducts.
Despite these challenges, I remain optimistic about the potential of metal-catalyzed cross-coupling reactions for peptide modification. Continued research into reaction conditions, catalyst design, and peptide structure will be crucial for achieving the desired outcomes.
In summary, my current work on developing a new bioorthogonal amide alkylation method has shifted from photochemical approaches to metal-catalyzed cross-coupling reactions using different peptides. While progress has been made, there are still significant challenges to overcome in achieving selectivity and confirming product identity.
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| Strategy for Future Research Activity |
My further research scheme involves optimizing the metal-catalyzed cross-coupling reaction conditions. By in depth screening of the effects of solvent additives, temperature, and other reaction parameters on the metal-catalyzed cross-coupling reaction, I hope to identify the conditions that will lead to the highest yield of the desired bioorthogonal amide alkylation product.
To optimize the reaction conditions, I also plan to explore a range of ligands, some of which are already available in our laboratory, varying in electron-donating and electron-withdrawing groups, as well as bulky and small ligands. By testing a wide variety of ligands, we should be able to identify catalysts capable of achieving a high conversion for the desired reaction.
Once successful conditions are identified, I plan to investigate the compatibility of this method with in vitro ribosomal peptide translation and mRNA display screening. These are important tools for identifying new peptide sequences and structures that are able to bind disease-related biomolecular targets of interest. Therefore, it will be critical to ensure that the metal-catalyzed cross-coupling reactions are compatible with these methods.
By systematically exploring these areas, I hope to develop a practical and effective method for bioorthogonal intramolecular amide alkylation leading to novel peptide drug candidates with favorable pharmacological properties.
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