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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Prange CJ, Hu X, Tang L. Smart chemistry for traceless release of anticancer therapeutics. Biomaterials 2023; 303:122353. [PMID: 37925794 DOI: 10.1016/j.biomaterials.2023.122353] [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: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
In the design of delivery strategies for anticancer therapeutics, the controlled release of intact cargo at the destined tumor and metastasis locations is of particular importance. To this end, stimuli-responsive chemical linkers have been extensively investigated owing to their ability to respond to tumor-specific physiological stimuli, such as lowered pH, altered redox conditions, increased radical oxygen species and pathological enzymatic activities. To prevent premature action and off-target effects, anticancer therapeutics are chemically modified to be transiently inactivated, a strategy known as prodrug development. Prodrugs are reactivated upon stimuli-dependent release at the sites of interest. As most drugs and therapeutic proteins have the optimal activity when released from carriers in their native and original forms, traceless release mechanisms are increasingly investigated. In this review, we summarize the chemical toolkit for developing innovative traceless prodrug strategies for stimuli-responsive drug delivery and discuss the applications of these chemical modifications in anticancer treatment including cancer immunotherapy.
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Affiliation(s)
- Céline Jasmin Prange
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland; Institute of Chemical Sciences and Engineering, EPFL, Lausanne, CH-1015, Switzerland
| | - Xile Hu
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, CH-1015, Switzerland.
| | - Li Tang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland; Institute of Materials Science & Engineering, EPFL, Lausanne, CH-1015, Switzerland.
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McFeely CAL, Shakya B, Makovsky CA, Haney AK, Ashton Cropp T, Hartman MCT. Extensive breaking of genetic code degeneracy with non-canonical amino acids. Nat Commun 2023; 14:5008. [PMID: 37591858 PMCID: PMC10435567 DOI: 10.1038/s41467-023-40529-x] [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: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic code expansion (GCE) offers many exciting opportunities for the creation of synthetic organisms and for drug discovery methods that utilize in vitro translation. One type of GCE, sense codon reassignment (SCR), focuses on breaking the degeneracy of the 61 sense codons which encode for only 20 amino acids. SCR has great potential for genetic code expansion, but extensive SCR is limited by the post-transcriptional modifications on tRNAs and wobble reading of these tRNAs by the ribosome. To better understand codon-tRNA pairing, here we develop an assay to evaluate the ability of aminoacyl-tRNAs to compete with each other for a given codon. We then show that hyperaccurate ribosome mutants demonstrate reduced wobble reading, and when paired with unmodified tRNAs lead to extensive and predictable SCR. Together, we encode seven distinct amino acids across nine codons spanning just two codon boxes, thereby demonstrating that the genetic code hosts far more re-assignable space than previously expected, opening the door to extensive genetic code engineering.
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Affiliation(s)
- Clinton A L McFeely
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Chelsea A Makovsky
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Aidan K Haney
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA.
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Zhang C, Talukder P, Dedkova LM, Hecht SM. Facilitated synthesis of proteins containing modified dipeptides. Bioorg Med Chem 2021; 41:116210. [PMID: 34022527 DOI: 10.1016/j.bmc.2021.116210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
The elaboration of peptides and proteins containing non-proteinogenic amino acids has been realized using several complementary strategies, including chemical synthesis, ribosome- or non-ribosome-mediated elaboration, intein-mediated polypeptide rearrangements, or some combination of these strategies. All of these have strengths and limitations, and significant efforts have been focused on minimizing the effects of limitations, to improve the overall utility of individual strategies. Our laboratory has studied ribosomally mediated peptide and protein synthesis involving a wide variety of non-proteinogenic amino acids, and in recent years we have described a novel strategy for the selection of modified bacterial ribosomes. These modified ribosomes have enabled the incorporation into peptides and proteins of numerous modified amino acids not accessible using wild-type ribosomes. This has included d-amino acids, β-amino acids, dipeptides and dipeptidomimetic species, as well as phosphorylated amino acids. Presently, we have considered novel strategies for incorporating non-proteinogenic amino acids in improved yields. This has included the incorporation of non-proteinogenic amino acids into contiguous positions, a transformation known to be challenging. We demonstrate the preparation of this type of protein modification by utilizing a suppressor tRNACUA activated with a dipeptide consisting of two identical non-proteinogenic amino acids, in the presence of modified ribosomes selected to recognize such dipeptides. Also, we demonstrate that the use of bis-aminoacylated suppressor tRNAs, shown previously to increase protein yields significantly in vitro, can be extended to the use of non-proteinogenic amino acids.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
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Evolution of KIPPIS as a versatile platform for evaluating intracellularly functional peptide aptamers. Sci Rep 2021; 11:11758. [PMID: 34083659 PMCID: PMC8175380 DOI: 10.1038/s41598-021-91287-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/18/2021] [Indexed: 11/18/2022] Open
Abstract
Chimeric proteins have been widely used to evaluate intracellular protein–protein interactions (PPIs) in living cells with various readouts. By combining an interleukin-3-dependent murine cells and chimeric proteins containing a receptor tyrosine kinase c-kit, we previously established a c-kit-based PPI screening (KIPPIS) system to evaluate and select protein binders. In the KIPPIS components, proteins of interest are connected with a chemically inducible helper module and the intracellular domain of the growth-signaling receptor c-kit, which detects PPIs based on cell proliferation as a readout. In this system, proteins of interest can be incorporated into chimeric proteins without any scaffold proteins, which would be advantageous for evaluating interaction between small peptides/domains. To prove this superiority, we apply KIPPIS to 6 peptide aptamer–polypeptide pairs, which are derived from endogenous, synthetic, and viral proteins. Consequently, all of the 6 peptide aptamer–polypeptide interactions are successfully detected by cell proliferation. The detection sensitivity can be modulated in a helper ligand-dependent manner. The assay results of KIPPIS correlate with the activation levels of Src, which is located downstream of c-kit-mediated signal transduction. Control experiments reveal that KIPPIS clearly discriminates interacting aptamers from non-interacting ones. Thus, KIPPIS proves to be a versatile platform for evaluating the binding properties of peptide aptamers.
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Liljeruhm J, Wang J, Kwiatkowski M, Sabari S, Forster AC. Kinetics of d-Amino Acid Incorporation in Translation. ACS Chem Biol 2019; 14:204-213. [PMID: 30648860 DOI: 10.1021/acschembio.8b00952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the stereospecificity of translation for l-amino acids (l-AAs) in vivo, synthetic biologists have enabled ribosomal incorporation of d-AAs in vitro toward encoding polypeptides with pharmacologically desirable properties. However, the steps in translation limiting d-AA incorporation need clarification. In this work, we compared d- and l-Phe incorporation in translation by quench-flow kinetics, measuring 250-fold slower incorporation into the dipeptide for the d isomer from a tRNAPhe-based adaptor (tRNAPheB). Incorporation was moderately hastened by tRNA body swaps and higher EF-Tu concentrations, indicating that binding by EF-Tu can be rate-limiting. However, from tRNAAlaB with a saturating concentration of EF-Tu, the slow d-Phe incorporation was unexpectedly very efficient in competition with incorporation of the l isomer, indicating fast binding to EF-Tu, fast binding of the resulting complex to the ribosome, and rate-limiting accommodation/peptide bond formation. Subsequent elongation with an l-AA was confirmed to be very slow and inefficient. This understanding helps rationalize incorporation efficiencies in vitro and stereospecific mechanisms in vivo and suggests approaches for improving incorporation.
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Affiliation(s)
- Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Samudra Sabari
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
| | - Anthony C. Forster
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 751 24 Uppsala, Sweden
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