1
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Schröder MP, Pfeiffer IPM, Mordhorst S. Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry. Beilstein J Org Chem 2024; 20:1652-1670. [PMID: 39076295 PMCID: PMC11285071 DOI: 10.3762/bjoc.20.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
This review article aims to highlight the role of methyltransferases within the context of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Methyltransferases play a pivotal role in the biosynthesis of diverse natural products with unique chemical structures and bioactivities. They are highly chemo-, regio-, and stereoselective allowing methylation at various positions. The different possible acceptor regions in ribosomally synthesised peptides are described in this article. Furthermore, we will discuss the potential application of these methyltransferases as powerful biocatalytic tools in the synthesis of modified peptides and other bioactive compounds. By providing an overview of the various methylation options available, this review is intended to emphasise the biocatalytic potential of RiPP methyltransferases and their impact on the field of natural product chemistry.
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Affiliation(s)
- Maria-Paula Schröder
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Isabel P-M Pfeiffer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Silja Mordhorst
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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2
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Zhang C, Chen S, Fu X, Dedkova LM, Hecht SM. Enhancement of N-Methyl Amino Acid Incorporation into Proteins and Peptides Using Modified Bacterial Ribosomes and Elongation Factor P. ACS Chem Biol 2024; 19:1330-1338. [PMID: 38769080 DOI: 10.1021/acschembio.4c00165] [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: 05/22/2024]
Abstract
N-Methylated amino acids are constituents of natural bioactive peptides and proteins. Nα-methylated amino acids appear abundantly in natural cyclic peptides, likely due to their constraint of peptide conformation and contribution to peptide stability. Peptides containing Nα-methylated amino acids have long been prepared by chemical synthesis. While such natural peptides are not produced ribosomally, recent ribosomal strategies have afforded Nα-methylated peptides. Presently, we define new strategies for the ribosomal incorporation of Nα-methylated amino acids into peptides and proteins. First, we identify modified ribosomes capable of facilitating the incorporation of six N-methylated amino acids into antibacterial scorpion peptide IsCT. Also synthesized analogously was a protein domain (RRM1) from hnRNP LL; improved yields were observed for nearly all tested N-methylated amino acids. Computational modeling of the ribosomal assembly illustrated how the distortion imposed by N-methylation could be compensated by altering the nucleotides in key 23S rRNA positions. Finally, it is known that incorporation of multiple prolines (an N-alkylated amino acid) ribosomally can be facilitated by bacterial elongation factor P. We report that supplementing endogenous EF-P during IsCT peptide and RRM1 protein synthesis gave improved yields for most of the N-methylated amino acids studied.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xuan Fu
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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3
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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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4
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Lu W, Terasaka N, Sakaguchi Y, Suzuki T, Suzuki T, Suga H. An anticodon-sensing T-boxzyme generates the elongator nonproteinogenic aminoacyl-tRNA in situ of a custom-made translation system for incorporation. Nucleic Acids Res 2024; 52:3938-3949. [PMID: 38477328 DOI: 10.1093/nar/gkae151] [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: 11/21/2023] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
In the hypothetical RNA world, ribozymes could have acted as modern aminoacyl-tRNA synthetases (ARSs) to charge tRNAs, thus giving rise to the peptide synthesis along with the evolution of a primitive translation apparatus. We previously reported a T-boxzyme, Tx2.1, which selectively charges initiator tRNA with N-biotinyl-phenylalanine (BioPhe) in situ in a Flexible In-vitro Translation (FIT) system to produce BioPhe-initiating peptides. Here, we performed in vitro selection of elongation-capable T-boxzymes (elT-boxzymes), using para-azido-l-phenylalanine (PheAZ) as an acyl-donor. We implemented a new strategy to enrich elT-boxzyme-tRNA conjugates that self-aminoacylated on the 3'-terminus selectively. One of them, elT32, can charge PheAZ onto tRNA in trans in response to its cognate anticodon. Further evolution of elT32 resulted in elT49, with enhanced aminoacylation activity. We have demonstrated the translation of a PheAZ-containing peptide in an elT-boxzyme-integrated FIT system, revealing that elT-boxzymes are able to generate the PheAZ-tRNA in response to the cognate anticodon in situ of a custom-made translation system. This study, together with Tx2.1, illustrates a scenario where a series of ribozymes could have overseen aminoacylation and co-evolved with a primitive RNA-based translation system.
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Affiliation(s)
- Wei Lu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Medical Biochemistry, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0125, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, 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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5
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Vinogradov AA, Zhang Y, Hamada K, Kobayashi S, Ogata K, Sengoku T, Goto Y, Suga H. A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides. J Am Chem Soc 2024; 146:8058-8070. [PMID: 38491946 PMCID: PMC10979747 DOI: 10.1021/jacs.3c12037] [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: 10/28/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/18/2024]
Abstract
Thiopeptides make up a group of structurally complex peptidic natural products holding promise in bioengineering applications. The previously established thiopeptide/mRNA display platform enables de novo discovery of natural product-like thiopeptides with designed bioactivities. However, in contrast to natural thiopeptides, the discovered structures are composed predominantly of proteinogenic amino acids, which results in low metabolic stability in many cases. Here, we redevelop the platform and demonstrate that the utilization of compact reprogrammed genetic codes in mRNA display libraries can lead to the discovery of thiopeptides predominantly composed of nonproteinogenic structural elements. We demonstrate the feasibility of our designs by conducting affinity selections against Traf2- and NCK-interacting kinase (TNIK). The experiment identified a series of thiopeptides with high affinity to the target protein (the best KD = 2.1 nM) and kinase inhibitory activity (the best IC50 = 0.15 μM). The discovered compounds, which bore as many as 15 nonproteinogenic amino acids in an 18-residue macrocycle, demonstrated high metabolic stability in human serum with a half-life of up to 99 h. An X-ray cocrystal structure of TNIK in complex with a discovered thiopeptide revealed how nonproteinogenic building blocks facilitate the target engagement and orchestrate the folding of the thiopeptide into a noncanonical conformation. Altogether, the established platform takes a step toward the discovery of thiopeptides with high metabolic stability for early drug discovery applications.
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Affiliation(s)
- Alexander A. Vinogradov
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yue Zhang
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keisuke Hamada
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Shunsuke Kobayashi
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kazuhiro Ogata
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toru Sengoku
- Department
of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yuki Goto
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 PMCID: PMC11151186 DOI: 10.1021/jacs.3c11306] [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] [Indexed: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
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Affiliation(s)
- Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joshua E. Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Patric W. Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Eugene N. Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, 27599, USA
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7
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Faris J, Adaligil E, Popovych N, Ono S, Takahashi M, Nguyen H, Plise E, Taechalertpaisarn J, Lee HW, Koehler MFT, Cunningham CN, Lokey RS. Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation. J Am Chem Soc 2024; 146:4582-4591. [PMID: 38330910 PMCID: PMC10885153 DOI: 10.1021/jacs.3c10949] [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: 10/17/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024]
Abstract
The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.
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Affiliation(s)
- Justin
H. Faris
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Emel Adaligil
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department
of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, United States
| | - Satoshi Ono
- Innovative
Research Division, Mitsubishi Tanabe Pharma
Corporation, Kanagawa 227-0033, Japan
| | - Mifune Takahashi
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Huy Nguyen
- Department
of Analytical Research, Genentech, South San Francisco, California 94080, United States
| | - Emile Plise
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Jaru Taechalertpaisarn
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Hsiau-Wei Lee
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Michael F. T. Koehler
- Department
of Medicinal Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
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8
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Li X, Wang N, Liu Y, Li W, Bai X, Liu P, He CY. Backbone N-methylation of peptides: Advances in synthesis and applications in pharmaceutical drug development. Bioorg Chem 2023; 141:106892. [PMID: 37776681 DOI: 10.1016/j.bioorg.2023.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the limited pharmacokinetic properties of peptides have hindered their full potential. One prominent strategy for enhancing the druggability of peptides is N-methylation, which involves the addition of a methyl group to the nitrogen atom of the peptide backbone. This modification significantly improves the stability, bioavailability, receptor binding affinity and selectivity of peptide drug candidates. In this review, we provide a comprehensive overview of the advancements in synthetic methods for N-methylated peptide synthesis, as well as the associated limitations. Moreover, we explore the versatile effects of N-methylation on various aspects of peptide properties. Furthermore, we emphasize the efforts dedicated to N-methylated peptide pharmaceuticals that have successfully obtained marketing approval.
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Affiliation(s)
- Xuefei Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Ningchao Wang
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Yuhang Liu
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Weipiao Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xinyu Bai
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ping Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Chun-Yang He
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China.
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9
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Dengler S, Howard RT, Morozov V, Tsiamantas C, Huang WE, Liu Z, Dobrzanski C, Pophristic V, Brameyer S, Douat C, Suga H, Huc I. Display Selection of a Hybrid Foldamer-Peptide Macrocycle. Angew Chem Int Ed Engl 2023; 62:e202308408. [PMID: 37707879 DOI: 10.1002/anie.202308408] [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: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/15/2023]
Abstract
Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential to bind biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A foldamer was first identified that undergoes flexizyme-mediated tRNA acylation and that is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer-peptide hybrids. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.
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Affiliation(s)
- Sebastian Dengler
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Ryan T Howard
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Vasily Morozov
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Wei-En Huang
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Zhiwei Liu
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Christopher Dobrzanski
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Sophie Brameyer
- Biozentrum, Microbiology, Ludwig-Maximilians-Universität, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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10
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Mou X, Kwok CK. Peptides Selected by G4-mRNA Display-Seq Enable RNA G-Quadruplex Recognition and Gene Regulation. J Am Chem Soc 2023; 145:18693-18697. [PMID: 37582058 DOI: 10.1021/jacs.3c04534] [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: 08/17/2023]
Abstract
G-quadruplexes (G4s) are noncanonical secondary structures that play critical roles in both chemistry and biology. Although several approaches have been developed for G4 targeting, such as chemicals and antibodies, there is currently no general and efficient platform for G4-specific peptides. In this study, we developed a new platform, G4-mRNA display-Seq, for selecting peptides that specifically recognize the G4 target of interest. By using an RNA G4 (rG4) found in human telomerase RNA (hTERC) as the target, we have identified a novel short peptide, namely, peptide 11 (pep11), which displays high affinity and selectivity to hTERC rG4. Furthermore, we designed tandem and cyclic versions of pep11 and found that both modified versions exhibit stronger binding affinity with preferential rG4 selectivity. Notably, we have demonstrated that these peptides can negatively regulate gene expression by targeting rG4. Our results provide a universal platform for the discovery of G4-targeting peptides and demonstrate the ability of these peptides to regulate G4-mediated gene functions.
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Affiliation(s)
- Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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11
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Katoh T, Suga H. Ribosomal incorporation of negatively charged d-α- and N-methyl-l-α-amino acids enhanced by EF-Sep. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220038. [PMID: 36633283 PMCID: PMC9835608 DOI: 10.1098/rstb.2022.0038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
Ribosomal incorporation of d-α-amino acids (dAA) and N-methyl-l-α-amino acids (MeAA) with negatively charged sidechains, such as d-Asp, d-Glu, MeAsp and MeGlu, into nascent peptides is far more inefficient compared to those with neutral or positively charged ones. This is because of low binding affinity of their aminoacyl-transfer RNA (tRNA) to elongation factor-thermo unstable (EF-Tu), a translation factor responsible for accommodation of aminoacyl-tRNA onto ribosome. It is well known that EF-Tu binds to two parts of aminoacyl-tRNA, the amino acid moiety and the T-stem; however, the amino acid binding pocket of EF-Tu bearing Glu and Asp causes electric repulsion against the negatively charged amino acid charged on tRNA. To circumvent this issue, here we adopted two strategies: (i) use of an EF-Tu variant, called EF-Sep, in which the Glu216 and Asp217 residues in EF-Tu are substituted with Asn216 and Gly217, respectively; and (ii) reinforcement of the T-stem affinity using an artificially developed chimeric tRNA, tRNAPro1E2, whose T-stem is derived from Escherichia coli tRNAGlu that has high affinity to EF-Tu. Consequently, we could successfully enhance the incorporation efficiencies of d-Asp, d-Glu, MeAsp and MeGlu and demonstrated for the first time, to our knowledge, ribosomal synthesis of macrocyclic peptides containing multiple d-Asp or MeAsp. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- 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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12
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Chan AI, Sawant MS, Burdick DJ, Tom J, Song A, Cunningham CN. Evaluating Translational Efficiency of Noncanonical Amino Acids to Inform the Design of Druglike Peptide Libraries. ACS Chem Biol 2023; 18:81-90. [PMID: 36607609 PMCID: PMC9872084 DOI: 10.1021/acschembio.2c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Advances in genetic code reprogramming have allowed the site-specific incorporation of noncanonical functionalities into polypeptides and proteins, providing access to wide swaths of chemical space via in vitro translation techniques like mRNA display. Prior efforts have established that the translation machinery can tolerate amino acids with modifications to both the peptide backbone and side chains, greatly broadening the chemical space that can be interrogated in ligand discovery efforts. However, existing methods for confirming the translation yield of new amino acid building blocks for these technologies necessitate multistep workups and, more importantly, are not relevant for measuring translation within the context of a combinatorial library consisting of multiple noncanonical amino acids. In this study, we developed a luminescence-based assay to rapidly assess the relative translation yield of any noncanonical amino acid in real time. Among the 59 amino acids tested here, we found that many translate with high efficiency, but translational yield is not necessarily correlated to whether the amino acid is proteinogenic or has high tRNA acylation efficiency. Interestingly, we found that single-template translation data can inform the library-scale translation yield and that shorter peptide libraries are more tolerant of lower-efficiency amino acid monomers. Together our data show that the luminescence-based assay described herein is an essential tool in evaluating new building blocks and codon table designs within mRNA display toward the goal of developing druglike peptide-based libraries for drug discovery campaigns.
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Affiliation(s)
- Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Manali S. Sawant
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Daniel J. Burdick
- Department
of Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Jeffrey Tom
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Aimin Song
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States,
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13
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Kuroda T, Huang Y, Nishio S, Goto Y, Suga H. Post-translational backbone-acyl shift yields natural product-like peptides bearing hydroxyhydrocarbon units. Nat Chem 2022; 14:1413-1420. [PMID: 36329180 DOI: 10.1038/s41557-022-01065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/09/2022] [Indexed: 11/06/2022]
Abstract
Hydroxyhydrocarbon (Hhc) moieties in the backbone of peptidic natural products can exert a substantial influence on the bioactivities of the products, making Hhc units an attractive class of building blocks for de novo peptides. However, despite advances in in vitro genetic code reprogramming, the ribosomal incorporation of Hhc units remains challenging. Here we report a method for in vitro ribosomal synthesis of natural-product-like peptides bearing Hhc units. A series of azide/hydroxy acids were designed as chemical precursors of Hhc units and incorporated into the nascent peptide chain by means of genetic code reprogramming. Post-translational reduction of the azide induced an O-to-N acyl shift to rearrange the peptide backbone. This method allows for one-pot ribosomal synthesis of designer macrocycles bearing various β-, γ- and δ-type Hhc units. We also report the synthesis of a statine-containing peptidomimetic inhibitor of β-secretase 1 as a showcase example.
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Affiliation(s)
- Tomohiro Kuroda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Soichiro Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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14
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van Neer RHP, Dranchak PK, Liu L, Aitha M, Queme B, Kimura H, Katoh T, Battaile KP, Lovell S, Inglese J, Suga H. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. ACS Chem Biol 2022; 17:2284-2295. [PMID: 35904259 PMCID: PMC9900472 DOI: 10.1021/acschembio.2c00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.
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Affiliation(s)
- R H P van Neer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - P K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - L Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - M Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - B Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - H Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K P Battaile
- New York Structural Biology Center, NSLS-II, Upton, New York 11973, United States
| | - S Lovell
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - H Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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15
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Katoh T, Suga H. In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids. Annu Rev Biochem 2022; 91:221-243. [PMID: 35729073 DOI: 10.1146/annurev-biochem-040320-103817] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic code reprogramming has enabled us to ribosomally incorporate various nonproteinogenic amino acids (npAAs) into peptides in vitro. The repertoire of usable npAAs has been expanded to include not only l-α-amino acids with noncanonical sidechains but also those with noncanonical backbones. Despite successful single incorporation of npAAs, multiple and consecutive incorporations often suffer from low efficiency or are even unsuccessful. To overcome this stumbling block, engineering approaches have been used to modify ribosomes, EF-Tu, and tRNAs. Here, we provide an overview of these in vitro methods that are aimed at optimal expansion of the npAA repertoire and their applications for the development of de novo bioactive peptides containing various npAAs.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan; ,
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16
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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Affiliation(s)
- Paddy R. A. Melsen
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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17
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Coronado JN, Ngo P, Anslyn EV, Ellington AD. Chemical insights into flexizyme-mediated tRNA acylation. Cell Chem Biol 2022; 29:1071-1112. [PMID: 35413283 DOI: 10.1016/j.chembiol.2022.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
A critical step in repurposing the cellular translation machinery for the synthesis of polymeric products is the acylation of transfer RNA (tRNA) with unnatural monomers. Toward this goal, flexizymes, ribozymes capable of aminoacylation, have emerged as a uniquely adept tool for charging tRNA with ever increasingly diverse substrates. In this review, we present a library of monomer substrates that have been tested for tRNA acylation with the flexizyme system. From this mile-high view, we provide insights for understanding the chemical factors that influence flexizyme-mediated tRNA acylation. We conclude that flexizymes are primitive esterification catalysts that display a modest binding affinity to the monomer's aromatic recognition element. Together, these robust, yet flexible, flexizyme systems provide researchers with unprecedented access for preparing unnatural acyl-tRNA and the opportunity to repurpose the translation machinery for the synthesis of novel biologically derived structures beyond native proteins and peptides.
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Affiliation(s)
- Jaime N Coronado
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Phuoc Ngo
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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18
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Wang H, Wang Y, Yuan Z, Wang Y, Li X, Song P, Lu F, Liu Y. Insight into the cross-linking preferences and characteristics of the transglutaminase from Bacillus subtilis by in vitro RNA display. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Wu Y, Bertran MT, Rowley J, Calder EDD, Joshi D, Walport LJ. Fluorescent Amino Acid Initiated de novo Cyclic Peptides for the Label-Free Assessment of Cell Permeability*. ChemMedChem 2021; 16:3185-3188. [PMID: 34236771 PMCID: PMC8597039 DOI: 10.1002/cmdc.202100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 11/11/2022]
Abstract
The major obstacle in applying peptides to intracellular targets is their low inherent cell permeability. Standard approaches to attach a fluorophore (e. g. FITC, TAMRA) can change the physicochemical properties of the parent peptide and influence their ability to penetrate and localize in cells. We report a label-free strategy for evaluating the cell permeability of cyclic peptide leads. Fluorescent tryptophan analogues 4-cyanotryptophan (4CNW) and β-(1-azulenyl)-L-alanine (AzAla) were incorporated into in vitro translated macrocyclic peptides by initiator reprogramming. We then demonstrate these efficient blue fluorescent emitters are good tools for monitoring peptide penetration into cells.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - M. Teresa Bertran
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
| | - James Rowley
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - Ewen D. D. Calder
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
| | - Dhira Joshi
- Peptide ChemistryThe Francis Crick InstituteLondonNW1 1ATUK
| | - Louise J. Walport
- Protein-Protein Interaction LaboratoryThe Francis Crick InstituteLondonNW1 1ATUK
- Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonW12 0BZUK
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20
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Lin C, Harner MJ, Douglas AE, Lafont V, Yu F, Lee VG, Poss MA, Swain JF, Wright M, Lipovšek D. A Selection of Macrocyclic Peptides That Bind STING From an mRNA‐Display Library With Split Degenerate Codons. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chi‐Wang Lin
- Bristol Myers Squibb 100 Binney Street Cambridge MA 02142 USA
| | - Mary J. Harner
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | - Andrew E. Douglas
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | - Virginie Lafont
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | - Fei Yu
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | - Ving G. Lee
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | - Michael A. Poss
- Bristol Myers Squibb Route 206 & Province Line Road Lawrenceville NJ 08543 USA
| | | | - Martin Wright
- Bristol Myers Squibb 100 Binney Street Cambridge MA 02142 USA
| | - Daša Lipovšek
- Bristol Myers Squibb 100 Binney Street Cambridge MA 02142 USA
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21
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In Vitro Selection of Thioether-Closed Macrocyclic Peptide Ligands by Means of the RaPID System. Methods Mol Biol 2021. [PMID: 34596852 DOI: 10.1007/978-1-0716-1689-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The Random nonstandard Peptides Integrated Discovery (RaPID) system enables efficient screening of macrocyclic peptides with high affinities against target molecules. Random peptide libraries are prepared by in vitro translation using the Flexible In vitro Translation (FIT) system, which allows for incorporation of diverse nonproteinogenic amino acids into peptides by genetic code reprogramming. By introducing an N-chloroacetyl amino acid at the N-terminus and a Cys at the downstream, macrocyclic peptide libraries can be readily generated via posttranslational thioether formation. Here, we describe how to prepare a thioether-closed macrocyclic peptide library, and its application to the RaPID screening.
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22
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Lin CW, Harner MJ, Douglas AE, Lafont V, Yu F, Lee VG, Poss MA, Swain JF, Wright M, Lipovšek D. A Selection of Macrocyclic Peptides That Bind STING From an mRNA-Display Library With Split Degenerate Codons. Angew Chem Int Ed Engl 2021; 60:22640-22645. [PMID: 34383389 PMCID: PMC8518765 DOI: 10.1002/anie.202103043] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/11/2021] [Indexed: 12/05/2022]
Abstract
Recent improvements in mRNA display have enabled the selection of peptides that incorporate non‐natural amino acids, thus expanding the chemical diversity of macrocycles beyond what is accessible in nature. Such libraries have incorporated non‐natural amino acids at the expense of natural amino acids by reassigning their codons. Here we report an alternative approach to expanded amino‐acid diversity that preserves all 19 natural amino acids (no methionine) and adds 6 non‐natural amino acids, resulting in the highest sequence complexity reported to date. We have applied mRNA display to this 25‐letter library to select functional macrocycles that bind human STING, a protein involved in immunoregulation. The resulting STING‐binding peptides include a 9‐mer macrocycle with a dissociation constant (KD) of 3.4 nM, which blocks binding of cGAMP to STING and induces STING dimerization. This approach is generalizable to expanding the amino‐acid alphabet in a library beyond 25 building blocks.
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Affiliation(s)
- Chi-Wang Lin
- Bristol Myers Squibb, 100 Binney Street, Cambridge, MA, 02142, USA
| | - Mary J Harner
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | - Andrew E Douglas
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | - Virginie Lafont
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | - Fei Yu
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | - Ving G Lee
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | - Michael A Poss
- Bristol Myers Squibb, Route 206 & Province Line Road, Lawrenceville, NJ, 08543, USA
| | | | - Martin Wright
- Bristol Myers Squibb, 100 Binney Street, Cambridge, MA, 02142, USA
| | - Daša Lipovšek
- Bristol Myers Squibb, 100 Binney Street, Cambridge, MA, 02142, USA
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23
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Abstract
![]()
Since the establishment
of site-specific mutagenesis of single
amino acids to interrogate protein function in the 1970s, biochemists
have sought to tailor protein structure in the native cell environment.
Fine-tuning the chemical properties of proteins is an indispensable
way to address fundamental mechanistic questions. Unnatural amino
acids (UAAs) offer the possibility to expand beyond the 20 naturally
occurring amino acids in most species and install new and useful chemical
functions. Here, we review the literature about advances in UAA incorporation
technology from chemoenzymatic aminoacylation of modified tRNAs to in vitro translation systems to genetic encoding of UAAs
in the native cell environment and whole organisms. We discuss innovative
applications of the UAA technology to challenges in bioengineering
and medicine.
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Affiliation(s)
- Mia A Shandell
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, U.K
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, New York 10027, United States.,Department of Systems Biology, Columbia University, New York, New York 10027, United States
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24
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Incorporation of backbone modifications in mRNA-displayable peptides. Methods Enzymol 2021; 656:521-544. [PMID: 34325797 DOI: 10.1016/bs.mie.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we comprehensively summarize the most recent efforts in our research team, aiming at installing N-methyl and azole backbones into peptides expressed in translation. The genetic code reprogramming using the Flexible In-vitro Translation system (FIT system) has proven to be the most reliable and versatile approach for ribosomally installing various exotic amino acids. However, it had been yet difficult in translating diverse kinds of multiple and consecutive sequences of N-methyl amino acids (MeAAs). We have recently reported that a semi-rational fine tuning of MeAA-tRNA affinities for EF-Tu by altering tRNA T-stem sequence achieves efficient delivery of MeAA-tRNAs to the ribosome. Indeed, this approach has made it possible to express N-methyl-peptides containing multiple MeAAs with a remarkably high fidelity. Another interesting backbone modification in peptides is azole moieties often found in natural products, but they are explicitly installed by post-translational modifying enzymes. We have recently devised a method to bypass such enzymatic processes where a bromovinyl group-containing amino acid is incorporated into the peptide by genetic code reprogramming and then chemically converted to an azole group via an intramolecular heterocyclization reaction. These methods will grant more drug-like properties to peptides than ordinary peptides in terms of protease resistance and cell membrane permeability. Particularly when they can be integrated with in vitro mRNA display, such as the RaPID system, the discovery of de novo bioactive peptides can be realized.
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25
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Song H, Burton AJ, Shirran SL, Fahrig-Kamarauskaitė J, Kaspar H, Muir TW, Künzler M, Naismith JH. Engineering of a Peptide α-N-Methyltransferase to Methylate Non-Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2021; 60:14319-14323. [PMID: 33856715 PMCID: PMC8251615 DOI: 10.1002/anie.202100818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Indexed: 12/24/2022]
Abstract
Introduction of α‐N‐methylated non‐proteinogenic amino acids into peptides can improve their biological activities, membrane permeability and proteolytic stability. This is commonly achieved, in nature and in the lab, by assembling pre‐methylated amino acids. The more appealing route of methylating amide bonds is challenging. Biology has evolved an α‐N‐automethylating enzyme, OphMA, which acts on the amide bonds of peptides fused to its C‐terminus. Due to the ribosomal biosynthesis of its substrate, the activity of this enzyme towards peptides with non‐proteinogenic amino acids has not been addressed. An engineered OphMA, intein‐mediated protein ligation and solid‐phase peptide synthesis have allowed us to demonstrate the methylation of amide bonds in the context of non‐natural amides. This approach may have application in the biotechnological production of therapeutic peptides.
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Affiliation(s)
- Haigang Song
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,The Research Complex at Harwell, Harwell Campus, Oxford, OX11 0FA, UK.,The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - Antony J Burton
- Department of Chemistry, Frick Chemistry Laboratory, Princeton University, Princeton, NJ, USA
| | - Sally L Shirran
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife, KY16 9ST, UK
| | - Jūratė Fahrig-Kamarauskaitė
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hannelore Kaspar
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tom W Muir
- Department of Chemistry, Frick Chemistry Laboratory, Princeton University, Princeton, NJ, USA
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - James H Naismith
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,The Research Complex at Harwell, Harwell Campus, Oxford, OX11 0FA, UK.,The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
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26
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Song H, Burton AJ, Shirran SL, Fahrig‐Kamarauskaitė J, Kaspar H, Muir TW, Künzler M, Naismith JH. Engineering of a Peptide α-N-Methyltransferase to Methylate Non-Proteinogenic Amino Acids. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:14440-14444. [PMID: 38505374 PMCID: PMC10947093 DOI: 10.1002/ange.202100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/23/2021] [Indexed: 11/07/2022]
Abstract
Introduction of α-N-methylated non-proteinogenic amino acids into peptides can improve their biological activities, membrane permeability and proteolytic stability. This is commonly achieved, in nature and in the lab, by assembling pre-methylated amino acids. The more appealing route of methylating amide bonds is challenging. Biology has evolved an α-N-automethylating enzyme, OphMA, which acts on the amide bonds of peptides fused to its C-terminus. Due to the ribosomal biosynthesis of its substrate, the activity of this enzyme towards peptides with non-proteinogenic amino acids has not been addressed. An engineered OphMA, intein-mediated protein ligation and solid-phase peptide synthesis have allowed us to demonstrate the methylation of amide bonds in the context of non-natural amides. This approach may have application in the biotechnological production of therapeutic peptides.
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Affiliation(s)
- Haigang Song
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOxfordOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOxfordOX11 0FAUK
| | - Antony J. Burton
- Department of ChemistryFrick Chemistry LaboratoryPrinceton UniversityPrincetonNJUSA
| | - Sally L. Shirran
- Biomedical Sciences Research Complex, North HaughUniversity of St. AndrewsFifeKY16 9STUK
| | - Jūratė Fahrig‐Kamarauskaitė
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - Hannelore Kaspar
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - Tom W. Muir
- Department of ChemistryFrick Chemistry LaboratoryPrinceton UniversityPrincetonNJUSA
| | - Markus Künzler
- Department of BiologyInstitute of MicrobiologyEidgenössische Technische Hochschule (ETH) ZürichZürichSwitzerland
| | - James H. Naismith
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOxfordOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOxfordOX11 0FAUK
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27
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Adaligil E, Song A, Hallenbeck KK, Cunningham CN, Fairbrother WJ. Ribosomal Synthesis of Macrocyclic Peptides with β 2- and β 2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries. ACS Chem Biol 2021; 16:1011-1018. [PMID: 34008946 DOI: 10.1021/acschembio.1c00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more β2-homo-amino acids (β2haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 β2-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of β2haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,β-disubstituted β2,3-homo-amino acids (β2,3haa) with different R-groups on the α- and β-carbons of the same amino acid. Incorporation of these β2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-β2hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of β-amino acid is suitable for development of large scale macrocyclic peptide libraries.
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Affiliation(s)
- Emel Adaligil
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wayne J. Fairbrother
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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28
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Hosseinzadeh P, Watson PR, Craven TW, Li X, Rettie S, Pardo-Avila F, Bera AK, Mulligan VK, Lu P, Ford AS, Weitzner BD, Stewart LJ, Moyer AP, Di Piazza M, Whalen JG, Greisen PJ, Christianson DW, Baker D. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat Commun 2021; 12:3384. [PMID: 34099674 PMCID: PMC8185074 DOI: 10.1038/s41467-021-23609-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
Abstract
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational "anchor extension" methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC50 values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.
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Affiliation(s)
- Parisa Hosseinzadeh
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Knight Campus Center, University of Oregon, Eugene, OR, USA
| | - Paris R Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy W Craven
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Xinting Li
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Stephen Rettie
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Molecular and Cellular Biology Ph.D. Program, University of Washington, Seattle, WA, USA
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Asim K Bera
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Vikram Khipple Mulligan
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Systems Biology, Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Peilong Lu
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Alexander S Ford
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Brian D Weitzner
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Lyell Immunopharma, Inc., Seattle, WA, USA
| | - Lance J Stewart
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Adam P Moyer
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA, USA
| | - Maddalena Di Piazza
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Joshua G Whalen
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
| | - Per Jr Greisen
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA
- Novo Nordisk A/S, Måløv, Denmark
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - David Baker
- University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.
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29
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Initiating protein synthesis with noncanonical monomers in vitro and in vivo. Methods Enzymol 2021; 656:495-519. [PMID: 34325796 DOI: 10.1016/bs.mie.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
With few exceptions, ribosomal protein synthesis begins with methionine (or its derivative N-formyl-methionine) across all domains of life. The role of methionine as the initiating amino acid is dictated by the unique structure of its cognate tRNA known as tRNAfMet. By mis-acylating tRNAfMet, we and others have shown that protein synthesis can be initiated with a variety of canonical and noncanonical amino acids both in vitro and in vivo. Furthermore, because the α-amine of the initiating amino acid is not required for peptide bond formation, translation can be initiated with a variety of structurally disparate carboxylic acids that bear little resemblance to traditional α-amino acids. Herein, we provide a detailed protocol to initiate in vitro protein synthesis with substituted benzoic acid and 1,3-dicarbonyl compounds. These moieties are introduced at the N-terminus of peptides by mis-acylated tRNAfMet, prepared by flexizyme-catalyzed tRNA acylation. In addition, we describe a protocol to initiate in vivo protein synthesis with aromatic noncanonical amino acids (ncAAs). This method relies on an engineered chimeric initiator tRNA that is acylated with ncAAs by an orthogonal aminoacyl-tRNA synthetase. Together, these systems are useful platforms for producing N-terminally modified proteins and for engineering the protein synthesis machinery of Escherichia coli to accept additional nonproteinogenic carboxylic acid monomers.
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Iwane Y, Kimura H, Katoh T, Suga H. Uniform affinity-tuning of N-methyl-aminoacyl-tRNAs to EF-Tu enhances their multiple incorporation. Nucleic Acids Res 2021; 49:10807-10817. [PMID: 33997906 PMCID: PMC8565323 DOI: 10.1093/nar/gkab288] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 01/13/2023] Open
Abstract
In ribosomal translation, the accommodation of aminoacyl-tRNAs into the ribosome is mediated by elongation factor thermo unstable (EF-Tu). The structures of proteinogenic aminoacyl-tRNAs (pAA-tRNAs) are fine-tuned to have uniform binding affinities to EF-Tu in order that all proteinogenic amino acids can be incorporated into the nascent peptide chain with similar efficiencies. Although genetic code reprogramming has enabled the incorporation of non-proteinogenic amino acids (npAAs) into the nascent peptide chain, the incorporation of some npAAs, such as N-methyl-amino acids (MeAAs), is less efficient, especially when MeAAs frequently and/or consecutively appear in a peptide sequence. Such poor incorporation efficiencies can be attributed to inadequate affinities of MeAA-tRNAs to EF-Tu. Taking advantage of flexizymes, here we have experimentally verified that the affinities of MeAA-tRNAs to EF-Tu are indeed weaker than those of pAA-tRNAs. Since the T-stem of tRNA plays a major role in interacting with EF-Tu, we have engineered the T-stem sequence to tune the affinity of MeAA-tRNAs to EF-Tu. The uniform affinity-tuning of the individual pairs has successfully enhanced the incorporation of MeAAs, achieving the incorporation of nine distinct MeAAs into both linear and thioether-macrocyclic peptide scaffolds.
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Affiliation(s)
- Yoshihiko Iwane
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kimura
- 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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31
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Imanishi S, Katoh T, Yin Y, Yamada M, Kawai M, Suga H. In Vitro Selection of Macrocyclic d/l-Hybrid Peptides against Human EGFR. J Am Chem Soc 2021; 143:5680-5684. [PMID: 33822597 DOI: 10.1021/jacs.1c02593] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
d/l-Hybrid peptides are an attractive class of molecular modality because they are able to exhibit high proteolytic stability and unique structural diversity which cannot be accessed by those consisting of only proteinogenic l-amino acids. Despite such an expectation, it has not been possible to devise de novo d/l-hybrid peptides capable of disrupting the function of a protein target(s) due to the lack of an effective method that reliably constructs a highly diverse library and screens active species. Here we report for the first time construction of a library consisting of 1012 members of macrocyclic d/l-hybrid peptides containing five kinds of d-amino acids and performance of the RaPID selection against human EGFR as a showcase to uncover PPI (protein-protein interaction) inhibitors.
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Affiliation(s)
- Sayaka Imanishi
- 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
| | - Yizhen Yin
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mituhiro Yamada
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marina Kawai
- 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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32
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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33
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Discovery of De Novo Macrocyclic Peptides by Messenger RNA Display. Trends Pharmacol Sci 2021; 42:385-397. [PMID: 33771353 DOI: 10.1016/j.tips.2021.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
Macrocyclic peptides are a promising class of compounds that can often engage challenging therapeutic targets. Display technologies, such as mRNA display, allow for the efficient discovery of macrocyclic peptides. This article reviews the current approaches for generating macrocyclic peptide libraries using mRNA display and highlights some recent examples of ribosomal incorporation of nonproteinogenic amino acids into macrocyclic peptides.
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34
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Katoh T, Suga H. Development of Bioactive Foldamers Using Ribosomally Synthesized Nonstandard Peptide Libraries. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- 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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35
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [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: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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36
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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37
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Wang H, Song P, Li X, Wang Y, Gui S, Liu Y, Lu F. Screening of the candidate inhibitory peptides of subtilisin by in vitro RNA display technique. Int J Biol Macromol 2020; 163:1162-1167. [PMID: 32673721 DOI: 10.1016/j.ijbiomac.2020.07.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 11/19/2022]
Abstract
The application of inhibitors facilitates the stable preservation of enzyme in liquid detergent by mitigating the proteolytic activity of subtilisin. The conventionally used subtilisin inhibitors such as boric acid pose a threat to the environment and human health. Thus, the formulation of novel subtilisin inhibitors demands immediate attention. In the current study, we have screened the peptide inhibitors for subtilisin by employing the in vitro mRNA display technique. It is a sensitive screening technique with a high library capacity. The affinity screening was performed between the biotin-modified subtilisin immobilized on the streptavidin magnetic beads and the cDNA-mRNA-peptide fusion molecular library acquired from the in vitro translation and reverse transcription. The candidate peptides with high affinity were obtained after multiple rounds of screening. Furthermore, the inhibitory effect was evaluated, showing that some candidate peptides had inhibitory effects, but the isothermal titration calorimetry and time dependent experiments ultimately proved that these candidate peptides were not stable inhibitors. However, the in vitro mRNA display method explored in this study can be used as a preliminary screening method to provide candidate peptides for the screening of subtilisin inhibitors.
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Affiliation(s)
- Hongbin Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Ping Song
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xue Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yufa Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuqi Gui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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38
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Abstract
Preventing the escape of hazardous genes from genetically modified organisms (GMOs) into the environment is one of the most important issues in biotechnology research. Various strategies were developed to create "genetic firewalls" that prevent the leakage of GMOs; however, they were not specially designed to prevent the escape of genes. To address this issue, we developed amino acid (AA)-swapped genetic codes orthogonal to the standard genetic code, namely SL (Ser and Leu were swapped) and SLA genetic codes (Ser, Leu, and Ala were swapped). From mRNAs encoded by the AA-swapped genetic codes, functional proteins were only synthesized in translation systems featuring the corresponding genetic codes. These results clearly demonstrated the orthogonality of the AA-swapped genetic codes against the standard genetic code and their potential to function as "genetic firewalls for genes". Furthermore, we propose "a codon-bypass strategy" to develop a GMO with an AA-swapped genetic code.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Masahiro Tozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan
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39
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Cui Z, Johnston WA, Alexandrov K. Cell-Free Approach for Non-canonical Amino Acids Incorporation Into Polypeptides. Front Bioeng Biotechnol 2020; 8:1031. [PMID: 33117774 PMCID: PMC7550873 DOI: 10.3389/fbioe.2020.01031] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.
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Affiliation(s)
- Zhenling Cui
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wayne A Johnston
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Synthetic Biology Laboratory, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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40
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Wu Y, Wang Z, Qiao X, Li J, Shu X, Qi H. Emerging Methods for Efficient and Extensive Incorporation of Non-canonical Amino Acids Using Cell-Free Systems. Front Bioeng Biotechnol 2020; 8:863. [PMID: 32793583 PMCID: PMC7387428 DOI: 10.3389/fbioe.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cell-free protein synthesis (CFPS) has emerged as a novel protein expression platform. Especially the incorporation of non-canonical amino acids (ncAAs) has led to the development of numerous flexible methods for efficient and extensive expression of artificial proteins. Approaches were developed to eliminate the endogenous competition for ncAAs and engineer translation factors, which significantly enhanced the incorporation efficiency. Furthermore, in vitro aminoacylation methods can be conveniently combined with cell-free systems, extensively expanding the available ncAAs with novel and unique moieties. In this review, we summarize the recent progresses on the efficient and extensive incorporation of ncAAs by different strategies based on the elimination of competition by endogenous factors, translation factors engineering and extensive incorporation of novel ncAAs coupled with in vitro aminoacylation methods in CFPS. We also aim to offer new ideas to researchers working on ncAA incorporation techniques in CFPS and applications in various emerging fields.
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Affiliation(s)
- Yang Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xin Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Xiangrong Shu
- Department of Pharmacy, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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41
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Nagano M, Suga H. Expansion of Modality: Peptides to Pseudo-Natural Macrocyclic Peptides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo
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42
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Ishida S, Terasaka N, Katoh T, Suga H. An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch. Nat Chem Biol 2020; 16:702-709. [PMID: 32203413 DOI: 10.1038/s41589-020-0500-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/11/2020] [Indexed: 12/20/2022]
Abstract
When the primitive translation system first emerged in the hypothetical RNA world, ribozymes could have been responsible for aminoacylation. Given that naturally occurring T-box riboswitches selectively sense the aminoacylation status of cognate tRNAs, we introduced a domain of random sequence into a T-box-tRNA conjugate and isolated ribozymes that were self-aminoacylating on the 3'-terminal hydroxyl group. One of them, named Tx2.1, recognizes the anticodon and D-loop of tRNA via interaction with its stem I domain, similarly to the parental T-box, and selectively charges N-biotinyl-L-phenylalanine (Bio-lPhe) onto the 3' end of the cognate tRNA in trans. We also demonstrated the ribosomal synthesis of a Bio-lPhe-initiated peptide in a Tx2.1-coupled in vitro translation system, in which Tx2.1 catalyzed specific tRNA aminoacylation in situ. This suggests that such ribozymes could have coevolved with a primitive translation system in the RNA world.
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Affiliation(s)
- Satoshi Ishida
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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43
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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44
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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45
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Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
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46
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Katoh T, Suga H. Flexizyme-catalyzed synthesis of 3'-aminoacyl-NH-tRNAs. Nucleic Acids Res 2019; 47:e54. [PMID: 30843032 PMCID: PMC6511858 DOI: 10.1093/nar/gkz143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/08/2019] [Accepted: 03/02/2019] [Indexed: 11/15/2022] Open
Abstract
Structural analysis of ribosomes in complex with aminoacyl- and/or peptidyl-transfer RNA (tRNA) often suffers from rapid hydrolysis of the ester bond of aminoacyl-tRNAs. To avoid this issue, several methods to introduce an unhydrolyzable amide bond instead of the canonical ester bond have been developed to date. However, the existing methodologies require rather complex steps of synthesis and are often inapplicable to a variety of amino acids including those with noncanonical structures. Here, we report a new method to synthesize 3'-aminoacyl-NH-tRNAs by means of flexizymes-ribozymes capable of charging amino acids onto tRNAs. We show that two types of flexizymes, dFx and eFx, are able to charge various amino acids, including nonproteinogenic ones, onto tRNA or microhelix RNA bearing the 3'-deoxy-3'-amino-adenosine. Due to the versatility of the flexizymes toward any pair of nonproteinogenic amino acids and full-length or fragment tRNAs, this method provides researchers an opportunity to use a wide array of hydrolytically stable 3'-aminoacyl-NH-tRNAs and analogs for various studies.
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Affiliation(s)
- 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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47
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Hirose H, Tsiamantas C, Katoh T, Suga H. In vitro expression of genetically encoded non-standard peptides consisting of exotic amino acid building blocks. Curr Opin Biotechnol 2019; 58:28-36. [DOI: 10.1016/j.copbio.2018.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/26/2018] [Indexed: 01/04/2023]
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48
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Li Q, Montalban-Lopez M, Kuipers OP. Feasability of Introducing a Thioether Ring in Vasopressin by nisBTC Co-expression in Lactococcus lactis. Front Microbiol 2019; 10:1508. [PMID: 31333616 PMCID: PMC6614560 DOI: 10.3389/fmicb.2019.01508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/17/2019] [Indexed: 11/13/2022] Open
Abstract
Introducing one or more intramolecular thioether bridges in a peptide provides a promising approach to create more stable molecules with improved pharmacodynamic properties and especially to protect peptides against proteolytic degradation. Lanthipeptides are compounds that naturally possess thioether bonds in their structure. The model lanthipeptide, nisin, is produced by Lactococcus lactis as a core peptide fused to a leader peptide. The modification machinery responsible for nisin production, including the Ser/Thr-dehydratase NisB and the cyclase NisC, can be applied for introducing a thioether bridge into peptides fused to the nisin leader peptide, e.g., to replace a disulfide bond. Vasopressin plays a key role in water homeostasis in the human body and helps to constrict blood vessels. There are two cysteine residues in the structure of wild type vasopressin, which form a disulfide bridge in the mature peptide. Here, we show it is possible to direct the biosynthesis of vasopressin variants in such a way that the disulfide bridge is replaced by a thioether bridge using the nisin modification machinery NisBTC, albeit at low efficiency. Vasopressin mutants were fused either to the nisin leader peptide directly (Type A), after the first three rings of nisin (Type B/C), or after full nisin (Type D). The type B strategy was optimal for expression. LC-MS/MS data verified the formation of a thioether bridge, which provides proof of principle for this modification in vasopressin. This is a first step prior to the necessary increase of the production yield and further purification of these peptides to finally test their biological activity in tissue and animal models.
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Affiliation(s)
- Qian Li
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Manuel Montalban-Lopez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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49
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Fujino T, Kondo T, Suga H, Murakami H. Exploring the Minimal RNA Substrate of Flexizymes. Chembiochem 2019; 20:1959-1965. [PMID: 30950544 DOI: 10.1002/cbic.201900150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Indexed: 02/06/2023]
Abstract
Flexizymes are tRNA acylation ribozymes that have been successfully used to facilitate genetic code reprogramming. They are capable of charging acid substrates onto various tRNAs and tRNA analogues. However, their minimal RNA substrate has not been investigated. Here we have designed fluorescently labeled short RNAs corresponding to the four, three, and two bases (4bRNA, 3bRNA, 2bRNA) at the tRNA 3'-end and explored the minimal RNA substrate of flexizymes, dFx and eFx. 3bRNA was the observed minimal RNA substrate of the flexizymes, but the efficiency of acylation of this short RNA was two to three times lower than that of 4bRNA. The efficiency of acylation of 4bRNA was comparable with that of the microhelix, a 22-base RNA conventionally used as a tRNA analogue for analyzing acylation efficiency. We also compared the efficiencies of acylation of the microhelix and 4bRNA with various acid substrates. Thanks to the short length of 4bRNA, its acyl-4bRNA products exhibited larger mobility shifts in gel electrophoresis than those exhibited by acyl-microhelix products with every substrate tested. This indicated that 4bRNA was an ideal RNA substrate for analyzing the efficiency of acylation by flexizymes.
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Affiliation(s)
- Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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50
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Katoh T, Suga H. Engineering Translation Components Improve Incorporation of Exotic Amino Acids. Int J Mol Sci 2019; 20:ijms20030522. [PMID: 30691159 PMCID: PMC6386890 DOI: 10.3390/ijms20030522] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
Methods of genetic code manipulation, such as nonsense codon suppression and genetic code reprogramming, have enabled the incorporation of various nonproteinogenic amino acids into the peptide nascent chain. However, the incorporation efficiency of such amino acids largely varies depending on their structural characteristics. For instance, l-α-amino acids with artificial, bulky side chains are poorer substrates for ribosomal incorporation into the nascent peptide chain, mainly owing to the lower affinity of their aminoacyl-tRNA toward elongation factor-thermo unstable (EF-Tu). Phosphorylated Ser and Tyr are also poorer substrates for the same reason; engineering EF-Tu has turned out to be effective in improving their incorporation efficiencies. On the other hand, exotic amino acids such as d-amino acids and β-amino acids are even poorer substrates owing to their low affinity to EF-Tu and poor compatibility to the ribosome active site. Moreover, their consecutive incorporation is extremely difficult. To solve these problems, the engineering of ribosomes and tRNAs has been executed, leading to successful but limited improvement of their incorporation efficiency. In this review, we comprehensively summarize recent attempts to engineer the translation systems, resulting in a significant improvement of the incorporation of exotic amino acids.
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Affiliation(s)
- 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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