1
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024. [PMID: 38953775 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G Koch
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
- Chemical Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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2
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Thombare VJ, Wu Y, Pamulapati K, Han M, Tailhades J, Cryle MJ, Roberts KD, Velkov T, Li J, Patil NA. Advancing Nitrile-Aminothiol Strategy for Dual and Sequential Bioconjugation. Chemistry 2024:e202401674. [PMID: 38839567 DOI: 10.1002/chem.202401674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Nitrile-aminothiol conjugation (NATC) stands out as a promising biocompatible ligation technique due to its high chemo-selectivity. Herein we investigated the reactivity and substrate scope of NAT conjugation chemistry, thus developing a novel pH dependent orthogonal NATC as a valuable tool for chemical biology. The study of reaction kinetics elucidated that the combination of heteroaromatic nitrile and aminothiol groups led to the formation of an optimal bioorthogonal pairing, which is pH dependent. This pairing system was effectively utilized for sequential and dual conjugation. Subsequently, these rapid (≈1 h) and high yield (>90 %) conjugation strategies were successfully applied to a broad range of complex biomolecules, including oligonucleotides, chelates, small molecules and peptides. The effectiveness of this conjugation chemistry was demonstrated by synthesizing a fluorescently labelled antimicrobial peptide-oligonucleotide complex as a dual conjugate to imaging in live cells. This first-of-its-kind sequential NATC approach unveils unprecedented opportunities in modern chemical biology, showcasing exceptional adaptability in rapidly creating structurally complex bioconjugates. Furthermore, the results highlight its potential for versatile applications across fundamental and translational biomedical research.
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Affiliation(s)
- Varsha J Thombare
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Yimin Wu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Kavya Pamulapati
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Meiling Han
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Julien Tailhades
- Department of Biochemistry Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Max J Cryle
- Department of Biochemistry Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Kade D Roberts
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Tony Velkov
- Department of Pharmacology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Jian Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Nitin A Patil
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
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3
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Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [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: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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4
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Pirhaghi M, Mamashli F, Moosavi-Movahedi F, Arghavani P, Amiri A, Davaeil B, Mohammad-Zaheri M, Mousavi-Jarrahi Z, Sharma D, Langel Ü, Otzen DE, Saboury AA. Cell-Penetrating Peptides: Promising Therapeutics and Drug-Delivery Systems for Neurodegenerative Diseases. Mol Pharm 2024; 21:2097-2117. [PMID: 38440998 DOI: 10.1021/acs.molpharmaceut.3c01167] [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] [Indexed: 03/06/2024]
Abstract
Currently, one of the most significant and rapidly growing unmet medical challenges is the treatment of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). This challenge encompasses the imperative development of efficacious therapeutic agents and overcoming the intricacies of the blood-brain barrier for successful drug delivery. Here we focus on the delivery aspect with particular emphasis on cell-penetrating peptides (CPPs), widely used in basic and translational research as they enhance drug delivery to challenging targets such as tissue and cellular compartments and thus increase therapeutic efficacy. The combination of CPPs with nanomaterials such as nanoparticles (NPs) improves the performance, accuracy, and stability of drug delivery and enables higher drug loads. Our review presents and discusses research that utilizes CPPs, either alone or in conjugation with NPs, to mitigate the pathogenic effects of neurodegenerative diseases with particular reference to AD and PD.
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Affiliation(s)
- Mitra Pirhaghi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 6673145137, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | | | - Payam Arghavani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Ahmad Amiri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Bagher Davaeil
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Mahya Mohammad-Zaheri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Zahra Mousavi-Jarrahi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Ülo Langel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C 1592-224, Denmark
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
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5
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Yano T, Yamada T, Isida H, Ohashi N, Itoh T. 2-cyanopyridine derivatives enable N-terminal cysteine bioconjugation and peptide bond cleavage of glutathione under aqueous and mild conditions. RSC Adv 2024; 14:6542-6547. [PMID: 38390509 PMCID: PMC10882492 DOI: 10.1039/d4ra00437j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Inspired by the chemical reactivity of apalutamide, we have developed an efficient method for N-terminal cysteine bioconjugation with 2-cyanopyridine derivatives. Systematic investigations of various 2-cyanopyridines revealed that 2-cyanopyridines with electron-withdrawing groups react efficiently with cysteine under aqueous and mild conditions. Moreover, the highly reactive 2-cyanopyridines enable the peptide bond cleavage of glutathione. The utility of our method is demonstrated by its application to the cysteine-selective chemical modification of bioactive peptides.
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Affiliation(s)
- Tetsuya Yano
- Showa Pharmaceutical University Machida Tokyo 194-8543 Japan
| | - Takahiro Yamada
- Showa Pharmaceutical University Machida Tokyo 194-8543 Japan
| | - Hiroaki Isida
- Showa Pharmaceutical University Machida Tokyo 194-8543 Japan
| | - Nami Ohashi
- Showa Pharmaceutical University Machida Tokyo 194-8543 Japan
| | - Toshimasa Itoh
- Showa Pharmaceutical University Machida Tokyo 194-8543 Japan
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6
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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7
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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8
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Abdelkader EH, Qianzhu H, Huber T, Otting G. Genetic Encoding of 7-Aza-l-tryptophan: Isoelectronic Substitution of a Single CH-Group in a Protein for a Nitrogen Atom for Site-Selective Isotope Labeling. ACS Sens 2023; 8:4402-4406. [PMID: 37890165 DOI: 10.1021/acssensors.3c01904] [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] [Indexed: 10/29/2023]
Abstract
Genetic encoding of a noncanonical amino acid (ncAA) in an in vivo expression system requires an aminoacyl-tRNA synthetase that specifically recognizes the ncAA, while the ncAA must not be recognized by the canonical protein expression machinery. We succeeded in genetically encoding 7-aza-tryptophan (7AW), which is isoelectronic with tryptophan. The system is fully orthogonal to protein expression in Escherichia coli, enabling high-yielding site-selective isotope labeling in vivo. 7AW is readily synthesized from serine and 7-aza-indole using a tryptophan synthetase β-subunit (TrpB) mutant, affording easy access to isotope-labeled 7AW. Using labeled 7AW produced from 15N/13C-labeled serine, we produced 7AW mutants of the 25 kDa Zika virus NS2B-NS3 protease. 15N-HSQC spectra display single cross-peaks at chemical shifts near those observed for the wild-type protein labeled with 15N/13C-tryptophan, confirming the structural integrity of the protein and yielding straightforward NMR resonance assignments for site-specific probing.
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Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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9
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Liu M, Morewood R, Yoshisada R, Pascha MN, Hopstaken AJP, Tarcoveanu E, Poole DA, de Haan CAM, Nitsche C, Jongkees SAK. Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis. Chem Sci 2023; 14:10561-10569. [PMID: 37799990 PMCID: PMC10548512 DOI: 10.1039/d3sc03117a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.
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Affiliation(s)
- Minglong Liu
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Richard Morewood
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Mirte N Pascha
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Antonius J P Hopstaken
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Eliza Tarcoveanu
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - David A Poole
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University Yalelaan 1 3584 CL Utrecht The Netherlands
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT 2601 Australia
| | - Seino A K Jongkees
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam Amsterdam The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam Amsterdam The Netherlands
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10
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Proj M, Strašek N, Pajk S, Knez D, Sosič I. Tunable Heteroaromatic Nitriles for Selective Bioorthogonal Click Reaction with Cysteine. Bioconjug Chem 2023. [PMID: 37354098 PMCID: PMC10360065 DOI: 10.1021/acs.bioconjchem.3c00163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
The binucleophilic properties of 1,2-aminothiol and its rare occurrence in nature make it a useful reporter for tracking molecules in living systems. The 1,2-aminothiol moiety is present in cysteine, which is a substrate for a biocompatible click reaction with heteroaromatic nitriles. Despite the wide range of applications for this reaction, the scope of nitrile substrates has been explored only to a limited extent. In this study, we expand the chemical space of heteroaromatic nitriles for bioconjugation under physiologically relevant conditions. We systematically assembled a library of 116 2-cyanobenzimidazoles, 1-methyl-2-cyanobenzimidazoles, 2-cyanobenzothiazoles, and 2-cyanobenzoxazoles containing electron-donating and electron-withdrawing substituents at all positions of the benzene ring. The compounds were evaluated for their stability, reactivity, and selectivity toward the N-terminal cysteine of model oligopeptides. In comparison to the benchmark 6-hydroxy-2-cyanobenzothiazole or 6-amino-2-cyanobenzothiazole, we provide highly selective and moderately reactive nitriles as well as highly reactive yet less selective analogs with a variety of enabling attachment chemistries to aid future applications in bioconjugation, chemical biology, and nanomaterial science.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Nika Strašek
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Stane Pajk
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, Ljubljana 1000, Slovenia
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11
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Tai J, Wang L, Chan WS, Cheng J, Chan YH, Lee MM, Chan MK. Pyrrolysine-Inspired in Cellulo Synthesis of an Unnatural Amino Acid for Facile Macrocyclization of Proteins. J Am Chem Soc 2023; 145:10249-10258. [PMID: 37125745 PMCID: PMC10176472 DOI: 10.1021/jacs.3c01291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Macrocyclization has been touted as an effective strategy to enhance the in vivo stability and efficacy of protein therapeutics. Herein, we describe a scalable and robust system based on the endogenous biosynthesis of a noncanonical amino acid coupled to the pyrrolysine translational machinery for the generation of lasso-grafted proteins. The in cellulo biosynthesis of the noncanonical amino acid d-Cys-ε-Lys was achieved by hijacking the pyrrolysine biosynthesis pathway, and then, its genetical incorporation into proteins was performed using an optimized PylRS/tRNAPyl pair and cell line. This system was then applied to the structurally inspired cyclization of a 23-mer therapeutic P16 peptide engrafted on a fusion protein, resulting in near-complete cyclization of the target cyclic subunit in under 3 h. The resulting cyclic P16 peptide fusion protein possessed much higher CDK4 binding affinity than its linear counterpart. Furthermore, a bifunctional bicyclic protein harboring a cyclic cancer cell targeting RGD motif on the one end and the cyclic P16 peptide on the other is produced and shown to be a potent cell cycle arrestor with improved serum stability.
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Affiliation(s)
- Jingxuan Tai
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Lin Wang
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Wai Shan Chan
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Jiahui Cheng
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuk Hei Chan
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Marianne M Lee
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Michael K Chan
- School of Life Sciences and Center of Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
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12
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Ekanayake KB, Mahawaththa MC, Qianzhu H, Abdelkader EH, George J, Ullrich S, Murphy RB, Fry SE, Johansen-Leete J, Payne RJ, Nitsche C, Huber T, Otting G. Probing Ligand Binding Sites on Large Proteins by Nuclear Magnetic Resonance Spectroscopy of Genetically Encoded Non-Canonical Amino Acids. J Med Chem 2023; 66:5289-5304. [PMID: 36920850 DOI: 10.1021/acs.jmedchem.3c00222] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
N6-(((trimethylsilyl)-methoxy)carbonyl)-l-lysine (TMSK) and N6-trifluoroacetyl-l-lysine (TFAK) are non-canonical amino acids, which can be installed in proteins by genetic encoding. In addition, we describe a new aminoacyl-tRNA synthetase specific for N6-(((trimethylsilyl)methyl)-carbamoyl)-l-lysine (TMSNK), which is chemically more stable than TMSK. Using the dimeric SARS-CoV-2 main protease (Mpro) as a model system with three different ligands, we show that the 1H and 19F nuclei of the solvent-exposed trimethylsilyl and CF3 groups produce intense signals in the nuclear magnetic resonance (NMR) spectrum. Their response to active-site ligands differed significantly when positioned near rather than far from the active site. Conversely, the NMR probes failed to confirm the previously reported binding site of the ligand pelitinib, which was found to enhance the activity of Mpro by promoting the formation of the enzymatically active dimer. In summary, the amino acids TMSK, TMSNK, and TFAK open an attractive path for site-specific NMR analysis of ligand binding to large proteins of limited stability and at low concentrations.
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Affiliation(s)
- Kasuni B Ekanayake
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Acton, Canberra, Australian Capital Territory 2601, Australia
| | - Mithun C Mahawaththa
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Acton, Canberra, Australian Capital Territory 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Elwy H Abdelkader
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Acton, Canberra, Australian Capital Territory 2601, Australia
| | - Josemon George
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Rhys B Murphy
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Sarah E Fry
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason Johansen-Leete
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Acton, Canberra 2601, Australia
| | - Gottfried Otting
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Acton, Canberra, Australian Capital Territory 2601, Australia
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13
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Yanagisawa T, Seki E, Tanabe H, Fujii Y, Sakamoto K, Yokoyama S. Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids. Int J Mol Sci 2023; 24:ijms24076256. [PMID: 37047230 PMCID: PMC10094482 DOI: 10.3390/ijms24076256] [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: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including Nε-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNAPyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of Nε-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis.
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Affiliation(s)
- Tatsuo Yanagisawa
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
| | - Eiko Seki
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Hiroaki Tanabe
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Yoshifumi Fujii
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
| | - Kensaku Sakamoto
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan;
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-Cho, Tsurumi, Yokohama 230-0045, Japan; (E.S.); (H.T.)
- Correspondence: (T.Y.); (S.Y.); Tel.: +81-45-503-9196 (S.Y.)
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14
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Liu M, Yoshisada R, Amedi A, Hopstaken AJP, Pascha MN, de Haan CAM, Geerke DP, Poole DA, Jongkees SAK. An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry 2023; 29:e202203923. [PMID: 36529683 DOI: 10.1002/chem.202203923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.
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Affiliation(s)
- Minglong Liu
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Ryoji Yoshisada
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Avand Amedi
- Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
| | - Antonius J P Hopstaken
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Mirte N Pascha
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Cornelis A M de Haan
- Section Virology Division of Infectious Diseases and Immunology Department of Biomolecular Health Sciences Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands
| | - Daan P Geerke
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - David A Poole
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands
| | - Seino A K Jongkees
- Chemistry and Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, the Netherlands.,Department Chemical Biology and Drug Discovery and Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, 3584 CG, the Netherlands
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15
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Iskandar SE, Pelton JM, Wick ET, Bolhuis DL, Baldwin AS, Emanuele MJ, Brown NG, Bowers AA. Enabling Genetic Code Expansion and Peptide Macrocyclization in mRNA Display via a Promiscuous Orthogonal Aminoacyl-tRNA Synthetase. J Am Chem Soc 2023; 145:1512-1517. [PMID: 36630539 PMCID: PMC10411329 DOI: 10.1021/jacs.2c11294] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
mRNA display is revolutionizing peptide drug discovery through its ability to quickly identify potent peptide binders of therapeutic protein targets. Methods to expand the chemical diversity of display libraries are continually needed to increase the likelihood of identifying clinically relevant peptide ligands. Orthogonal aminoacyl-tRNA synthetases (ORSs) have proven utility in cellular genetic code expansion, but are relatively underexplored for in vitro translation (IVT) and mRNA display. Herein, we demonstrate that the promiscuous ORS p-CNF-RS can incorporate noncanonical amino acids at amber codons in IVT, including the novel substrate p-cyanopyridylalanine (p-CNpyrA), to enable a pyridine-thiazoline (pyr-thn) macrocyclization in mRNA display. Pyr-thn-based selections against the deubiquitinase USP15 yielded a potent macrocyclic binder that exhibits good selectivity for USP15 and close homologues over other ubiquitin-specific proteases (USPs). Overall, this work exemplifies how promiscuous ORSs can both expand side chain diversity and provide structural novelty in mRNA display libraries through a heterocycle forming macrocyclization.
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Affiliation(s)
- Sabrina E. Iskandar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizaveta T. Wick
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Derek L. Bolhuis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Michael J. Emanuele
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 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, North Carolina 27599, USA
- Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, 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, North Carolina 27599, USA
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16
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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