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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Arafiles JV, Franke J, Franz L, Gómez-González J, Kemnitz-Hassanin K, Hackenberger CPR. Cell-Surface-Retained Peptide Additives for the Cytosolic Delivery of Functional Proteins. J Am Chem Soc 2023; 145. [PMID: 37906525 PMCID: PMC10655119 DOI: 10.1021/jacs.3c05365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
The delivery of functional proteins remains a major challenge in advancing biological and pharmaceutical sciences. Herein, we describe a powerful, simple, and highly effective strategy for the intracellular delivery of functional cargoes. Previously, we demonstrated that cell-penetrating peptide (CPP) additives equipped with electrophilic thiol-reactive moieties temporarily attach to the cellular membrane, thereby facilitating the cellular uptake of protein- and antibody-CPP cargoes through direct membrane transduction at low concentrations. Now, we hypothesize that CPP-additives with an increased retention on the cellular membrane will further enhance intracellular uptake. We discovered that adding a small hydrophobic peptide sequence to an arginine-rich electrophilic CPP-additive further improved the uptake of protein-CPP conjugates, whereas larger hydrophobic anchors showed increased cytotoxicity. Cell viability and membrane integrity measurements, structure-activity relationship studies, and quantitative evaluation of protein-CPP uptake revealed important design principles for cell-surface-retained CPP-additives. These investigations allowed us to identify a nontoxic, thiol-reactive CPP-additive containing the hydrophobic ILFF sequence, which can deliver fluorescent model proteins at low micromolar concentrations. This hydrophobic CPP-additive allowed the addition of protein cargoes for intracellular delivery after initial additive incubation. Time-lapse fluorescence microscopy and membrane tension analysis of cells treated with fluorescent ILFF-CPP-additives supported the claim of increased cell surface retention and suggested that the protein-CPP cargoes enter the cell through a mechanism involving lowered cell membrane tension. Finally, we demonstrated that our newly engineered hydrophobic CPP-additive enabled the uptake of a functional macrocyclic peptidic MDM2-inhibitor and a recombinant genome editing protein. This indicates that the developed hydrophobic CPP-additive holds promise as a tool to enhance the intracellular delivery of peptide and protein cargoes.
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Affiliation(s)
- Jan Vincent
V. Arafiles
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Jonathan Franke
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institut
für Chemie, Humboldt Universität
zu Berlin, Brook-Taylor-Str.
2, Berlin 12489, Germany
| | - Luise Franz
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Berlin 14195, Germany
| | - Jacobo Gómez-González
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Kristin Kemnitz-Hassanin
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, Berlin 13125, Germany
- Institut
für Chemie, Humboldt Universität
zu Berlin, Brook-Taylor-Str.
2, Berlin 12489, Germany
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3
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Tréton G, Sayer C, Schürz M, Jaritsch M, Müller A, Matea CT, Stanojlovic V, Melo-Benirschke H, Be C, Krembel C, Rodde S, Haffke M, Hintermann S, Marzinzik A, Ripoche S, Blöchl C, Hollerweger J, Auer D, Cabrele C, Huber CG, Hintersteiner M, Wagner T, Lingel A, Meisner-Kober N. Quantitative and functional characterisation of extracellular vesicles after passive loading with hydrophobic or cholesterol-tagged small molecules. J Control Release 2023; 361:694-716. [PMID: 37567507 DOI: 10.1016/j.jconrel.2023.08.010] [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: 03/27/2023] [Revised: 07/03/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Extracellular vesicles (EVs) are nanosized intercellular messengers that bear enormous application potential as biological drug delivery vehicles. Much progress has been made for loading or decorating EVs with proteins, peptides or RNAs using genetically engineered donor cells, but post-isolation loading with synthetic drugs and using EVs from natural sources remains challenging. In particular, quantitative and unambiguous data assessing whether and how small molecules associate with EVs versus other components in the samples are still lacking. Here we describe the systematic and quantitative characterisation of passive EV loading with small molecules based on hydrophobic interactions - either through direct adsorption of hydrophobic compounds, or by membrane anchoring of hydrophilic ligands via cholesterol tags. As revealed by single vesicle imaging, both ligand types bind to CD63 positive EVs (exosomes), however also non-specifically to other vesicles, particles, and serum proteins. The hydrophobic compounds Curcumin and Terbinafine aggregate on EVs with no apparent saturation up to 106-107 molecules per vesicle as quantified by liquid chromatography - high resolution mass spectrometry (LC-HRMS). For both compounds, high density EV loading resulted in the formation of a population of large, electron-dense vesicles as detected by quantitative cryo-transmission electron microscopy (TEM), a reduced EV cell uptake and a toxic gain of function for Curcumin-EVs. In contrast, cholesterol tagging of a hydrophilic mdm2-targeted cyclic peptide saturated at densities of ca 104-105 molecules per vesicle, with lipidomics showing addition to, rather than replacement of endogenous cholesterol. Cholesterol anchored ligands did not change the EVs' size or morphology, and such EVs retained their cell uptake activity without inducing cell toxicity. However, the cholesterol-anchored ligands were rapidly shed from the vesicles in presence of serum. Based on these data, we conclude that (1) both methods allow loading of EVs with small molecules but are prone to unspecific compound binding or redistribution to other components if present in the sample, (2) cholesterol anchoring needs substantial optimization of formulation stability for in vivo applications, whereas (3) careful titration of loading densities is warranted when relying on hydrophobic interactions of EVs with hydrophobic compounds to mitigate changes in physicochemical properties, loss of EV function and potential cell toxicity.
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Affiliation(s)
- Gwenola Tréton
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Claudia Sayer
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Melanie Schürz
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Maria Jaritsch
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Anna Müller
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Cristian-Tudor Matea
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Heloisa Melo-Benirschke
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Celine Be
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Caroline Krembel
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Matthias Haffke
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Samuel Hintermann
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Marzinzik
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sébastien Ripoche
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Constantin Blöchl
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Julia Hollerweger
- GMP Unit, Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Daniela Auer
- GMP Unit, Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Chiara Cabrele
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Christian G Huber
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | | | - Trixie Wagner
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
| | - Nicole Meisner-Kober
- University of Salzburg, Department of Biosciences and Medical Biology, Hellbrunnerstrasse 34, 5020 Salzburg, Austria.
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4
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Mesrouze Y, Gubler H, Villard F, Boesch R, Ottl J, Kallen J, Reid PC, Scheufler C, Marzinzik AL, Chène P. Biochemical and Structural Characterization of a Peptidic Inhibitor of the YAP:TEAD Interaction That Binds to the α-Helix Pocket on TEAD. ACS Chem Biol 2023; 18:643-651. [PMID: 36825662 DOI: 10.1021/acschembio.2c00936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The TEAD transcription factors are the most distal elements of the Hippo pathway, and their transcriptional activity is regulated by several proteins, including YAP. In some cancers, the Hippo pathway is deregulated and inhibitors of the YAP:TEAD interaction are foreseen as new anticancer drugs. The binding of YAP to TEAD is driven by the interaction of an α-helix and an Ω-loop present in its TEAD-binding domain with two distinct pockets at the TEAD surface. Using the mRNA-based display technique to screen a library of in vitro-translated cyclic peptides, we identified a peptide that binds with a nanomolar affinity to TEAD. The X-ray structure of this peptide in complex with TEAD reveals that it interacts with the α-helix pocket. Under our experimental conditions, this peptide can form a ternary complex with TEAD and YAP. Furthermore, combining it with a peptide binding to the Ω-loop pocket gives an additive inhibitory effect on the YAP:TEAD interaction. Overall, our results show that it is possible to identify nanomolar inhibitors of the YAP:TEAD interaction that bind to the α-helix pocket, suggesting that developing such compounds might be a strategy to treat cancers where the Hippo pathway is deregulated.
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Affiliation(s)
- Yannick Mesrouze
- Disease Area Oncology, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Hanspeter Gubler
- NIBR Informatics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Frédéric Villard
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Ralf Boesch
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Johannes Ottl
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Joerg Kallen
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Patrick C Reid
- PeptiDream, 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Clemens Scheufler
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Andreas L Marzinzik
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Patrick Chène
- Disease Area Oncology, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
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5
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Hibino E, Hiroaki H. Potential of rescue and reactivation of tumor suppressor p53 for cancer therapy. Biophys Rev 2022; 14:267-275. [PMID: 35340607 PMCID: PMC8921420 DOI: 10.1007/s12551-021-00915-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/14/2021] [Indexed: 01/13/2023] Open
Abstract
The tumor suppressor protein p53, a transcription product of the anti-oncogene TP53, is a critical factor in preventing cellular cancerization and killing cancer cells by inducing apoptosis. As a result, p53 is often referred to as the "guardian of the genome." Almost half of cancers possess genetic mutations in the TP53 gene, and most of these mutations result in the malfunction of p53, which promotes aggregation. In some cases, the product of the TP53 mutant allele shows higher aggregation propensity; the mutant co-aggregates with the normal (functional) p53 protein, thus losing cellular activity of the p53 guardian. Cancer might also progress because of the proteolytic degradation of p53 by activated E3 ubiquitination enzymes, MDM2 and MDM4. The inhibition of the specific interaction between MDM2 (MDM4) and p53 also results in increased p53 activity in cancer cells. Although the molecular targets of the drugs are different, two drug discovery strategies with a common goal, "rescuing p53 protein," have recently emerged. To conduct this approach, various biophysical methods of protein characterization were employed. In this review, we focus on these two independent strategies based on the unique biophysical features of the p53 protein.
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Affiliation(s)
- Emi Hibino
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
- Business Incubation Building, BeCellBar LLC, Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
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