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Scherer D, Burger M, Leroux JC. Revival of Bioengineered Proteins as Carriers for Nucleic Acids. Bioconjug Chem 2024; 35:561-566. [PMID: 38621363 PMCID: PMC11099893 DOI: 10.1021/acs.bioconjchem.4c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Affiliation(s)
- David Scherer
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Michael Burger
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
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2
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Eweje F, Walsh ML, Ahmad K, Ibrahim V, Alrefai A, Chen J, Chaikof EL. Protein-based nanoparticles for therapeutic nucleic acid delivery. Biomaterials 2024; 305:122464. [PMID: 38181574 PMCID: PMC10872380 DOI: 10.1016/j.biomaterials.2023.122464] [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: 09/23/2023] [Revised: 12/25/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
To realize the full potential of emerging nucleic acid therapies, there is a need for effective delivery agents to transport cargo to cells of interest. Protein materials exhibit several unique properties, including biodegradability, biocompatibility, ease of functionalization via recombinant and chemical modifications, among other features, which establish a promising basis for therapeutic nucleic acid delivery systems. In this review, we highlight progress made in the use of non-viral protein-based nanoparticles for nucleic acid delivery in vitro and in vivo, while elaborating on key physicochemical properties that have enabled the use of these materials for nanoparticle formulation and drug delivery. To conclude, we comment on the prospects and unresolved challenges associated with the translation of protein-based nucleic acid delivery systems for therapeutic applications.
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Affiliation(s)
- Feyisayo Eweje
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Michelle L Walsh
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115
| | - Kiran Ahmad
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Vanessa Ibrahim
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Assma Alrefai
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jiaxuan Chen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Zhu H, Luo H, Chang R, Yang Y, Liu D, Ji Y, Qin H, Rong H, Yin J. Protein-based delivery systems for RNA delivery. J Control Release 2023; 363:253-274. [PMID: 37741460 DOI: 10.1016/j.jconrel.2023.09.032] [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: 06/18/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
RNA-based therapeutics have emerged as promising approaches to modulate gene expression and generate therapeutic proteins or antigens capable of inducing immune responses to treat a variety of diseases, such as infectious diseases, cancers, immunologic disorders, and genetic disorders. However, the efficient delivery of RNA molecules into cells poses significant challenges due to their large molecular weight, negative charge, and susceptibility to degradation by RNase enzymes. To overcome these obstacles, viral and non-viral vectors have been developed, including lipid nanoparticles, viral vectors, proteins, dendritic macromolecules, among others. Among these carriers, protein-based delivery systems have garnered considerable attention due to their potential to address specific issues associated with nanoparticle-based systems, such as liver accumulation and immunogenicity. This review provides an overview of currently marketed RNA drugs, underscores the significance of RNA delivery vector development, delineates the essential characteristics of an ideal RNA delivery vector, and introduces existing protein carriers for RNA delivery. By offering valuable insights, this review aims to serve as a reference for the future development of protein-based delivery vectors for RNA therapeutics.
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Affiliation(s)
- Haichao Zhu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hong Luo
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Ruilong Chang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yifan Yang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Dingkang Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yue Ji
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hai Qin
- Department of Clinical Laboratory, Beijing Jishuitan Hospital Guizhou Hospital, No. 206, Sixian Street, Baiyun District, Guiyang City 550014, Guizhou Province, China.
| | - Haibo Rong
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China.
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
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Klipp A, Burger M, Leroux JC. Get out or die trying: Peptide- and protein-based endosomal escape of RNA therapeutics. Adv Drug Deliv Rev 2023; 200:115047. [PMID: 37536508 DOI: 10.1016/j.addr.2023.115047] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
RNA therapeutics offer great potential to transform the biomedical landscape, encompassing the treatment of hereditary conditions and the development of better vaccines. However, the delivery of RNAs into the cell is hampered, among others, by poor endosomal escape. This major hurdle is often tackled using special lipids, polymers, or protein-based delivery vectors. In this review, we will focus on the most prominent peptide- and protein-based endosomal escape strategies with focus on RNA drugs. We discuss cell penetrating peptides, which are still incorporated into novel transfection systems today to promote endosomal escape. However, direct evidence for enhanced endosomal escape by the action of such peptides is missing and their transfection efficiency, even in permissive cell culture conditions, is rather low. Endosomal escape by the help of pore forming proteins or phospholipases, on the other hand, allowed to generate more efficient transfection systems. These are, however, often hampered by considerable toxicity and immunogenicity. We conclude that the perfect enhancer of endosomal escape has yet to be devised. To increase the chances of success, any new transfection system should be tested under relevant conditions and guided by assays that allow direct quantification of endosomal escape.
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Affiliation(s)
- Alexander Klipp
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
| | - Michael Burger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland.
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Hedlund H, Du Rietz H, Johansson JM, Eriksson HC, Zedan W, Huang L, Wallin J, Wittrup A. Single-cell quantification and dose-response of cytosolic siRNA delivery. Nat Commun 2023; 14:1075. [PMID: 36841822 PMCID: PMC9968291 DOI: 10.1038/s41467-023-36752-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Endosomal escape and subsequent cytosolic delivery of small interfering RNA (siRNA) therapeutics is believed to be highly inefficient. Since it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determining delivery bottlenecks and total efficiency has been difficult. Here, we present a confocal microscopy-based method to quantify cytosolic delivery of fluorescently labeled siRNA during lipid-mediated delivery. This method enables detection and quantification of sub-nanomolar cytosolic siRNA release amounts from individual release events with measures of quantitation confidence for each event. Single-cell kinetics of siRNA-mediated knockdown in cells expressing destabilized eGFP unveiled a dose-response relationship with respect to knockdown induction, depth and duration in the range from several hundred to thousands of cytosolic siRNA molecules. Accurate quantification of cytosolic siRNA, and the establishment of the intracellular dose-response relationships, will aid the development and characterization of novel delivery strategies for nucleic acid therapeutics.
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Affiliation(s)
- Hampus Hedlund
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hampus Du Rietz
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Johanna M Johansson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hanna C Eriksson
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Wahed Zedan
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Linfeng Huang
- Wang-Cai Biochemistry Lab, Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Jonas Wallin
- Department of Mathematical Statistics, Lund University, Lund, Sweden
| | - Anders Wittrup
- Department of Clinical Sciences Lund, Oncology, Faculty of Medicine, Lund University, Lund, Sweden. .,Skane University Hospital, Oncology, Lund, Sweden. .,Wallenberg Center for Molecular Medicine, Lund, Sweden.
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Nakamura M, Fujiwara K, Doi N. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide. J Nanobiotechnology 2022; 20:458. [PMID: 36303212 DOI: 10.1186/s12951-022-01667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although protein-based methods using cell-penetrating peptides such as TAT have been expected to provide an alternative approach to siRNA delivery, the low efficiency of endosomal escape of siRNA/protein complexes taken up into cells by endocytosis remains a problem. Here, to overcome this problem, we adopted the membrane penetration-enhancing peptide S19 from human syncytin 1 previously identified in our laboratory. RESULTS We prepared fusion proteins in which the S19 and TAT peptides were fused to the viral RNA-binding domains (RBDs) as carrier proteins, added the RBD-S19-TAT/siRNA complex to human cultured cells, and investigated the cytoplasmic delivery of the complex and the knockdown efficiency of target genes. We found that the intracellular uptake of the RBD-S19-TAT/siRNA complex was increased compared to that of the RBD-TAT/siRNA complex, and the expression level of the target mRNA was decreased. Because siRNA must dissociate from RBD and bind to Argonaute 2 (Ago2) to form the RNA-induced silencing complex (RISC) after the protein/siRNA complex is delivered into the cytoplasm, a dilemma arises: stronger binding between RBD and siRNA increases intracellular uptake but makes RISC formation more difficult. Thus, we next prepared fusion proteins in which the S19 and TAT peptides were fused with Ago2 instead of RBD and found that the efficiencies of siRNA delivery and knockdown obtained using TAT-S19-Ago2 were higher than those using TAT-Ago2. In addition, we found that the smallest RISC delivery induced faster knockdown than traditional siRNA lipofection, probably due to the decreased time required for RISC formation in the cytoplasm. CONCLUSION These results indicated that S19 and TAT-fused siRNA-binding proteins, especially Ago2, should be useful for the rapid and efficient delivery of siRNA without the addition of any endosome-disrupting agent.
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Affiliation(s)
- Momoko Nakamura
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
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Yang NJ. Kinetic Competition Screening of Yeast-Displayed Libraries for Isolating High Affinity Binders. Methods Mol Biol 2022; 2491:105-115. [PMID: 35482187 DOI: 10.1007/978-1-0716-2285-8_6] [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: 06/14/2023]
Abstract
Yeast surface display is a robust platform for obtaining binders with high affinity. Kinetic competition screening is an effective method for maturing the affinity of binders with strong starting affinities, or when dissociation kinetics are a key consideration for the protein of interest. In this chapter, we describe detailed protocols for setting up and performing a kinetic competition screen. The duration of competition is determined based on the dissociation rate constant of the parental clone measured on the yeast surface. This methodology was successfully used to improve the affinity of a viral double-stranded RNA binding protein with starting affinity in the sub-nanomolar range.
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Affiliation(s)
- Nicole J Yang
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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8
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Wang W, Tai W. RNA binding protein as monodisperse carriers for siRNA delivery. MEDICINE IN DRUG DISCOVERY 2019. [DOI: 10.1016/j.medidd.2019.100011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Pottash AE, Kuffner C, Noonan-Shueh M, Jay SM. Protein-based vehicles for biomimetic RNAi delivery. J Biol Eng 2019; 13:19. [PMID: 30891095 PMCID: PMC6390323 DOI: 10.1186/s13036-018-0130-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022] Open
Abstract
Broad translational success of RNA interference (RNAi) technology depends on the development of effective delivery approaches. To that end, researchers have developed a variety of strategies, including chemical modification of RNA, viral and non-viral transfection approaches, and incorporation with delivery vehicles such as polymer- and lipid-based nanoparticles, engineered and native proteins, extracellular vesicles (EVs), and others. Among these, EVs and protein-based vehicles stand out as biomimetically-inspired approaches, as both proteins (e.g. Apolipoprotein A-1, Argonaute 2, and Arc) and EVs mediate intercellular RNA transfer physiologically. Proteins specifically offer significant therapeutic potential due to their biophysical and biochemical properties as well as their ability to facilitate and tolerate manipulation; these characteristics have made proteins highly successful translational therapeutic molecules in the last two decades. This review covers engineered protein vehicles for RNAi delivery along with what is currently known about naturally-occurring extracellular RNA carriers towards uncovering design rules that will inform future engineering of protein-based vehicles.
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Affiliation(s)
- Alex Eli Pottash
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Christopher Kuffner
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Madeleine Noonan-Shueh
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA
| | - Steven M Jay
- 1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA.,2Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 USA.,3Program in Molecular and Cellular Biology, University of Maryland, College Park, MD 20742 USA
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