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Tatarūnas V, Čiapienė I, Giedraitienė A. Precise Therapy Using the Selective Endogenous Encapsidation for Cellular Delivery Vector System. Pharmaceutics 2024; 16:292. [PMID: 38399346 PMCID: PMC10893373 DOI: 10.3390/pharmaceutics16020292] [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: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Interindividual variability in drug response is a major problem in the prescription of pharmacological treatments. The therapeutic effect of drugs can be influenced by human genes. Pharmacogenomic guidelines for individualization of treatment have been validated and used for conventional dosage forms. However, drugs can often target non-specific areas and produce both desired and undesired pharmacological effects. The use of nanoparticles, liposomes, or other available forms for drug formulation could help to overcome the latter problem. Virus-like particles based on retroviruses could be a potential envelope for safe and efficient drug formulations. Human endogenous retroviruses would make it possible to overcome the host immune response and deliver drugs to the desired target. PEG10 is a promising candidate that can bind to mRNA because it is secreted like an enveloped virus-like extracellular vesicle. PEG10 is a retrotransposon-derived gene that has been domesticated. Therefore, formulations with PEG10 may have a lower immunogenicity. The use of existing knowledge can lead to the development of suitable drug formulations for the precise treatment of individual diseases.
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Affiliation(s)
- Vacis Tatarūnas
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania; (V.T.); (I.Č.)
| | - Ieva Čiapienė
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania; (V.T.); (I.Č.)
| | - Agnė Giedraitienė
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Eiveniu 4, LT 50161 Kaunas, Lithuania
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2
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Wendlandt T, Koch C, Britz B, Liedek A, Schmidt N, Werner S, Gleba Y, Vahidpour F, Welden M, Poghossian A, Schöning MJ, Eber FJ, Jeske H, Wege C. Facile Purification and Use of Tobamoviral Nanocarriers for Antibody-Mediated Display of a Two-Enzyme System. Viruses 2023; 15:1951. [PMID: 37766357 PMCID: PMC10536799 DOI: 10.3390/v15091951] [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: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Immunosorbent turnip vein clearing virus (TVCV) particles displaying the IgG-binding domains D and E of Staphylococcus aureus protein A (PA) on every coat protein (CP) subunit (TVCVPA) were purified from plants via optimized and new protocols. The latter used polyethylene glycol (PEG) raw precipitates, from which virions were selectively re-solubilized in reverse PEG concentration gradients. This procedure improved the integrity of both TVCVPA and the wild-type subgroup 3 tobamovirus. TVCVPA could be loaded with more than 500 IgGs per virion, which mediated the immunocapture of fluorescent dyes, GFP, and active enzymes. Bi-enzyme ensembles of cooperating glucose oxidase and horseradish peroxidase were tethered together on the TVCVPA carriers via a single antibody type, with one enzyme conjugated chemically to its Fc region, and the other one bound as a target, yielding synthetic multi-enzyme complexes. In microtiter plates, the TVCVPA-displayed sugar-sensing system possessed a considerably increased reusability upon repeated testing, compared to the IgG-bound enzyme pair in the absence of the virus. A high coverage of the viral adapters was also achieved on Ta2O5 sensor chip surfaces coated with a polyelectrolyte interlayer, as a prerequisite for durable TVCVPA-assisted electrochemical biosensing via modularly IgG-assembled sensor enzymes.
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Affiliation(s)
- Tim Wendlandt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Claudia Koch
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Beate Britz
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Anke Liedek
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Nora Schmidt
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Stefan Werner
- Nambawan Biotech GmbH/Now at Icon Genetics GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Yuri Gleba
- Nomad Bioscience GmbH, Weinbergweg 22, 06120 Halle, Germany;
| | - Farnoosh Vahidpour
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | - Melanie Welden
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
| | | | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany; (F.V.); (M.W.); (M.J.S.)
- Institute of Biological Information Processing (IBI-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabian J. Eber
- Department of Mechanical and Process Engineering, Offenburg University of Applied Sciences, 77652 Offenburg, Germany;
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany; (T.W.); (C.K.); (N.S.)
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Harun-Ur-Rashid M, Jahan I, Foyez T, Imran AB. Bio-Inspired Nanomaterials for Micro/Nanodevices: A New Era in Biomedical Applications. MICROMACHINES 2023; 14:1786. [PMID: 37763949 PMCID: PMC10536921 DOI: 10.3390/mi14091786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
Exploring bio-inspired nanomaterials (BINMs) and incorporating them into micro/nanodevices represent a significant development in biomedical applications. Nanomaterials, engineered to imitate biological structures and processes, exhibit distinctive attributes such as exceptional biocompatibility, multifunctionality, and unparalleled versatility. The utilization of BINMs demonstrates significant potential in diverse domains of biomedical micro/nanodevices, encompassing biosensors, targeted drug delivery systems, and advanced tissue engineering constructs. This article thoroughly examines the development and distinctive attributes of various BINMs, including those originating from proteins, DNA, and biomimetic polymers. Significant attention is directed toward incorporating these entities into micro/nanodevices and the subsequent biomedical ramifications that arise. This review explores biomimicry's structure-function correlations. Synthesis mosaics include bioprocesses, biomolecules, and natural structures. These nanomaterials' interfaces use biomimetic functionalization and geometric adaptations, transforming drug delivery, nanobiosensing, bio-inspired organ-on-chip systems, cancer-on-chip models, wound healing dressing mats, and antimicrobial surfaces. It provides an in-depth analysis of the existing challenges and proposes prospective strategies to improve the efficiency, performance, and reliability of these devices. Furthermore, this study offers a forward-thinking viewpoint highlighting potential avenues for future exploration and advancement. The objective is to effectively utilize and maximize the application of BINMs in the progression of biomedical micro/nanodevices, thereby propelling this rapidly developing field toward its promising future.
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Affiliation(s)
- Mohammad Harun-Ur-Rashid
- Department of Chemistry, International University of Business Agriculture and Technology, Dhaka 1230, Bangladesh;
| | - Israt Jahan
- Department of Cell Physiology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan;
| | - Tahmina Foyez
- Department of Pharmacy, United International University, Dhaka 1212, Bangladesh;
| | - Abu Bin Imran
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
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Ikwuagwu B, Tullman-Ercek D. Virus-like particles for drug delivery: a review of methods and applications. Curr Opin Biotechnol 2022; 78:102785. [PMID: 36099859 DOI: 10.1016/j.copbio.2022.102785] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/06/2022] [Accepted: 08/04/2022] [Indexed: 12/14/2022]
Abstract
Virus-like particles (VLPs) are self-assembling protein nanoparticles that have great promise as vectors for drug delivery. VLPs are derived from viruses but retain none of their infection or replication capabilities. These protein particles have defined surface chemistries, uniform sizes, and stability properties that make them attractive starting points for drug-delivery scaffolds. Here, we review recent advances in tailoring VLPs for drug-delivery applications, including VLP platform engineering approaches as well as methods for cargo loading, activation, and release. Finally, we highlight several successes using VLPs for drug delivery in model systems.
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Affiliation(s)
- Bon Ikwuagwu
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological Institute B486, Evanston, IL 60208, USA.
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5
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Shahgolzari M, Dianat-Moghadam H, Fiering S. Multifunctional plant virus nanoparticles in the next generation of cancer immunotherapies. Semin Cancer Biol 2022; 86:1076-1085. [PMID: 34375725 PMCID: PMC8821734 DOI: 10.1016/j.semcancer.2021.07.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/27/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Plant virus nanoparticles (PVNPs) have inherent immune stimulatory ability, and have been investigated as immune adjuvants to stimulate an anti-tumor immune response. The combination of immune stimulation, nanoparticle structure and the ability to deliver other therapeutic molecules provides a flexible platform for cancer immunotherapy. Researching multifunctional PVNPs and their modification will generate novel reagents for cancer immunotherapy. Here we review the properties of PVNPs, and their potential for clinical utilization to activate anti-tumor innate and lymphoid immune responses. PVNPs have potential utility for cancer immunotherapy as vaccine adjuvant, and delivery systems for other reagents as mono immunotherapy or combined with other immunotherapies. This review outlines the potential and challenges in developing PVNPs as cancer immunotherapy reagents.
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Affiliation(s)
- Mehdi Shahgolzari
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Dianat-Moghadam
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Steven Fiering
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth and Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States.
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6
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Plug-and-Display Photo-Switchable Systems on Plant Virus Nanoparticles. BIOTECH (BASEL (SWITZERLAND)) 2022; 11:biotech11040049. [PMID: 36278561 PMCID: PMC9589989 DOI: 10.3390/biotech11040049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Light can be used to regulate protein interactions with a high degree of spatial and temporal precision. Photo-switchable systems therefore allow the development of controllable protein complexes that can influence various cellular and molecular processes. Here, we describe a plant virus-based nanoparticle shuttle for the distribution of proteins that can be released when exposed to light. Potato virus X (PVX) is often used as a presentation system for heterologous proteins and epitopes, and has ideal properties for biomedical applications such as good tissue penetration and the ability to form hydrogels that present signaling molecules and promote cell adhesion. In this study, we describe three different systems attached to the surface of PVX particles: LOVTRAP, BphP1/QPAS1 and Dronpa145N. We demonstrated the functionality of all three photo-switchable protein complexes in vitro and the successful loading and unloading of PVX particles. The new systems provide the basis for promising applications in the biomedical and biomaterial sciences.
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7
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Shih CP, Tang X, Kuo CW, Chueh DY, Chen P. Design principles of bioinspired interfaces for biomedical applications in therapeutics and imaging. Front Chem 2022; 10:990171. [PMID: 36405322 PMCID: PMC9673126 DOI: 10.3389/fchem.2022.990171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/08/2022] [Indexed: 09/29/2023] Open
Abstract
In the past two decades, we have witnessed rapid developments in nanotechnology, especially in biomedical applications such as drug delivery, biosensing, and bioimaging. The most commonly used nanomaterials in biomedical applications are nanoparticles, which serve as carriers for various therapeutic and contrast reagents. Since nanomaterials are in direct contact with biological samples, biocompatibility is one of the most important issues for the fabrication and synthesis of nanomaterials for biomedical applications. To achieve specific recognition of biomolecules for targeted delivery and biomolecular sensing, it is common practice to engineer the surfaces of nanomaterials with recognition moieties. This mini-review summarizes different approaches for engineering the interfaces of nanomaterials to improve their biocompatibility and specific recognition properties. We also focus on design strategies that mimic biological systems such as cell membranes of red blood cells, leukocytes, platelets, cancer cells, and bacteria.
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Affiliation(s)
- Chun-Pei Shih
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Xiaofang Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Chiung Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Di-Yen Chueh
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Physics, Academia Sinica, Taipei, Taiwan
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8
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Hou C, Xu H, Jiang X, Li Y, Deng S, Zang M, Xu J, Liu J. Virus-Based Supramolecular Structure and Materials: Concept and Prospects. ACS APPLIED BIO MATERIALS 2021; 4:5961-5974. [PMID: 35006905 DOI: 10.1021/acsabm.1c00633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rodlike and spherelike viruses are various monodisperse nanoparticles that can display small molecules or polymers with unique distribution following chemical modifications. Because of the monodisperse property, aggregates in synthetic protein-polymer nanoparticles could be eliminated, thus improving the probability for application in protein-polymer drug. In addition, the monodisperse virus could direct the growth of metal materials or inorganic materials, finding applications in hydrogel, drug delivery, and optoelectronic and catalysis materials. Benefiting from the advantages, the virus or viruslike particles have been widely explored in the field of supramolecular chemistry. In this review, we describe the modification and application of virus and viruslike particles in surpramolecular structures and biomedical research.
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Affiliation(s)
- Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Hanxin Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xiaojia Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yijia Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shengchao Deng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Mingsong Zang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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Li J, Zhao H, Zheng L, An W. Advances in Synthetic Biology and Biosafety Governance. Front Bioeng Biotechnol 2021; 9:598087. [PMID: 33996776 PMCID: PMC8120004 DOI: 10.3389/fbioe.2021.598087] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/17/2021] [Indexed: 11/22/2022] Open
Abstract
Tremendous advances in the field of synthetic biology have been witnessed in multiple areas including life sciences, industrial development, and environmental bio-remediation. However, due to the limitations of human understanding in the code of life, any possible intended or unintended uses of synthetic biology, and other unknown reasons, the development and application of this technology has raised concerns over biosafety, biosecurity, and even cyberbiosecurity that they may expose public health and the environment to unknown hazards. Over the past decades, some countries in Europe, America, and Asia have enacted laws and regulations to control the application of synthetic biology techniques in basic and applied research and this has resulted in some benefits. The outbreak of the COVID-19 caused by novel coronavirus SARS-CoV-2 and various speculations about the origin of this virus have attracted more attention on bio-risk concerns of synthetic biology because of its potential power and uncertainty in the synthesis and engineering of living organisms. Therefore, it is crucial to scrutinize the control measures put in place to ensure appropriate use, promote the development of synthetic biology, and strengthen the governance of pathogen-related research, although the true origin of coronavirus remains hotly debated and unresolved. This article reviews the recent progress made in the field of synthetic biology and combs laws and regulations in governing bio-risk issues. We emphasize the urgent need for legislative and regulatory constraints and oversight to address the biological risks of synthetic biology.
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Affiliation(s)
- Jing Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huimiao Zhao
- College of Humanities and Law, Beijing University of Chemical Technology, Beijing, China
| | - Lanxin Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wenlin An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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10
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Matsuura K, Fujita S. A Photoresponsive Artificial Viral Capsid Self-Assembled from an Azobenzene-Containing β-Annulus Peptide. Int J Mol Sci 2021; 22:ijms22084028. [PMID: 33919771 PMCID: PMC8070682 DOI: 10.3390/ijms22084028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
Photoinduced structural changes in peptides can dynamically control the formation and dissociation of supramolecular peptide materials. However, the existence of photoresponsive viral capsids in nature remains unknown. In this study, we constructed an artificial viral capsid possessing a photochromic azobenzene moiety on the peptide backbone. An azobenzene-containing β-annulus peptide derived from the tomato bushy stunt virus was prepared through solid-phase synthesis using Fmoc-3-[(3-aminomethyl)-phenylazo]phenylacetic acid. The azobenzene-containing β-annulus (β-Annulus-Azo) peptide showed a reversible trans/cis isomerization property. The β-annulus-azo peptide self-assembled at 25 μM into capsids with the diameters of 30–50 nm before UV irradiation (trans-form rich), whereas micrometer-sized aggregates were formed after UV irradiation (cis-form rich). The artificial viral capsid possessing azobenzene facilitated the encapsulation of fluorescent-labeled dextrans and their photoinduced release from the capsid.
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Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan;
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
- Correspondence: ; Tel.: +81-857-31-5262
| | - Seiya Fujita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan;
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11
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Thadani NN, Zhou Q, Reyes Gamas K, Butler S, Bueno C, Schafer NP, Morcos F, Wolynes PG, Suh J. Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophys J 2020; 120:489-503. [PMID: 33359833 DOI: 10.1016/j.bpj.2020.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 01/03/2023] Open
Abstract
Adeno-associated virus (AAV) is a promising gene therapy vector because of its efficient gene delivery and relatively mild immunogenicity. To improve delivery target specificity, researchers use combinatorial and rational library design strategies to generate novel AAV capsid variants. These approaches frequently propose high proportions of nonforming or noninfective capsid protein sequences that reduce the effective depth of synthesized vector DNA libraries, thereby raising the discovery cost of novel vectors. We evaluated two computational techniques for their ability to estimate the impact of residue mutations on AAV capsid protein-protein interactions and thus predict changes in vector fitness, reasoning that these approaches might inform the design of functionally enriched AAV libraries and accelerate therapeutic candidate identification. The Frustratometer computes an energy function derived from the energy landscape theory of protein folding. Direct-coupling analysis (DCA) is a statistical framework that captures residue coevolution within proteins. We applied the Frustratometer to select candidate protein residues predicted to favor assembled or disassembled capsid states, then predicted mutation effects at these sites using the Frustratometer and DCA. Capsid mutants were experimentally assessed for changes in virus formation, stability, and transduction ability. The Frustratometer-based metric showed a counterintuitive correlation with viral stability, whereas a DCA-derived metric was highly correlated with virus transduction ability in the small population of residues studied. Our results suggest that coevolutionary models may be able to elucidate complex capsid residue-residue interaction networks essential for viral function, but further study is needed to understand the relationship between protein energy simulations and viral capsid metastability.
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Affiliation(s)
| | - Qin Zhou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas
| | | | - Susan Butler
- Department of Bioengineering, Rice University, Houston, Texas
| | - Carlos Bueno
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas; Center for Systems Biology, University of Texas at Dallas, Richardson, Texas; Department of Bioengineering, University of Texas at Dallas, Richardson, Texas
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas; Department of Biosciences, Rice University, Houston, Texas; Department of Physics, Rice University, Houston, Texas
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas; Department of Biosciences, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, Texas.
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12
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Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments. Proc Natl Acad Sci U S A 2020; 117:19643-19652. [PMID: 32759221 DOI: 10.1073/pnas.2011125117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
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Dickmeis C, Kauth L, Commandeur U. From infection to healing: The use of plant viruses in bioactive hydrogels. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1662. [PMID: 32677315 DOI: 10.1002/wnan.1662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Plant viruses show great diversity in shape and size, but each species forms unique nucleoprotein particles that are symmetrical and monodisperse. The genetically programed structure of plant viruses allows them to be modified by genetic engineering, bioconjugation, or encapsulation to form virus nanoparticles (VNPs) that are suitable for a broad range of applications. Plant VNPs can be used to present foreign proteins or epitopes, to construct inorganic hybrid materials, or to carry molecular cargos, allowing their utilization as imaging reagents, immunomodulators, therapeutics, nanoreactors, and biosensors. The medical applications of plant viruses benefit from their inability to infect and replicate in human cells. The structural properties of plant viruses also make them useful as components of hydrogels for tissue engineering. Hydrogels are three-dimensional networks composed of hydrophilic polymers that can absorb large amounts of water. They are used as supports for tissue regeneration, as reservoirs for controlled drug release, and are found in contact lenses, many wound healing materials, and hygiene products. They are also useful in ecological applications such as wastewater treatment. Hydrogel-based matrices are structurally similar to the native extracellular matrix (ECM) and provide a scaffold for the attachment of cells. To fully replicate the functions of the ECM it is necessary to augment hydrogels with biological cues that regulate cellular interactions. This can be achieved by incorporating functionalized VNPs displaying ligands that influence the mechanical characteristics of hydrogels and their biological properties, promoting the survival, proliferation, migration, and differentiation of embedded cells. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement.
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Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Louisa Kauth
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
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14
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Thadani NN, Yang J, Moyo B, Lee CM, Chen MY, Bao G, Suh J. Site-Specific Post-translational Surface Modification of Adeno-Associated Virus Vectors Using Leucine Zippers. ACS Synth Biol 2020; 9:461-467. [PMID: 32068391 PMCID: PMC7323921 DOI: 10.1021/acssynbio.9b00341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Adeno-associated virus (AAV) is widely favored as a gene therapy vector, tested in over 200 clinical trials internationally. To improve targeted delivery a variety of genetic capsid modifications, such as insertion of targeting proteins/peptides into the capsid shell, have been explored with some success but larger insertions often have unpredictable deleterious impacts on capsid formation and gene delivery. Here, we demonstrate a modular platform for the integration of exogenous peptides and proteins onto the AAV capsid post-translationally while preserving vector functionality. We decorated the AAV capsid with leucine-zipper coiled-coil binding motifs that exhibit specific noncovalent heterodimerization. AAV capsids successfully display hexahistidine tagged-peptides using this approach, as demonstrated through nickel column affinity. This protein display platform may facilitate the incorporation of biological moieties on the AAV surface, expanding possibilities for vector enhancement and engineering.
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Affiliation(s)
- Nicole N Thadani
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Joanna Yang
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Buhle Moyo
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Maria Y Chen
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77030, United States
- Systems, Synthetic and Physical Biology Program, Rice University, Houston, Texas 77030, United States
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15
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Poghossian A, Jablonski M, Molinnus D, Wege C, Schöning MJ. Field-Effect Sensors for Virus Detection: From Ebola to SARS-CoV-2 and Plant Viral Enhancers. FRONTIERS IN PLANT SCIENCE 2020; 11:598103. [PMID: 33329662 PMCID: PMC7732584 DOI: 10.3389/fpls.2020.598103] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/26/2020] [Indexed: 05/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a novel human infectious disease provoked by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, no specific vaccines or drugs against COVID-19 are available. Therefore, early diagnosis and treatment are essential in order to slow the virus spread and to contain the disease outbreak. Hence, new diagnostic tests and devices for virus detection in clinical samples that are faster, more accurate and reliable, easier and cost-efficient than existing ones are needed. Due to the small sizes, fast response time, label-free operation without the need for expensive and time-consuming labeling steps, the possibility of real-time and multiplexed measurements, robustness and portability (point-of-care and on-site testing), biosensors based on semiconductor field-effect devices (FEDs) are one of the most attractive platforms for an electrical detection of charged biomolecules and bioparticles by their intrinsic charge. In this review, recent advances and key developments in the field of label-free detection of viruses (including plant viruses) with various types of FEDs are presented. In recent years, however, certain plant viruses have also attracted additional interest for biosensor layouts: Their repetitive protein subunits arranged at nanometric spacing can be employed for coupling functional molecules. If used as adapters on sensor chip surfaces, they allow an efficient immobilization of analyte-specific recognition and detector elements such as antibodies and enzymes at highest surface densities. The display on plant viral bionanoparticles may also lead to long-time stabilization of sensor molecules upon repeated uses and has the potential to increase sensor performance substantially, compared to conventional layouts. This has been demonstrated in different proof-of-concept biosensor devices. Therefore, richly available plant viral particles, non-pathogenic for animals or humans, might gain novel importance if applied in receptor layers of FEDs. These perspectives are explained and discussed with regard to future detection strategies for COVID-19 and related viral diseases.
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Affiliation(s)
| | - Melanie Jablonski
- Institute of Nano- and Biotechnologies, FH Aachen University of Applied Sciences, Jülich, Germany
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Denise Molinnus
- Institute of Nano- and Biotechnologies, FH Aachen University of Applied Sciences, Jülich, Germany
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
- *Correspondence: Christina Wege,
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, FH Aachen University of Applied Sciences, Jülich, Germany
- Institute of Complex Systems (ICS-8), Research Centre Jülich GmbH, Jülich, Germany
- Michael J. Schöning,
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16
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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