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Thanaskody K, Natashah FN, Nordin F, Kamarul Zaman WSW, Tye GJ. Designing molecules: directing stem cell differentiation. Front Bioeng Biotechnol 2024; 12:1396405. [PMID: 38803845 PMCID: PMC11129639 DOI: 10.3389/fbioe.2024.1396405] [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: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Stem cells have been widely applied in regenerative and therapeutic medicine for their unique regenerative properties. Although much research has shown their potential, it remains tricky in directing stem cell differentiation. The advancement of genetic and therapeutic technologies, however, has facilitated this issue through development of design molecules. These molecules are designed to overcome the drawbacks previously faced, such as unexpected differentiation outcomes and insufficient migration of endogenous or exogenous MSCs. Here, we introduced aptamer, bacteriophage, and biological vectors as design molecules and described their characteristics. The methods of designing/developing discussed include various Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedures, in silico approaches, and non-SELEX methods for aptamers, and genetic engineering methods such as homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), Bacteriophage Recombineering with Infectious Particles (BRIP), and genome rebooting for bacteriophage. For biological vectors, methods such as alternate splicing, multiple promoters, internal ribosomal entry site, CRISPR-Cas9 system and Cre recombinase mediated recombination were used to design viral vectors, while non-viral vectors like exosomes are generated through parental cell-based direct engineering. Besides that, we also discussed the pros and cons, and applications of each design molecule in directing stem cell differentiation to illustrate their great potential in stem cells research. Finally, we highlighted some safety and efficacy concerns to be considered for future studies.
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Affiliation(s)
- Kalaiselvaan Thanaskody
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fajriyah Nur Natashah
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Fazlina Nordin
- Centre for Tissue Engineering and Regenerative Medicine (CTERM), Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Wan Safwani Wan Kamarul Zaman
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
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Mallick B, Dutta A, Mondal P, Dutta M. Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches. Proteins 2024; 92:637-648. [PMID: 38146101 DOI: 10.1002/prot.26653] [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: 08/26/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Bacteriophages are the natural predators of bacteria and are available abundantly everywhere in nature. Lytic phages can specifically infect their bacterial host (through attachment to the receptor) and use their host replication machinery to replicate rapidly, a feature that enables them to kill a disease-causing bacteria. Hence, phage attachment to the host bacteria is the first important step of the infection process. It is reported in this study that the receptor could be an LPS which is responsible for the attachment of the Sfk20 phage to its host (Shigella flexneri 2a). Phage Sfk20 bacteriolytic activity was examined for preliminary optimization of phage titer. The phage Sfk20 viability at different saline conditions was conducted. The LC-MS/MS technique used here for detecting and identifying 40 Sfk20 phage proteins helped us to get an initial understanding of the structural landscape of phage Sfk20. From the identified proteins, six structurally significant proteins were selected for structure prediction using two neural network systems: AlphaFold2 and ESMFold, and one homology modeling software: Phyre2. Later the performance of these modeling systems was compared using various metrics. We conclude from the available and generated information that AlphaFold2 and Phyre2 perform better than ESMFold for predicting Sfk20 phage protein structures.
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Affiliation(s)
- Bani Mallick
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Aninda Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Payel Mondal
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Moumita Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
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3
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Sittiju P, Wudtiwai B, Chongchai A, Hajitou A, Kongtawelert P, Pothacharoen P, Suwan K. Bacteriophage-based particles carrying the TNF-related apoptosis-inducing ligand (TRAIL) gene for targeted delivery in hepatocellular carcinoma. NANOSCALE 2024; 16:6603-6617. [PMID: 38470366 PMCID: PMC10977282 DOI: 10.1039/d3nr05660k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The TRAIL (Tumour Necrosis Factor-Related Apoptosis-Inducing Ligand) is a promising candidate for cancer treatment due to its unique ability to selectively induce programmed cell death, or apoptosis, in cancer cells while sparing healthy ones. This selectivity arises from the preferential binding of the TRAIL to death receptors on cancer cells, triggering a cascade of events that lead to their demise. However, significant limitations in using the TRAIL for cancer treatment are the administration of the TRAIL protein that can potentially lead to tissue toxicity (off-target) and the short half-life of the TRAIL in the body which may necessitate frequent and sustained administration; these can pose logistical challenges for long-term treatment regimens. We have devised a novel approach for surmounting these limitations by introducing the TRAIL gene directly into cancer cells, enabling them to produce the TRAIL locally and subsequently trigger apoptosis. A novel gene delivery system such as a bacteriophage-based particle TPA (transmorphic phage/AAV) was utilized to address these limitations. TPA is a hybrid M13 filamentous bacteriophage particle encapsulating a therapeutic gene cassette with inverted terminal repeats (ITRs) from adeno-associated viruses (AAVs). The particle also showed a tumour targeting ligand, CDCRGDCFC (RGD4C), on its capsid (RGD4C.TPA) to target the particle to cancer cells. RGD4C selectively binds to αvβ3 and αvβ5 integrins overexpressed on the surface of most of the cancer cells but is barely present on normal cells. Hepatocellular carcinoma (HCC) was chosen as a model because it has one of the lowest survival rates among cancers. We demonstrated that human HCC cell lines (Huh-7 and HepG2) express αvβ5 integrin receptors on their surface. These HCC cells also express death receptors and TRAIL-binding receptors. We showed that the targeted TPA particle carrying the transmembrane TRAIL gene (RGD4C.TPA-tmTRAIL) selectively and efficiently delivered the tmTRAIL gene to HCC cells resulting in the production of tmTRAIL from transduced cells and subsequently induced apoptotic death of HCC cells. This tumour-targeted particle can be an excellent candidate for the targeted gene therapy of HCC.
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Affiliation(s)
- Pattaralawan Sittiju
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
- Cancer Phage Therapy Group, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Benjawan Wudtiwai
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Aitthiphon Chongchai
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Amin Hajitou
- Cancer Phage Therapy Group, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Peraphan Pothacharoen
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.
| | - Keittisak Suwan
- Cancer Phage Therapy Group, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, UK.
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4
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Mucke HA. Patent Highlights June-July 2023. Pharm Pat Anal 2024. [PMID: 38497750 DOI: 10.4155/ppa-2023-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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Muikham I, Thongsum O, Jaranathummakul S, Wathammawut A, Chotwiwatthanakun C, Jariyapong P, Weerachatyanukul W. Interior modification of Macrobrachium rosenbergii nodavirus-like particle enhances encapsulation of VP37-dsRNA against shrimp white spot syndrome infection. BMC Vet Res 2024; 20:91. [PMID: 38459500 PMCID: PMC10921773 DOI: 10.1186/s12917-024-03936-w] [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: 09/08/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Application of a virus-like particle (VLP) as a nanocontainer to encapsulate double stranded (ds)RNA to control viral infection in shrimp aquaculture has been extensively reported. In this study, we aimed at improving VLP's encapsulation efficiency which should lead to a superior fighting weapon with disastrous viruses. RESULTS We constructed 2 variants of chimeric Macrobrachium rosenbergii nodavirus (MrNV)-like particles (V1- and V2-MrN-VLPs) and tested their efficiency to encapsulate VP37 double stranded RNA as well as WSSV protection in P. vannamei. Two types of short peptides, RNA-binding domain (RBD) and deca-arginine (10R) were successfully engineered into the interior surface of VLP, the site where the contact with VP37-dsRNA occurs. TEM and dynamic light scattering (DLS) analyses revealed that the chimeric VLPs remained their assembling property to be an icosahedral symmetric particle with a diameter of about 30 nm, similar to the original MrN-VLP particle. The superior encapsulation efficiency of VP37-dsRNA into V2-MrN-VLP was achieved, which was slightly better than that of V1-MrN-VLP but far better (1.4-fold) than its parental V0-MrN-VLP which the mole ratio of 7.5-10.5 for all VLP variants. The protection effect against challenging WSSV (as gauged from the level of VP37 gene and the remaining viral copy number in shrimp) was significantly improved in both V1- and V2-MrN-VLP compared with an original V0-MrN-VLP template. CONCLUSION MrN-VLP (V0-) were re-engineered interiorly with RBD (V1-) and 10R (V2-) peptides which had an improved VP37-dsRNA encapsulation capability. The protection effect against WSSV infection through shrimp administration with dsRNA + V1-/V2-MrN VLPs was experimentally evident.
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Affiliation(s)
- Itsares Muikham
- Department of Anatomy, Faculty of Science, Mahidol University, Rama 6 Rd., Rachathewi, Bangkok, 10400, Thailand
| | - Orawan Thongsum
- Department of Anatomy, Faculty of Science, Mahidol University, Rama 6 Rd., Rachathewi, Bangkok, 10400, Thailand
| | - Somkid Jaranathummakul
- Department of Anatomy, Faculty of Science, Mahidol University, Rama 6 Rd., Rachathewi, Bangkok, 10400, Thailand
| | - Atthaboon Wathammawut
- Department of Anatomy, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
| | - Charoonroj Chotwiwatthanakun
- Faculty of Science, Mahidol University, Nakhonsawan Campus, Nakhonsawan, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Mahidol University, Bangkok, Thailand
| | - Pitchanee Jariyapong
- Department of Medical Science, School of Medicine, Walailak University, Thasala District, Nakhonsrithammarat, 80160, Thailand.
| | - Wattana Weerachatyanukul
- Department of Anatomy, Faculty of Science, Mahidol University, Rama 6 Rd., Rachathewi, Bangkok, 10400, Thailand.
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Li Y, Yang KD, Kong DC, Li XM, Duan HY, Ye JF. Harnessing filamentous phages for enhanced stroke recovery. Front Immunol 2024; 14:1343788. [PMID: 38299142 PMCID: PMC10829096 DOI: 10.3389/fimmu.2023.1343788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Stroke poses a critical global health challenge, leading to substantial morbidity and mortality. Existing treatments often miss vital timeframes and encounter limitations due to adverse effects, prompting the pursuit of innovative approaches to restore compromised brain function. This review explores the potential of filamentous phages in enhancing stroke recovery. Initially antimicrobial-centric, bacteriophage therapy has evolved into a regenerative solution. We explore the diverse role of filamentous phages in post-stroke neurological restoration, emphasizing their ability to integrate peptides into phage coat proteins, thereby facilitating recovery. Experimental evidence supports their efficacy in alleviating post-stroke complications, immune modulation, and tissue regeneration. However, rigorous clinical validation is essential to address challenges like dosing and administration routes. Additionally, genetic modification enhances their potential as injectable biomaterials for complex brain tissue issues. This review emphasizes innovative strategies and the capacity of filamentous phages to contribute to enhanced stroke recovery, as opposed to serving as standalone treatment, particularly in addressing stroke-induced brain tissue damage.
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Affiliation(s)
- Yang Li
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
- School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- School of Nursing, Jilin University, Changchun, China
| | - De-cai Kong
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiao-meng Li
- School of Nursing, Jilin University, Changchun, China
| | - Hao-yu Duan
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jun-feng Ye
- General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
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Peng H, Chen IA. Preparation of Bioconjugates of Chimeric M13 Phage and Gold Nanorods. Methods Mol Biol 2024; 2793:131-141. [PMID: 38526728 DOI: 10.1007/978-1-0716-3798-2_9] [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: 03/27/2024]
Abstract
Phage-nanomaterial conjugates are functional bio-nanofibers with various applications. While phage display can select for phages with desired genetically encoded functions and properties, nanomaterials can endow the phages with additional features at nanoscale dimensions. Therefore, combining phages with nanotechnology can construct bioconjugates with unique characteristics. One strategy for filamentous phages is to adsorb nanoparticles onto the side wall, composed of pVIII subunits, through electrostatic interactions. However, a noncovalent approach may cause offloading if the environment changes, potentially causing side effects especially for in vivo applications. Therefore, building stable phage-bioconjugates is an important need. We previously reported the construction of chimeric M13 phage conjugated with gold nanorods, named "phanorods," without weakening the binding affinity to the bacterial host cells. Herein, we give a detailed protocol for preparing the chimeric M13 phage and covalently conjugating gold nanorods to the phage.
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Affiliation(s)
- Huan Peng
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
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8
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Zhang YW, Zheng N, Chou DHC. Serine-mediated hydrazone ligation displaying insulin-like peptides on M13 phage pIII. Org Biomol Chem 2023; 21:8902-8909. [PMID: 37905463 DOI: 10.1039/d3ob01487h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phage display has emerged as a tool for the discovery of therapeutic antibodies and proteins. However, the effective display and engineering of structurally complex proteins, such as insulin, pose significant challenges due to the sequence of insulin, which is composed of two peptide chains linked by three disulfide bonds. In this study, we developed a new approach for the display of insulin-like peptides on M13 phage pIII, employing N-terminal serine-mediated hydrazone ligation. The insulin-displaying phage retains the biological binding affinity of human insulin. To address the viability loss after ligation, we introduced a trypsin-cleavable spacer on pIII, enabling insulin-displayed phage library selection. This method offers a general pathway for the display of structurally complex proteins on pIII, enhancing the practicality of selecting chemically modified phage libraries and opening avenues for the engineering of new insulin analogs for the treatment of diabetes by using phage display.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nan Zheng
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, CA 94304, USA.
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9
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De Plano LM, Oddo S, Guglielmino SPP, Caccamo A, Conoci S. Generation of a helper phage for the fluorescent detection of peptide-target interactions by dual-display phages. Sci Rep 2023; 13:18927. [PMID: 37919374 PMCID: PMC10622537 DOI: 10.1038/s41598-023-45087-2] [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: 07/27/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
Phage display is a molecular biology technique that allows the presentation of foreign peptides on the surface of bacteriophages. It is widely utilized for applications such as the discovery of biomarkers, the development of therapeutic antibodies, and the investigation of protein-protein interactions. When employing phages in diagnostic and therapeutic monitoring assays, it is essential to couple them with a detection system capable of revealing and quantifying the interaction between the peptide displayed on the phage capsid and the target of interest. This process is often technically challenging and costly. Here, we generated a fluorescent helper phage vector displaying sfGFP in-frame to the pIII of the capsid proteins. Further, we developed an exchangeable dual-display phage system by combining our newly developed fluorescent helper phage vector with a phagemid vector harboring the engineered pVIII with a peptide-probe. By doing so, the sfGFP and a peptide-probe are displayed on the same phage particle. Notably, our dual-display approach is highly flexible as it allows for easy exchange of the displayed peptide-probe on the pVIII to gain the desired selectivity, while maintaining the sfGFP gene, which allows easy visualization and quantification of the interaction peptide-probe. We anticipate that this system will reduce time and costs compared to the current phage-based detection systems.
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Affiliation(s)
- Laura Maria De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Salvatore Oddo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Salvatore P P Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Antonella Caccamo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy.
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
- Department of Chemistry G. Ciamician, University of Bologna, Via F. Selmi 2, Bologna, Italy
- LAB Sense Beyond Nano-DSFTM CNR, Viale F. Stagno d'Alcontres 31, Messina, Italy
- CNR Institute for Microelectronics and Microsystems, Strada VIII, 5, Catania, Italy
- STMicroelectronics, Stradale Primosole 50, 95121, Catania, Italy
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10
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Carmody CM, Nugen SR. Monomeric streptavidin phage display allows efficient immobilization of bacteriophages on magnetic particles for the capture, separation, and detection of bacteria. Sci Rep 2023; 13:16207. [PMID: 37758721 PMCID: PMC10533843 DOI: 10.1038/s41598-023-42626-9] [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: 02/21/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Immobilization of bacteriophages onto solid supports such as magnetic particles has demonstrated ultralow detection limits as biosensors for the separation and detection of their host bacteria. While the potential impact of magnetized phages is high, the current methods of immobilization are either weak, costly, inefficient, or laborious making them less viable for commercialization. In order to bridge this gap, we have developed a highly efficient, site-specific, and low-cost method to immobilize bacteriophages onto solid supports. While streptavidin-biotin represents an ideal conjugation method, the functionalization of magnetic particles with streptavidin requires square meters of coverage and therefore is not amenable to a low-cost assay. Here, we genetically engineered bacteriophages to allow synthesis of a monomeric streptavidin during infection of the bacterial host. The monomeric streptavidin was fused to a capsid protein (Hoc) to allow site-specific self-assembly of up to 155 fusion proteins per capsid. Biotin coated magnetic nanoparticles were functionalized with mSA-Hoc T4 phage demonstrated in an E. coli detection assay with a limit of detection of < 10 CFU in 100 mLs of water. This work highlights the creation of genetically modified bacteriophages with a novel capsid modification, expanding the potential for bacteriophage functionalized biotechnologies.
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Affiliation(s)
- Caitlin M Carmody
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sam R Nugen
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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11
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Liu Y, Yu W, Wang Q, Cao Z, Li J. Artificially engineered bacteria to treat gastrointestinal disease and cancer. Drug Discov Today 2023; 28:103667. [PMID: 37302541 DOI: 10.1016/j.drudis.2023.103667] [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: 04/11/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Therapeutics based on living organisms provide a roadmap for next-generation biomedicine. Bacteria have an essential role in the development, regulation, and treatment of gastrointestinal disease and cancer through similar mechanisms. However, primitive bacteria lack the stability to overcome complex drug delivery barriers, and their multifunctionality in reinforcing both conventional and emerging therapeutics is limited. Artificially engineered bacteria (ArtBac) with modified surfaces and genetic functions show promise for tackling these problems. Herein, we discuss recent applications of ArtBac as living biomedicine for the treatment of gastrointestinal diseases and tumors. Future perspectives are given to guide the rational design of ArtBac toward safe multifunctional medicine.
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Affiliation(s)
- Yong Liu
- School of Science, Hainan University, Haikou 570228, China
| | - Wenqin Yu
- School of Life Sciences, Hainan University, Haikou 570228, China
| | - Qian Wang
- College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China.
| | - Zhenping Cao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou 570228, China.
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12
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Hussain W, Yang X, Ullah M, Wang H, Aziz A, Xu F, Asif M, Ullah MW, Wang S. Genetic engineering of bacteriophages: Key concepts, strategies, and applications. Biotechnol Adv 2023; 64:108116. [PMID: 36773707 DOI: 10.1016/j.biotechadv.2023.108116] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.
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Affiliation(s)
- Wajid Hussain
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaohan Yang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Department of Biotechnology, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huan Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ayesha Aziz
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fang Xu
- Huazhong University of Science and Technology Hospital, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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13
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Wang R, Li HD, Cao Y, Wang ZY, Yang T, Wang JH. M13 phage: a versatile building block for a highly specific analysis platform. Anal Bioanal Chem 2023:10.1007/s00216-023-04606-w. [PMID: 36867197 PMCID: PMC9982796 DOI: 10.1007/s00216-023-04606-w] [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: 11/14/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/04/2023]
Abstract
Viruses are changing the biosensing and biomedicine landscape due to their multivalency, orthogonal reactivities, and responsiveness to genetic modifications. As the most extensively studied phage model for constructing a phage display library, M13 phage has received much research attention as building blocks or viral scaffolds for various applications including isolation/separation, sensing/probing, and in vivo imaging. Through genetic engineering and chemical modification, M13 phages can be functionalized into a multifunctional analysis platform with various functional regions conducting their functionality without mutual disturbance. Its unique filamentous morphology and flexibility also promoted the analytical performance in terms of target affinity and signal amplification. In this review, we mainly focused on the application of M13 phage in the analytical field and the benefit it brings. We also introduced several genetic engineering and chemical modification approaches for endowing M13 with various functionalities, and summarized some representative applications using M13 phages to construct isolation sorbents, biosensors, cell imaging probes, and immunoassays. Finally, current issues and challenges remaining in this field were discussed and future perspectives were also proposed.
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Affiliation(s)
- Rui Wang
- grid.412252.20000 0004 0368 6968Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819 China
| | - Hui-Da Li
- grid.412252.20000 0004 0368 6968Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819 China
| | - Ying Cao
- grid.412252.20000 0004 0368 6968Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819 China
| | - Zi-Yi Wang
- grid.412252.20000 0004 0368 6968Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819 China
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819, China.
| | - Jian-Hua Wang
- grid.412252.20000 0004 0368 6968Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, 110819 China
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14
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Chabi M, Vu B, Brosamer K, Smith M, Chavan D, Conrad JC, Willson RC, Kourentzi K. Smartphone-read phage lateral flow assay for point-of-care detection of infection. Analyst 2023; 148:839-848. [PMID: 36645184 PMCID: PMC10503656 DOI: 10.1039/d2an01499h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The COVID-19 pandemic has highlighted the urgent need for sensitive, affordable, and widely accessible testing at the point of care. Here we demonstrate a new, universal LFA platform technology using M13 phage conjugated with antibodies and HRP enzymes that offers high analytical sensitivity and excellent performance in a complex clinical matrix. We also report its complete integration into a sensitive chemiluminescence-based smartphone-readable lateral flow assay for the detection of SARS-CoV-2 nucleoprotein. We screened 84 anti-nucleoprotein monoclonal antibody pairs in phage LFA and identified an antibody pair that gave an LoD of 25 pg mL-1 nucleoprotein in nasal swab extract using a FluorChem gel documentation system and 100 pg mL-1 when the test was imaged and analyzed by an in-house-developed smartphone reader. The smartphone-read LFA signals for positive clinical samples tested (N = 15, with known Ct) were statistically different (p < 0.001) from signals for negative clinical samples (N = 11). The phage LFA technology combined with smartphone chemiluminescence imaging can enable the timely development of ultrasensitive, affordable point-of-care testing platforms for SARS-CoV-2 and beyond.
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Affiliation(s)
- Maede Chabi
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Binh Vu
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Kristen Brosamer
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Maxwell Smith
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Dimple Chavan
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Jacinta C Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
| | - Richard C Willson
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA.
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
- Escuela de Medicina y Ciencias de Salud, Tecnológico de Monterrey, Monterrey, Nuevo León 64710, Mexico
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA.
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15
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Shen Y, Wang J, Li Y, Yang CT, Zhou X. Modified Bacteriophage for Tumor Detection and Targeted Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13040665. [PMID: 36839030 PMCID: PMC9963578 DOI: 10.3390/nano13040665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 05/07/2023]
Abstract
Malignant tumor is one of the leading causes of death in human beings. In recent years, bacteriophages (phages), a natural bacterial virus, have been genetically engineered for use as a probe for the detection of antigens that are highly expressed in tumor cells and as an anti-tumor reagent. Furthermore, phages can also be chemically modified and assembled with a variety of nanoparticles to form a new organic/inorganic composite, thus extending the application of phages in biological detection and tumor therapeutic. This review summarizes the studies on genetically engineered and chemically modified phages in the diagnosis and targeting therapy of tumors in recent years. We discuss the advantages and limitations of modified phages in practical applications and propose suitable application scenarios based on these modified phages.
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Affiliation(s)
- Yuanzhao Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Jingyu Wang
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Yuting Li
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
| | - Chih-Tsung Yang
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, Adelaide, SA 5095, Australia
- Correspondence: (X.Z.); (C.-T.Y.)
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.Z.); (C.-T.Y.)
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16
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Hufziger KA, Farquharson EL, Werner BG, Chen Q, Goddard JM, Nugen SR. In Vivo Capsid Engineering of Bacteriophages for Oriented Surface Conjugation. ACS APPLIED BIO MATERIALS 2022; 5:5104-5112. [PMID: 36264000 PMCID: PMC10184791 DOI: 10.1021/acsabm.2c00428] [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] [Indexed: 01/25/2023]
Abstract
The current state-of-the-art in bacteriophage (phage) immobilization onto magnetic particles is limited to techniques that are less expensive and/or facile but nonspecific or those that are more expensive and/or complicated but ensure capsid-down orientation of the phages, as necessary to preserve infectivity and performance in subsequent applications (e.g., therapeutics, detection). These cost, complexity, and effectiveness limitations constitute the major hurdles that limit the scale-up of phage-based strategies and thus their accessibility in low-resource settings. Here, we report a plasmid-based technique that incorporates a silica-binding protein, L2, into the T7 phage capsid, during viral assembly, with and without inclusion of a flexible linker peptide, allowing for targeted binding of the phage capsid to silica without requiring the direct modification of the phage genome. L2-tagged phages were then immobilized onto silica-coated magnetic nanoparticles. Inclusion of the flexible linker between the phage capsid protein and the L2 protein improved immobilization density compared to both wild type T7 phages and L2-tagged phages without the flexible linker. Taken together, this work demonstrates phage capsid modification without engineering the phage genome, which provides an important step toward reducing the cost and increasing the specificity/directionality of phage immobilization methods and could be more broadly applied in the future for other phages for a range of other capsid tags and nanomaterials.
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Affiliation(s)
| | | | - Brenda G. Werner
- Department of Food Science and Technology, Cornell University, Ithaca, NY 14853 (USA)
| | - Qingmin Chen
- Department of Food Science and Technology, Cornell University, Ithaca, NY 14853 (USA)
| | - Julie M. Goddard
- Department of Food Science and Technology, Cornell University, Ithaca, NY 14853 (USA)
| | - Sam R. Nugen
- Department of Food Science and Technology, Cornell University, Ithaca, NY 14853 (USA)
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17
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He L, Jiang C, Chen Z, Ma D, Yi L, Xi Z. A triple-diazonium reagent for virus crosslinking and the synthesis of an azo-linked molecular cage. Org Biomol Chem 2022; 20:7577-7581. [PMID: 36131636 DOI: 10.1039/d2ob01583h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first bench-stable triple-diazonium reagent (TDA-1) was rationally designed and synthesized for coupling and crosslinking. The three reactive sites of TDA-1 can react with phenol-containing molecules as well as plant viruses in aqueous buffers efficiently. In addition, a new-type azo-linked cage was constructed by the direct reaction of TDA-1 with a triple-phenol molecule and was characterized by X-ray crystallography.
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Affiliation(s)
- Lijun He
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhuoyue Chen
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Dejun Ma
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
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18
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Allen GL, Grahn AK, Kourentzi K, Willson RC, Waldrop S, Guo J, Kay BK. Expanding the chemical diversity of M13 bacteriophage. Front Microbiol 2022; 13:961093. [PMID: 36003937 PMCID: PMC9393631 DOI: 10.3389/fmicb.2022.961093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
Bacteriophage M13 virions are very stable nanoparticles that can be modified by chemical and genetic methods. The capsid proteins can be functionalized in a variety of chemical reactions without loss of particle integrity. In addition, Genetic Code Expansion (GCE) permits the introduction of non-canonical amino acids (ncAAs) into displayed peptides and proteins. The incorporation of ncAAs into phage libraries has led to the discovery of high-affinity binders with low nanomolar dissociation constant (K D) values that can potentially serve as inhibitors. This article reviews how bioconjugation and the incorporation of ncAAs during translation have expanded the chemistry of peptides and proteins displayed by M13 virions for a variety of purposes.
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Affiliation(s)
| | | | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Richard C. Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, United States
| | - Sean Waldrop
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Brian K. Kay
- Tango Biosciences, Inc., Chicago, IL, United States
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19
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Ulfo L, Cantelli A, Petrosino A, Costantini PE, Nigro M, Starinieri F, Turrini E, Zadran SK, Zuccheri G, Saporetti R, Di Giosia M, Danielli A, Calvaresi M. Orthogonal nanoarchitectonics of M13 phage for receptor targeted anticancer photodynamic therapy. NANOSCALE 2022; 14:632-641. [PMID: 34792088 DOI: 10.1039/d1nr06053h] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Photodynamic therapy (PDT) represents a promising therapeutic modality for cancer. Here we used an orthogonal nanoarchitectonics approach (genetic/chemical) to engineer M13 bacteriophages as targeted vectors for efficient photodynamic killing of cancer cells. M13 was genetically refactored to display on the phage tip a peptide (SYPIPDT) able to bind the epidermal growth factor receptor (EGFR). The refactored M13EGFR phages demonstrated EGFR-targeted tropism and were internalized by A431 cancer cells, that overexpress EGFR. Using an orthogonal approach to the genetic display, M13EGFR phages were then chemically modified, conjugating hundreds of Rose Bengal (RB) photosensitizing molecules on the capsid surface, without affecting the selective recognition of the SYPIPDT peptides. Upon internalization, the M13EGFR-RB derivatives generated intracellularly reactive oxygen species, activated by an ultralow intensity white light irradiation. The killing activity of cancer cells is observed at picomolar concentrations of the M13EGFR phage.
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Affiliation(s)
- Luca Ulfo
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Andrea Cantelli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy.
| | - Annapaola Petrosino
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Paolo Emidio Costantini
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Michela Nigro
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Francesco Starinieri
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Eleonora Turrini
- Dipartimento di Scienze per la Qualità della Vita, Alma Mater Studiorum-Università di Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Suleman Khan Zadran
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Giampaolo Zuccheri
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Roberto Saporetti
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy.
| | - Matteo Di Giosia
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy.
| | - Alberto Danielli
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum - Università di Bologna, via Francesco Selmi 3, 40126 Bologna, Italy.
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy.
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