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Pei J, Tian Y, Ye W, Han J, Dang Y, Cheng T, Wang W, Zhao Y, Ye W, Huangfu S, Li Y, Zhang F, Lei Y, Qian A. A novel recombinant ORF7-siRNA delivered by flexible nano-liposomes inhibits varicella zoster virus infection. Cell Biosci 2023; 13:167. [PMID: 37700336 PMCID: PMC10496174 DOI: 10.1186/s13578-023-01108-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Varicella zoster virus (VZV), which is a human restricted alpha-herpesvirus, causes varicella (chickenpox) and zoster (shingles). The subsequent post-herpetic neuralgia (PHN) due to VZV infection is excruciating for most patients. Thus, developing specific therapeutics against VZV infection is imperative. RNA interference (RNAi) represents an effective approach for alternative antiviral therapy. This study aimed to develop a novel anti-VZV therapeutics based on RNAi. RESULTS In this study, we screened and found the open reading frame 7 (ORF7) of the VZV genome was an ideal antiviral target based on RNAi. Therefore, a novel siRNA targeting ORF7 (si-ORF7) was designed to explore the potential of RNAi antiviral treatment strategy toward VZV. We used a bio-engineering approach to manufacture recombinant siRNA agents with high yield in E. coli. Then, the efficacy of recombinant ORF7-siRNA (r/si-ORF7) in inhibiting VZV infection both in cellular level and 3D human epidermal skin model was evaluated. The r/si-ORF7 was proved to inhibit the VZV replication and reduce the virus copy numbers significantly in vitro. Furthermore, flexible nano-liposomes were established to deliver r/si-ORF7 to 3D human epidermal skin model and found r/si-ORF7 also could inhibit the VZV infection, thus maintaining normal skin morphology. CONCLUSIONS Taken together, our results highlighted that transdermal administration of antiviral r/si-ORF7 was a promising therapeutic strategy for functional cure of VZV infection.
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Affiliation(s)
- Jiawei Pei
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Ye Tian
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wei Ye
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jiangfan Han
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yamei Dang
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Wei Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
| | - Yipu Zhao
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Weiliang Ye
- Department of Pharmaceutics, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Shuyuan Huangfu
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Yu Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
| | - Fanglin Zhang
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Yingfeng Lei
- Department of Microbiology, School of Preclinical Medicine, Airforce Medical University: Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Airong Qian
- key Lab for Space Biosciences and Biotechnology, School of Life Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
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siRNA Functionalized Lipid Nanoparticles (LNPs) in Management of Diseases. Pharmaceutics 2022; 14:pharmaceutics14112520. [PMID: 36432711 PMCID: PMC9694336 DOI: 10.3390/pharmaceutics14112520] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
RNAi (RNA interference)-based technology is emerging as a versatile tool which has been widely utilized in the treatment of various diseases. siRNA can alter gene expression by binding to the target mRNA and thereby inhibiting its translation. This remarkable potential of siRNA makes it a useful candidate, and it has been successively used in the treatment of diseases, including cancer. However, certain properties of siRNA such as its large size and susceptibility to degradation by RNases are major drawbacks of using this technology at the broader scale. To overcome these challenges, there is a requirement for versatile tools for safe and efficient delivery of siRNA to its target site. Lipid nanoparticles (LNPs) have been extensively explored to this end, and this paper reviews different types of LNPs, namely liposomes, solid lipid NPs, nanostructured lipid carriers, and nanoemulsions, to highlight this delivery mode. The materials and methods of preparation of the LNPs have been described here, and pertinent physicochemical properties such as particle size, surface charge, surface modifications, and PEGylation in enhancing the delivery performance (stability and specificity) have been summarized. We have discussed in detail various challenges facing LNPs and various strategies to overcome biological barriers to undertake the safe delivery of siRNA to a target site. We additionally highlighted representative therapeutic applications of LNP formulations with siRNA that may offer unique therapeutic benefits in such wide areas as acute myeloid leukaemia, breast cancer, liver disease, hepatitis B and COVID-19 as recent examples.
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Gerber PP, Donde MJ, Matheson NJ, Taylor AI. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nat Commun 2022; 13:6716. [PMID: 36385143 PMCID: PMC9668987 DOI: 10.1038/s41467-022-34339-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The unprecedented emergence and spread of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, underscores the need for diagnostic and therapeutic technologies that can be rapidly tailored to novel threats. Here, we show that site-specific RNA endonuclease XNAzymes - artificial catalysts composed of single-stranded synthetic xeno-nucleic acid oligonucleotides (in this case 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid) - may be designed, synthesised and screened within days, enabling the discovery of a range of enzymes targeting SARS-CoV-2 ORF1ab, ORF7b, spike- and nucleocapsid-encoding RNA. Three of these are further engineered to self-assemble into a catalytic nanostructure with enhanced biostability. This XNA nanostructure is capable of cleaving genomic SARS-CoV-2 RNA under physiological conditions, and when transfected into cells inhibits infection with authentic SARS-CoV-2 virus by RNA knockdown. These results demonstrate the potential of XNAzymes to provide a platform for the rapid generation of antiviral reagents.
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Affiliation(s)
- Pehuén Pereyra Gerber
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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Li T, Luo KQ. Recipients of COVID-19 vaccines face challenges of SARS-CoV-2 variants. Int J Biol Sci 2022; 18:4642-4647. [PMID: 35874950 PMCID: PMC9305267 DOI: 10.7150/ijbs.72424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/02/2022] [Indexed: 01/15/2023] Open
Abstract
The coronavirus disease 19 (COVID-19) has been rampant since 2019, severely affecting global public health, and causing 5.75 million deaths worldwide. So far, many vaccines have been developed to prevent the infection of SARS-CoV-2 virus. However, the emergence of new variants may threat vaccine recipients as they might evade immunological surveillance that depends on the using of anti-SARS-CoV-2 antibody to neutralize the viral particles. Recent studies have found that recipients who received two doses of vaccination plus an additional booster shoot were able to quickly elevate neutralization response and immune response against wild-type SARS-CoV-2 virus and some initially appeared viral variants. In this review, we assessed the real-world effectiveness of different COVID-19 vaccines by population studies and neutralization assays and compared neutralization responses of booster vaccines in vitro. Finally, as the efficacy of COVID-19 vaccine is expected to decline over time, continued vaccination should be considered to achieve a long-term immune protection against coronavirus.
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Affiliation(s)
- Tianhong Li
- Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Kathy Qian Luo
- Faculty of Health Sciences, University of Macau, Macao SAR, China.,Ministry of Education-Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macao SAR, China
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Sartaj Sohrab S, Aly El-Kafrawy S, Ibraheem Azhar E. In silico prediction and experimental evaluation of potential siRNAs against SARS-CoV-2 inhibition in Vero E6 cells. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102049. [PMID: 35493709 PMCID: PMC9040457 DOI: 10.1016/j.jksus.2022.102049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Accepted: 04/18/2022] [Indexed: 11/21/2022]
Abstract
Objective The acute cases of pneumonia (COVID-19) were first reported from China in December 2019, and the pathogen was identified as SARS-CoV-2. Currently, many vaccines have been developed against this virus by using multiple genes, applying different platforms, and used for the vaccinations of the human population. Spike protein genes play an important role in host cell attachment and viral entry and have been extensively used for the development of vaccine and antiviral therapeutics. Short interfering RNA is also known as silencing RNA and contribute a significant role to regulate the expression of a specific gene. By using this technology, virus inhibition has been demonstrated against many viral diseases. Methods In this work, we have reported the Insilico prediction, designing, and experimental validation of siRNAs antiviral potency against SARS-CoV-2-S-RBD. The siDirect 2.0 was selected for siRNAs prediction, and secondary structure was predicted by RNAfold while the HNADOCK was used for molecular docking analysis and specific binding of siRNAs to the selected target. We have used and evaluated four siRNAs for cellular toxicity and determination of antiviral efficiency based on the Ct value of q-real-time PCR in Vero E6 cells. Results Based on the experimental evaluation and analysis of results from generated data, we observed that there is no cytotoxicity for any tested siRNAs in Vero E6 cells. Total four siRNA were filtered out from twenty-one siRNAs following the strict selection and scoring criteria. The better antiviral efficiency was observed in 3rd siRNAs based on the Ct value of q-real-time PCR. The results that emerged from this study encouraged us to validate the efficiency of these siRNAs in multiple cells by using alone and in a combination of two or more siRNAs to inhibit the SARS-CoV-2 proliferation. Conclusion The Insilico prediction, molecular docking analysis provided the selection of better siRNAs. Based on the experimental evaluation only 3rd siRNA was found to be more effective than others and showed better antiviral efficiency. These siRNAs should also be evaluated in other cell lines either separately or in combination against SARS-CoV-2 to determine their antiviral efficiency.
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Sohrab SS, El-Kafrawy SA, Azhar EI. Effect of insilico predicted and designed potential siRNAs on inhibition of SARS-CoV-2 in HEK-293 cells. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:101965. [PMID: 35313445 PMCID: PMC8925144 DOI: 10.1016/j.jksus.2022.101965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022]
Abstract
Objectives The COVID-19 was identified for the first time from the sea food market, Wuhan city, China in 2019 and the pathogenic organism was identified as SARS-CoV-2. Currently, this virus has spread to 223 countries and territories and known as a serious issue for the global human community. Many vaccines have been developed and used for immunization. Methods We have reported the insilico prediction, designing, secondary structure prediction, molecular docking analysis, and in vitro assessment of siRNAs against SARS-CoV-2. The online bioinformatic approach was used for siRNAs selection and designing. The selected siRNAs were evaluated for antiviral efficacy by using Lipofectamine 2000 as delivery agent to HEK-293 cells. The MTT assay was used for cytotoxicity determination. The antiviral efficacy of potential siRNAs was determined based on the Ct value of q-RT-PCR and the data analysis was done by Prism-GraphPad software. Results The analyzed data resulted in the selection of only three siRNAs out of twenty-six siRNAs generated by online software. The secondary structure prediction and molecular docking analysis of siRNAs revealed the efficient binding to the target. There was no cellular toxicity observed in the HEK-293 cells at any tested concentrations of siRNAs. The purification of RNA was completed from inoculated cells and subjected to q-RT-PCR. The highest Ct value was observed in siRNA 3 than the others. The results offered valuable evidence and invigorated us to assess the potency of siRNAs by using alone or in combination in other human cells. Conclusion The data generated from this study indicates the significance of in silico prediction and narrow down the potential siRNA' against SARS-CoV-2, and molecular docking investigation offered the effective siRNAs binding with the target. Finally, it is concluded that the online bioinformatics approach provided the prediction and selection of siRNAs with better antiviral efficacy. The siRNA-3 was observed to be the best for reduction of viral RNA in cells.
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Semple SL, Au SKW, Jacob RA, Mossman KL, DeWitte-Orr SJ. Discovery and Use of Long dsRNA Mediated RNA Interference to Stimulate Antiviral Protection in Interferon Competent Mammalian Cells. Front Immunol 2022; 13:859749. [PMID: 35603190 PMCID: PMC9120774 DOI: 10.3389/fimmu.2022.859749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
In invertebrate cells, RNA interference (RNAi) acts as a powerful immune defense that stimulates viral gene knockdown thereby preventing infection. With this pathway, virally produced long dsRNA (dsRNA) is cleaved into short interfering RNA (siRNA) by Dicer and loaded into the RNA-induced silencing complex (RISC) which can then destroy/disrupt complementary viral mRNA sequences. Comparatively, in mammalian cells it is believed that the type I interferon (IFN) pathway is the cornerstone of the innate antiviral response. In these cells, dsRNA acts as a potent inducer of the IFN system, which is dependent on dsRNA length, but not sequence, to stimulate an antiviral state. Although the cellular machinery for RNAi is intact and functioning in mammalian cells, its role to trigger an antiviral response using long dsRNA (dsRNAi) remains controversial. Here we show that dsRNAi is not only functional but has a significant antiviral effect in IFN competent mammalian cells. We found that pre-soaking mammalian cells with concentrations of sequence specific dsRNA too low to induce IFN production could significantly inhibit vesicular stomatitis virus expressing green fluorescent protein (VSV-GFP), and the human coronaviruses (CoV) HCoV-229E and SARS-CoV-2 replication. This phenomenon was shown to be dependent on dsRNA length, was comparable in effect to transfected siRNAs, and could knockdown multiple sequences at once. Additionally, knockout cell lines revealed that functional Dicer was required for viral inhibition, revealing that the RNAi pathway was indeed responsible. These results provide the first evidence that soaking with gene-specific long dsRNA can generate viral knockdown in mammalian cells. We believe that this novel discovery provides an explanation as to why the mammalian lineage retained its RNAi machinery and why vertebrate viruses have evolved methods to suppress RNAi. Furthermore, demonstrating RNAi below the threshold of IFN induction has uses as a novel therapeutic platform, both antiviral and gene targeting in nature.
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Affiliation(s)
- Shawna L. Semple
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Sarah K. W. Au
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Rajesh A. Jacob
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Stephanie J. DeWitte-Orr
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
- *Correspondence: Stephanie J. DeWitte-Orr,
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Becker J, Stanifer ML, Leist SR, Stolp B, Maiakovska O, West A, Wiedtke E, Börner K, Ghanem A, Ambiel I, Tse LV, Fackler OT, Baric RS, Boulant S, Grimm D. Ex vivo and in vivo suppression of SARS-CoV-2 with combinatorial AAV/RNAi expression vectors. Mol Ther 2022; 30:2005-2023. [PMID: 35038579 PMCID: PMC8758558 DOI: 10.1016/j.ymthe.2022.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022] Open
Abstract
Despite rapid development and deployment of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinically relevant modalities to curb the pandemic by directly attacking the virus on a genetic level remain highly desirable and are urgently needed. Here we comprehensively illustrate the capacity of adeno-associated virus (AAV) vectors co-expressing a cocktail of three short hairpin RNAs (shRNAs; RNAi triggers) directed against the SARS-CoV-2 RdRp and N genes as versatile and effective antiviral agents. In cultured monkey cells and human gut organoids, our most potent vector, SAVIOR (SARS virus repressor), suppressed SARS-CoV-2 infection to background levels. Strikingly, in control experiments using single shRNAs, multiple SARS-CoV-2 escape mutants quickly emerged from infected cells within 24-48 h. Importantly, such adverse viral adaptation was fully prevented with the triple-shRNA AAV vector even during long-term cultivation. In addition, AAV-SAVIOR efficiently purged SARS-CoV-2 in a new model of chronically infected human intestinal cells. Finally, intranasal AAV-SAVIOR delivery using an AAV9 capsid moderately diminished viral loads and/or alleviated disease symptoms in hACE2-transgenic or wild-type mice infected with human or mouse SARS-CoV-2 strains, respectively. Our combinatorial and customizable AAV/RNAi vector complements ongoing global efforts to control the coronavirus disease 2019 (COVID-19) pandemic and holds great potential for clinical translation as an original and flexible preventive or therapeutic antiviral measure.
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Affiliation(s)
- Jonas Becker
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Megan Lynn Stanifer
- Department of Infectious Diseases/Molecular Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Sarah Rebecca Leist
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Bettina Stolp
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Olena Maiakovska
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ande West
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Ellen Wiedtke
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Ali Ghanem
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ina Ambiel
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Longping Victor Tse
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Oliver Till Fackler
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ralph Steven Baric
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, 69120 Heidelberg, Germany.
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Friedrich M, Pfeifer G, Binder S, Aigner A, Vollmer Barbosa P, Makert GR, Fertey J, Ulbert S, Bodem J, König EM, Geiger N, Schambach A, Schilling E, Buschmann T, Hauschildt S, Koehl U, Sewald K. Selection and Validation of siRNAs Preventing Uptake and Replication of SARS-CoV-2. Front Bioeng Biotechnol 2022; 10:801870. [PMID: 35309990 PMCID: PMC8925020 DOI: 10.3389/fbioe.2022.801870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
In 2019, the novel highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak rapidly led to a global pandemic with more than 346 million confirmed cases worldwide, resulting in 5.5 million associated deaths (January 2022). Entry of all SARS-CoV-2 variants is mediated by the cellular angisin-converting enzyme 2 (ACE2). The virus abundantly replicates in the epithelia of the upper respiratory tract. Beyond vaccines for immunization, there is an imminent need for novel treatment options in COVID-19 patients. So far, only a few drugs have found their way into the clinics, often with modest success. Specific gene silencing based on small interfering RNA (siRNA) has emerged as a promising strategy for therapeutic intervention, preventing/limiting SARS-CoV-2 entry into host cells or interfering with viral replication. Here, we pursued both strategies. We designed and screened nine siRNAs (siA1-9) targeting the viral entry receptor ACE2. SiA1, (siRNA against exon1 of ACE2 mRNA) was most efficient, with up to 90% knockdown of the ACE2 mRNA and protein for at least six days. In vitro, siA1 application was found to protect Vero E6 and Huh-7 cells from infection with SARS-CoV-2 with an up to ∼92% reduction of the viral burden indicating that the treatment targets both the endosomal and the viral entry at the cytoplasmic membrane. Since the RNA-encoded genome makes SARS-CoV-2 vulnerable to RNA interference (RNAi), we designed and analysed eight siRNAs (siV1-8) directly targeting the Orf1a/b region of the SARS-CoV-2 RNA genome, encoding for non-structural proteins (nsp). As a significant hallmark of this study, we identified siV1 (siRNA against leader protein of SARS-CoV-2), which targets the nsp1-encoding sequence (a.k.a. ‘host shutoff factor’) as particularly efficient. SiV1 inhibited SARS-CoV-2 replication in Vero E6 or Huh-7 cells by more than 99% or 97%, respectively. It neither led to toxic effects nor induced type I or III interferon production. Of note, sequence analyses revealed the target sequence of siV1 to be highly conserved in SARS-CoV-2 variants. Thus, our results identify the direct targeting of the viral RNA genome (ORF1a/b) by siRNAs as highly efficient and introduce siV1 as a particularly promising drug candidate for therapeutic intervention.
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Affiliation(s)
- Maik Friedrich
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- *Correspondence: Maik Friedrich,
| | - Gabriele Pfeifer
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Stefanie Binder
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Achim Aigner
- Rudolf Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | | | - Gustavo R. Makert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jasmin Fertey
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Sebastian Ulbert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jochen Bodem
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Erik Schilling
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Tilo Buschmann
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | | | - Ulrike Koehl
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Katherina Sewald
- Fraunhofer Institute of Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) of the German Center for Lung Research (DZL), Hannover, Germany
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10
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Zhang Y, Almazi JG, Ong HX, Johansen MD, Ledger S, Traini D, Hansbro PM, Kelleher AD, Ahlenstiel CL. Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract. Int J Mol Sci 2022; 23:2408. [PMID: 35269550 PMCID: PMC8909959 DOI: 10.3390/ijms23052408] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Since December 2019, a pandemic of COVID-19 disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread across the globe. At present, the Food and Drug Administration (FDA) has issued emergency approval for the use of some antiviral drugs. However, these drugs still have limitations in the specific treatment of COVID-19, and as such, new treatment strategies urgently need to be developed. RNA-interference-based gene therapy provides a tractable target for antiviral treatment. Ensuring cell-specific targeted delivery is important to the success of gene therapy. The use of nanoparticles (NPs) as carriers for the delivery of small interfering RNA (siRNAs) to specific tissues or organs of the human body could play a crucial role in the specific therapy of severe respiratory infections, such as COVID-19. In this review, we describe a variety of novel nanocarriers, such as lipid NPs, star polymer NPs, and glycogen NPs, and summarize the pre-clinical/clinical progress of these nanoparticle platforms in siRNA delivery. We also discuss the application of various NP-capsulated siRNA as therapeutics for SARS-CoV-2 infection, the challenges with targeting these therapeutics to local delivery in the lung, and various inhalation devices used for therapeutic administration. We also discuss currently available animal models that are used for preclinical assessment of RNA-interference-based gene therapy. Advances in this field have the potential for antiviral treatments of COVID-19 disease and could be adapted to treat a range of respiratory diseases.
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Affiliation(s)
- Yuan Zhang
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Juhura G. Almazi
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Hui Xin Ong
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Scott Ledger
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Daniela Traini
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Anthony D. Kelleher
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
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11
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Chang YC, Yang CF, Chen YF, Yang CC, Chou YL, Chou HW, Chang TY, Chao TL, Hsu SC, Ieong SM, Tsai YM, Liu PC, Chin YF, Fang JT, Kao HC, Lu HY, Chang JY, Weng RS, Tu QW, Chang FY, Huang KY, Lee TY, Chang SY, Yang PC. A siRNA targets and inhibits a broad range of SARS-CoV-2 infections including Delta variant. EMBO Mol Med 2022; 14:e15298. [PMID: 35138028 PMCID: PMC8988202 DOI: 10.15252/emmm.202115298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/22/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variants has altered the trajectory of the COVID‐19 pandemic and raised some uncertainty on the long‐term efficiency of vaccine strategy. The development of new therapeutics against a wide range of SARS‐CoV‐2 variants is imperative. We, here, have designed an inhalable siRNA, C6G25S, which covers 99.8% of current SARS‐CoV‐2 variants and is capable of inhibiting dominant strains, including Alpha, Delta, Gamma, and Epsilon, at picomolar ranges of IC50in vitro. Moreover, C6G25S could completely inhibit the production of infectious virions in lungs by prophylactic treatment, and decrease 96.2% of virions by cotreatment in K18‐hACE2‐transgenic mice, accompanied by a significant prevention of virus‐associated extensive pulmonary alveolar damage, vascular thrombi, and immune cell infiltrations. Our data suggest that C6G25S provides an alternative and effective approach to combating the COVID‐19 pandemic.
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Affiliation(s)
| | - Chi-Fan Yang
- Microbio (Shanghai) Biotech Company, Shanghai, China
| | - Yi-Fen Chen
- Oneness Biotech Company Limited, Taipei, Taiwan
| | | | - Yuan-Lin Chou
- Microbio (Shanghai) Biotech Company, Shanghai, China
| | | | - Tein-Yao Chang
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Chen Hsu
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - Si-Man Ieong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ya-Min Tsai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Cheng Liu
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - Yuan-Fan Chin
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - Jun-Tung Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Han-Chieh Kao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsuan-Ying Lu
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | - Jia-Yu Chang
- Institute of Preventive Medicine, National Defense Medical Center, Taiwan
| | | | - Qian-Wen Tu
- Oneness Biotech Company Limited, Taipei, Taiwan
| | | | - Kuo-Yen Huang
- Institute of Microbiology and Immunology, National Defense Medical Center, Taiwan
| | | | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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12
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Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res 2021; 50:333-349. [PMID: 34928377 PMCID: PMC8754636 DOI: 10.1093/nar/gkab1248] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/10/2021] [Accepted: 12/05/2021] [Indexed: 01/08/2023] Open
Abstract
A promising approach to tackle the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. So far it is unclear, which viral replication steps can be efficiently inhibited with siRNAs. Here, we report that siRNAs can target genomic RNA (gRNA) of SARS-CoV-2 after cell entry, and thereby terminate replication before start of transcription and prevent virus-induced cell death. Coronaviruses replicate via negative sense RNA intermediates using a unique discontinuous transcription process. As a result, each viral RNA contains identical sequences at the 5′ and 3′ end. Surprisingly, siRNAs were not active against intermediate negative sense transcripts. Targeting common sequences shared by all viral transcripts allowed simultaneous suppression of gRNA and subgenomic (sg)RNAs by a single siRNA. The most effective suppression of viral replication and spread, however, was achieved by siRNAs that targeted open reading frame 1 (ORF1) which only exists in gRNA. In contrast, siRNAs that targeted the common regions of transcripts were outcompeted by the highly abundant sgRNAs leading to an impaired antiviral efficacy. Verifying the translational relevance of these findings, we show that a chemically modified siRNA that targets a highly conserved region of ORF1, inhibited SARS-CoV-2 replication ex vivo in explants of the human lung. Our work encourages the development of siRNA-based therapies for COVID-19 and suggests that early therapy start, or prophylactic application, together with specifically targeting gRNA, might be key for high antiviral efficacy.
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Affiliation(s)
- Shubhankar Ambike
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Stoyan Velkov
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Domizia Baldassi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Suliman Qadir Afridi
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Diana Porras-Gonzalez
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Xin Wei
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Philipp Hagen
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mircea Gabriel Stoleriu
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Pulmonary Hospital; Marchioninistraße 15, 81377 Munich and Robert-Koch-Allee 2, 82131 Gauting, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany.,Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,Infectious Diseases Therapeutic Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), 34114 Daejeon, Republic of Korea
| | - Thomas Michler
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
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13
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Khanali J, Azangou-Khyavy M, Asaadi Y, Jamalkhah M, Kiani J. Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs. Front Microbiol 2021; 12:758948. [PMID: 34858370 PMCID: PMC8630580 DOI: 10.3389/fmicb.2021.758948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023] Open
Abstract
Despite significant efforts, there are currently no approved treatments for COVID-19. However, biotechnological approaches appear to be promising in the treatment of the disease. Accordingly, nucleic acid-based treatments including aptamers and siRNAs are candidates that might be effective in COVID-19 treatment. Aptamers can hamper entry and replication stages of the SARS-CoV-2 infection, while siRNAs can cleave the viral genomic and subgenomic RNAs to inhibit the viral life cycle and reduce viral loads. As a conjugated molecule, aptamer–siRNA chimeras have proven to be dual-functioning antiviral therapy, acting both as virus-neutralizing and replication-interfering agents as well as being a siRNA targeted delivery approach. Previous successful applications of these compounds against various stages of the pathogenesis of diseases and viral infections, besides their advantages over other alternatives, might provide sufficient rationale for the application of these nucleic acid-based drugs against the SARS-CoV-2. However, none of them are devoid of limitations. Here, the literature was reviewed to assess the plausibility of using aptamers, siRNAs, and aptamer–siRNA chimeras against the SARS-CoV-2 based on their previously established effectiveness, and discussing challenges lie in applying these molecules.
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Affiliation(s)
- Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Monire Jamalkhah
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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14
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Tolksdorf B, Nie C, Niemeyer D, Röhrs V, Berg J, Lauster D, Adler JM, Haag R, Trimpert J, Kaufer B, Drosten C, Kurreck J. Inhibition of SARS-CoV-2 Replication by a Small Interfering RNA Targeting the Leader Sequence. Viruses 2021; 13:v13102030. [PMID: 34696460 PMCID: PMC8539227 DOI: 10.3390/v13102030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected almost 200 million people worldwide and led to approximately 4 million deaths as of August 2021. Despite successful vaccine development, treatment options are limited. A promising strategy to specifically target viral infections is to suppress viral replication through RNA interference (RNAi). Hence, we designed eight small interfering RNAs (siRNAs) targeting the highly conserved 5′-untranslated region (5′-UTR) of SARS-CoV-2. The most promising candidate identified in initial reporter assays, termed siCoV6, targets the leader sequence of the virus, which is present in the genomic as well as in all subgenomic RNAs. In assays with infectious SARS-CoV-2, it reduced replication by two orders of magnitude and prevented the development of a cytopathic effect. Moreover, it retained its activity against the SARS-CoV-2 alpha variant and has perfect homology against all sequences of the delta variant that were analyzed by bioinformatic means. Interestingly, the siRNA was even highly active in virus replication assays with the SARS-CoV-1 family member. This work thus identified a very potent siRNA with a broad activity against various SARS-CoV viruses that represents a promising candidate for the development of new treatment options.
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Affiliation(s)
- Beatrice Tolksdorf
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Chuanxiong Nie
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Daniela Niemeyer
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Viola Röhrs
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Johanna Berg
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Julia M. Adler
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; (C.N.); (D.L.); (R.H.)
| | - Jakob Trimpert
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Benedikt Kaufer
- Department of Veterinary Medicine, Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.M.A.); (J.T.); (B.K.)
| | - Christian Drosten
- German Centre for Infection Research (DZIF), Charitéplatz 1, 10117 Berlin, Germany; (D.N.); (C.D.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jens Kurreck
- Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; (B.T.); (V.R.); (J.B.)
- Correspondence: ; Tel.:+ 49-30-314-27581
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