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Madanagopal P, Muthukumar H, Thiruvengadam K. Computational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains. Comput Biol Chem 2022; 98:107687. [PMID: 35537364 PMCID: PMC9052778 DOI: 10.1016/j.compbiolchem.2022.107687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 01/26/2023]
Abstract
SARS-CoV-2 is a highly transmissible and pathogenic coronavirus that first emerged in late 2019 and has since triggered a pandemic of acute respiratory disease named COVID-19 which poses a significant threat to all public health institutions in the absence of specific antiviral treatment. Since the outbreak began in March 2020, India has reported 4.77 lakh Coronavirus deaths, according to the World Health Organization (WHO). The innate RNA interference (RNAi) pathway, on the other hand, allows for the development of nucleic acid-based antiviral drugs in which complementary small interfering RNAs (siRNAs) mediate the post-transcriptional gene silencing (PTGS) of target mRNA. Therefore, in this current study, the potential of RNAi was harnessed to construct siRNA molecules that target the consensus regions of specific structural proteins associated genes of SARS-CoV-2, such as the envelope protein gene (E), membrane protein gene (M), nucleocapsid phosphoprotein gene (N), and surface glycoprotein gene (S) which are important for the viral pathogenesis. Conserved sequences of 811 SARS-CoV-2 strains from around India were collected to design 21 nucleotides long siRNA duplex based on various computational algorithms and parameters targeting E, M, N and S genes. The proposed siRNA molecules possessed sufficient nucleotide-based and other features for effective gene silencing and BLAST results revealed that siRNAs' targets have no significant matches across the whole human genome. Hence, siRNAs were found to have no off-target effects on the genome, ruling out the possibility of off-target silencing. Finally, out of 157 computationally identified siRNAs, only 4 effective siRNA molecules were selected for each target gene which is proposed to exert the best action based on GC content, free energy of folding, free energy of binding, melting temperature, heat capacity and molecular docking analysis with Human AGO2 protein. Our engineered siRNA candidates could be used as a genome-level therapeutic treatment against various sequenced SARS-CoV-2 strains in India. However, future applications will necessitate additional validations in vitro and in vivo animal models.
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Murtaza S, Tabassum B, Tariq M, Riaz S, Yousaf I, Jabbar B, Khan A, Samuel AO, Zameer M, Nasir IA. Silencing a Myzus persicae Macrophage Inhibitory Factor by Plant-Mediated RNAi Induces Enhanced Aphid Mortality Coupled with Boosted RNAi Efficacy in Transgenic Potato Lines. Mol Biotechnol 2022; 64:1152-1163. [PMID: 35460447 DOI: 10.1007/s12033-022-00498-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/08/2022] [Indexed: 11/28/2022]
Abstract
Myzus persicae causes considerable losses to crops as a major pest. The damage is direct by feeding and also partly indirect because it vectors plant viruses. The currently available control strategies rely on unsafe and nonecofriendly chemical pesticide applications. Plant-mediated RNA interference (RNAi) has emerged as a powerful tool in crop protection from insect pests. Aphid salivary proteins are essential for phloem feeding and act as mediators of the complex interactions between aphids and their host plants. We documented the efficacy of dsRNA directed against macrophage inhibitory factor (MIF1) of M. persicae to induce aphid mortality and gene silencing through the generation of transgenic potato lines. A binary construct harbouring dsMIF1 driven by the CaMV35S promoter was introduced into the local potato variety 'AGB-white' by Agrobacterium-mediated transformation. PCR and Southern blotting validated the transgene presence and genomic integration in seven transgenic potato lines. An in vitro detached leaf assay revealed a significantly high aphid mortality of 65% in the transgenic potato line sDW-2, while the aphid mortality was 77% in the sDW-2 transgenic line during the in planta bioassay in comparison with 19% aphid mortality in the control nontransgenic potato line. A significantly high silencing effect was observed in the mRNA expression of MIF1, which was reduced to 21% in aphids fed on the transgenic potato line sDW-2. However, variable knockdown effects were found among six other transgenic potato lines, ranging from 30 to 62%. The study concluded that plant-mediated silencing of aphid RNA induces significant RNAi in M. persicae, along with enhanced aphid mortality.
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Affiliation(s)
- Shahid Murtaza
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Tabassum
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. .,School of Biological Sciences, University of the Punjab Quaid-I-Azam Campus, Lahore, 54590, Pakistan.
| | - Muhammad Tariq
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Saman Riaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Iqra Yousaf
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Anwar Khan
- Department of Microbiology, BUITEMS, Quetta, Pakistan
| | | | - Mariam Zameer
- Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Rahman A, Gupta SD, Rahman MA, Tamanna S. An in-silico approach to design potential siRNAs against the ORF57 of Kaposi's sarcoma-associated herpesvirus. Genomics Inform 2021; 19:e47. [PMID: 35012290 PMCID: PMC8752988 DOI: 10.5808/gi.21057] [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: 09/17/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.
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Affiliation(s)
- Anisur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Shipan Das Gupta
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Md. Anisur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Saheda Tamanna
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Shawan MMAK, Sharma AR, Bhattacharya M, Mallik B, Akhter F, Shakil MS, Hossain MM, Banik S, Lee SS, Hasan MA, Chakraborty C. Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 93:104951. [PMID: 34089909 PMCID: PMC8170914 DOI: 10.1016/j.meegid.2021.104951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
The devastating outbreak of COVID-19 has spread all over the world and has become a global health concern. There is no specific therapeutics to encounter the COVID-19. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control human viral infections employing post-transcriptional gene silencing (PTGS) through neutralizing target complementary mRNA. RNA-dependent RNA polymerase (RdRp) encoded by the viral RdRp gene as a part of the replication-transcription complex can be adopted as an acceptable target for controlling SARS-CoV-2 mediated infection. Therefore, in the current study, accessible siRNA designing tools, including significant algorithms and parameters, were rationally used to design the candidate siRNAs against SARS-COV-2 encoded RdRp. The designed siRNA molecules possessed adequate nucleotide-based and other features for potent gene silencing. The targets of the designed siRNAs revealed no significant matches within the whole human genome, ruling out any possibilities for off-target silencing by the siRNAs. Characterization with different potential parameters of efficacy allowed selecting the finest siRNA among all the designed siRNA molecules. Further, validation assessment and target site accessibility prediction also rationalized the suitability of this siRNA molecule. Molecular docking study between the selected siRNA molecule and component of RNA interference (RNAi) pathway gave an excellent outcome. Molecular dynamics of two complexes: siRNA and argonaute complex, guide RNA, and target protein complex, have shown structural stability of these proteins. Therefore, the designed siRNA molecule might act as an effective therapeutic agent against the SARS-CoV-2 at the genome level and can prevent further outbreaks of COVID-19 in humans.
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Affiliation(s)
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Bidyut Mallik
- Department of Applied Science, Galgotias College of Engineering and Technology, Knowledge Park-II, Greater Noida, Uttar Pradesh 201306, India
| | - Farhana Akhter
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Government Unani and Ayurvedic Medical College Hospital, Mirpur-13, Dhaka 1221, Bangladesh
| | - Md Salman Shakil
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; Department of Pharmacology & Toxicology, University of Otago, Dunedin, New Zealand
| | - Md Mozammel Hossain
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Subrata Banik
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea.
| | - Md Ashraful Hasan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh.
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Jagannathpur, Kolkata, West Bengal 700126, India.
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Hasan M, Ashik AI, Chowdhury MB, Tasnim AT, Nishat ZS, Hossain T, Ahmed S. Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021; 24:100569. [PMID: 33846694 PMCID: PMC8028608 DOI: 10.1016/j.imu.2021.100569] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by an RNA virus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 possesses an almost 30kbp long genome. The genome contains open-reading frame 1ab (ORF1ab) gene, the largest one of SARS-CoV-2, encoding polyprotein PP1ab and PP1a responsible for viral transcription and replication. Several vaccines have already been approved by the respective authorities over the world to develop herd immunity among the population. In consonance with this effort, RNA interference (RNAi) technology holds the possibility to strengthen the fight against this virus. Here, we have implemented a computational approach to predict potential short interfering RNAs including small interfering RNAs (siRNAs) and microRNAs (miRNAs), which are presumed to be intrinsically active against SARS-CoV-2. In doing so, we have screened miRNA library and siRNA library targeting the ORF1ab gene. We predicted the potential miRNA and siRNA candidate molecules utilizing an array of bioinformatic tools. By extending the analysis, out of 24 potential pre-miRNA hairpins and 131 siRNAs, 12 human miRNA and 10 siRNA molecules were sorted as potential therapeutic agents against SARS-CoV-2 based on their GC content, melting temperature (Tm), heat capacity (Cp), hybridization and minimal free energy (MFE) of hybridization. This computational study is focused on lessening the extensive time and labor needed in conventional trial and error based wet lab methods and it has the potential to act as a decent base for future researchers to develop a successful RNAi therapeutic.
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Key Words
- ACE-2, Angiotensin-converting enzyme 2
- COVID-19
- COVID-19, coronavirus disease 2019
- Cp, heat capacity
- Gene silencing
- ORF, open reading frame
- Posttranscriptional regulation
- RNAi Therapeutics
- RNAi, RNA interference
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane protease serine 2
- Tm, melting temperature
- UTR, untranslated region
- hsa-miR, human microRNA
- miRNA
- miRNA, microRNA
- sgRNA, sub-genomic RNA
- siRNA
- siRNA, small interfering RNA
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Affiliation(s)
- Mahedi Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Arafat Islam Ashik
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Belal Chowdhury
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Atiya Tahira Tasnim
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zakia Sultana Nishat
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Shamim Ahmed
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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Perez-Mendez M, Zárate-Segura P, Salas-Benito J, Bastida-González F. siRNA Design to Silence the 3'UTR Region of Zika Virus. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6759346. [PMID: 32802864 PMCID: PMC7421096 DOI: 10.1155/2020/6759346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/16/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
The disease caused by the Zika virus (ZIKV) has positioned itself as one of the main public health problems in Mexico. One of the main reasons is it causes microcephaly and other birth defects. The transmission of ZIKV is through Aedes aegypti and Ae. albopictus mosquitoes, which are found in a larger space of the national territory. In addition, it can also be transmitted via blood transfusion, sexual relations, and maternal-fetal route. So far, there are no vaccines or specific treatments to deal with this infection. Currently, some new therapeutics such as small interfering RNAs (siRNAs) are able to regulate or suppress transcription in viruses. Therefore, in this project, an in silico siRNA was designed for the 3'UTR region of ZIKV via bioinformatics tools. The designed siRNA was synthesized and transfected into the C6/36 cell line, previously infected with ZIKV in order to assess the ability of the siRNA to inhibit viral replication. The designed siRNA was able to inhibit significantly (p < 0.05) ZIKV replication; this siRNA could be considered a potential therapeutic towards the disease that causes ZIKV and the medical problems generated.
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Affiliation(s)
- María Perez-Mendez
- Laboratorio de Medicina Traslacional, Escuela Superior de Medicina, Instituto Politécnico Nacional, St. Salvador Díaz Mirón Esquina Plan de San Luis, Santo Tomas, Miguel Hidalgo, CDMX 11340, Mexico
| | - Paola Zárate-Segura
- Laboratorio de Medicina Traslacional, Escuela Superior de Medicina, Instituto Politécnico Nacional, St. Salvador Díaz Mirón Esquina Plan de San Luis, Santo Tomas, Miguel Hidalgo, CDMX 11340, Mexico
| | - Juan Salas-Benito
- Laboratorio de Biomedicina Molecular 3, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, La Escalera-Ticomán, Gustavo A. Madero, CDMX 07329, Mexico
| | - Fernando Bastida-González
- Laboratorio de Biología Molecular, Laboratorio Estatal de Salud Pública del Estado de México, Paseo Tollocan s/n, La Moderna de la Cruz, EDOMEX, Toluca, 50180, Mexico
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Da BL, Heller T, Koh C. Hepatitis D infection: from initial discovery to current investigational therapies. Gastroenterol Rep (Oxf) 2019; 7:231-245. [PMID: 32477569 DOI: 10.1093/gastro/goz023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/15/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatitis D is the most severe form of viral hepatitis associated with a more rapid progression to cirrhosis and an increased risk of hepatocellular carcinoma and mortality compared with hepatitis B mono-infection. Although once thought of as a disappearing disease, hepatitis D is now becoming recognized as a serious worldwide issue due to improvement in diagnostic testing and immigration from endemic countries. Despite these concerns, there is currently only one accepted medical therapy (pegylated-interferon-α) for the treatment of hepatitis D with less than desirable efficacy and significant side effects. Due to these reasons, many patients never undergo treatment. However, increasing knowledge about the virus and its life cycle has led to the clinical development of multiple promising new therapies that hope to alter the natural history of this disease and improve patient outcome. In this article, we will review the literature from discovery to the current investigational therapies.
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Affiliation(s)
- Ben L Da
- Digestive Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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Tabernero D, Cortese MF, Buti M, Rodriguez-Frias F. HDV evolution-will viral resistance be an issue in HDV infection? Curr Opin Virol 2018; 32:100-107. [PMID: 30415162 DOI: 10.1016/j.coviro.2018.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis D virus (HDV) is a hepatotropic subviral infectious agent, obligate satellite of the Hepatitis B virus (HBV) and is highly related to viroids. HDV affects around 5% of the 257 million chronic HBV-carriers worldwide, leading to the most severe form of chronic viral hepatitis. Interferon alpha is the only approved treatment for chronic hepatitis D, albeit with low response rates (around 20%-30%). New antiviral strategies are currently under study. Due to the high viral evolution rates (10-3 to 10-4 substitutions/site/year) HDV forms an extremely complex viral population (quasispecies) that can be studied by Next-Generation Sequencing. Therefore, although specific viral resistance in HDV infection has not been reported, it cannot be completely discarded.
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Affiliation(s)
- David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
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Sharif Shohan MU, Paul A, Hossain M. Computational design of potential siRNA molecules for silencing nucleoprotein gene of rabies virus. Future Virol 2018. [DOI: 10.2217/fvl-2017-0117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aim: Rabies virus infections are a global threat to human and animal health, yet no progressive curative therapy has been developed. In this study, the nucleoprotein gene of rabies virus which is responsible for viral infection was used as a target to design our desired siRNA. Methods: The conserved regions were analyzed by doing alignment of sequences from different strains. Subsequently, different computational tools were used for designing and validation of siRNA molecules. Results: We identified four probable siRNA molecules from twelve different strains of rabies virus which may silence the nucleoprotein gene and inhibit the multiplication of the virus. Conclusion: Our study may help to take an effective therapeutic approach against rabies virus and lead to better control of rabies in humans.
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Affiliation(s)
| | - Anik Paul
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Motaher Hossain
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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Abstract
INTRODUCTION Treatment of chronic hepatitis D still relies on Interferon. To improve efficacy, new therapeutic strategies are in development which aim to deprive the Hepatitis D Virus (HDV) of functions of the Hepatitis B Virus and of the host required for its life-cycle. Areas covered: The therapeutic options are; 1) The inhibition of the farnesylation of the large HD-protein permissive of virion assembly with Lonafarnib, 2) The blocking of HBsAg entry into cells with Myrcludex B via the inhibition of the Sodium Taurocholate Cotransporting Receptor, to prevent the spreading of HDV to uninfected hepatocytes, 3) The reduction of subviral HBsAg particles by REP 2139, leading to diminished virion morphogenesis . Expert opinion: Lonafarnib and Myrcludex reduced serum HVD-RNA; neither diminished serum HBsAg. NAP REP-2139 diminished both HDV-RNA and HBsAg in serum; a full report is awaited. In combination with Peg-Interferon, these new drugs may provide additional efficacy.
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Affiliation(s)
- Mario Rizzetto
- a Department of Medicine , University of Torino , Torino , Italy
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Structural Dynamics of Human Argonaute2 and Its Interaction with siRNAs Designed to Target Mutant tdp43. Adv Bioinformatics 2016; 2016:8792814. [PMID: 27110240 PMCID: PMC4824133 DOI: 10.1155/2016/8792814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
The human Argonaute2 protein (Ago2) is a key player in RNA interference pathway and small RNA recognition by Ago2 is the crucial step in siRNA mediated gene silencing mechanism. The present study highlights the structural and functional dynamics of human Ago2 and the interaction mechanism of Ago2 with a set of seven siRNAs for the first time. The human Ago2 protein adopts two conformations such as “open” and “close” during the simulation of 25 ns. One of the domains named as PAZ, which is responsible for anchoring the 3′-end of siRNA guide strand, is observed as a highly flexible region. The interaction between Ago2 and siRNA, analyzed using a set of siRNAs (targeting at positions 128, 251, 341, 383, 537, 1113, and 1115 of mRNA) designed to target tdp43 mutants causing Amyotrophic Lateral Sclerosis (ALS) disease, revealed the stable and strong recognition of siRNA by the Ago2 protein during dynamics. Among the studied siRNAs, the siRNA341 is identified as a potent siRNA to recognize Ago2 and hence could be used further as a possible siRNA candidate to target the mutant tdp43 protein for the treatment of ALS patients.
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12
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Soriano V, Labarga P, de Mendoza C, Fernández-Montero JV, Treviño A, Benítez-Gutiérrez L, Peña JM, Barreiro P. Delta hepatitis: new approaches to therapy. Future Virol 2016. [DOI: 10.2217/fvl-2015-0009] [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
Hepatitis delta virus (HDV) infection is a neglected disease despite causing the most severe form of viral hepatitis. Over 15 million people are infected worldwide. IFN-α is largely inefficient and poorly tolerated. The discovery of sodium taurocholate cotransporting polypeptide as the cell receptor for HBV (and consequently for HDV) has allowed development of viral entry inhibitors (i.e., myrcludex-B). More recently, prenylation inhibitors (i.e., lonafarnib) that disrupt virion assembly are being tested. At this time, sustained suppression of HDV replication is the primary goal of hepatitis delta treatment, being associated with normalization of liver enzymes and histological improvement. The lack of persistent forms of HDV-RNA could provide unique opportunities for hepatitis delta cure using specific antivirals, even in the face of persistent HBV cccDNA.
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Affiliation(s)
- Vincent Soriano
- Infectious Diseases Unit, La Paz University Hospital, Madrid, Spain
| | - Pablo Labarga
- Department of Internal Medicine, La Luz Clinic, Madrid, Spain
| | - Carmen de Mendoza
- Department of Internal Medicine, Puerta de Hierro Research Institute & University Hospital, Majadahonda, Spain
| | | | - Ana Treviño
- Infectious Diseases Unit, La Paz University Hospital, Madrid, Spain
| | - Laura Benítez-Gutiérrez
- Department of Internal Medicine, Puerta de Hierro Research Institute & University Hospital, Majadahonda, Spain
| | - José M Peña
- Infectious Diseases Unit, La Paz University Hospital, Madrid, Spain
| | - Pablo Barreiro
- Infectious Diseases Unit, La Paz University Hospital, Madrid, Spain
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Guo Z, King T. Therapeutic Strategies and New Intervention Points in Chronic Hepatitis Delta Virus Infection. Int J Mol Sci 2015; 16:19537-52. [PMID: 26295228 PMCID: PMC4581312 DOI: 10.3390/ijms160819537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
Chronic hepatitis delta virus infection (CHD) is a condition arising from super-infection of hepatitis B virus (HBV)-infected patients, resulting in a more rapid advance in liver pathology and hepatocellular carcinoma than is observed for HBV mono-infection. Although hepatitis delta virus (HDV) is structurally simple, its life cycle involves the complex participation of host enzymes, HBV-derived surface antigen (HBsAg), and HDV-auto-ribozyme and hepatitis delta antigen (HDAg) activities. Unsatisfactory clinical trial results with interferon-based therapies are motivating researchers to adjust and redirect the approach to CHD drug development. This new effort will likely require additional structural and functional studies of the viral and cellular/host components involved in the HDV replication cycle. This review highlights recent work aimed at new drug interventions for CHD, with interpretation of key pre-clinical- and clinical trial outcomes and a discussion of promising new technological approaches to antiviral drug design.
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Affiliation(s)
- Zhimin Guo
- Huron Peak Ave., Superior, CO 80027, USA.
| | - Thomas King
- Allevagen, LLC, 4105 Perry St., Denver, CO 80212, USA.
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Aldabe R, Suárez-Amarán L, Usai C, González-Aseguinolaza G. Animal models of chronic hepatitis delta virus infection host-virus immunologic interactions. Pathogens 2015; 4:46-65. [PMID: 25686091 PMCID: PMC4384072 DOI: 10.3390/pathogens4010046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/05/2015] [Indexed: 02/08/2023] Open
Abstract
Hepatitis delta virus (HDV) is a defective RNA virus that has an absolute requirement for a virus belonging to the hepadnaviridae family like hepatitis B virus (HBV) for its replication and formation of new virions. HDV infection is usually associated with a worsening of HBV-induced liver pathogenesis, which leads to more frequent cirrhosis, increased risk of hepatocellular carcinoma (HCC), and fulminant hepatitis. Importantly, no selective therapies are available for HDV infection. The mainstay of treatment for HDV infection is pegylated interferon alpha; however, response rates to this therapy are poor. A better knowledge of HDV–host cell interaction will help with the identification of novel therapeutic targets, which are urgently needed. Animal models like hepadnavirus-infected chimpanzees or the eastern woodchuck have been of great value for the characterization of HDV chronic infection. Recently, more practical animal models in which to perform a deeper study of host virus interactions and to evaluate new therapeutic strategies have been developed. Therefore, the main focus of this review is to discuss the current knowledge about HDV host interactions obtained from cell culture and animal models.
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Affiliation(s)
- Rafael Aldabe
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra (UNAV), Pamplona 31008, Spain.
| | - Lester Suárez-Amarán
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra (UNAV), Pamplona 31008, Spain
| | - Carla Usai
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra (UNAV), Pamplona 31008, Spain.
| | - Gloria González-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra (UNAV), Pamplona 31008, Spain.
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Abstract
Immigration is fuelling a new reservoir of hepatitis D virus (HDV) in Europe, and hepatitis D still represents an important medical problem in the USA. The disease continues to be a major medical scourge in the developing world, in particular in countries such as Pakistan, Mongolia and Mauritania. New therapeutic strategies are being developed to disrupt interactions between HDV and its viral partner HBV, or with the host. Blocking or modifying the hepatitis B surface antigen (HBsAg) might interfere with the uptake or release of the hepatitis D virion; interference with host-mediated post-translational changes of proteins that are crucial to the HDV life cycle, such as prenylation, is another potential therapeutic option. At present, however, the only realistic option is to optimize IFN-α therapy. As eradication of HBsAg is the ultimate end point of therapy, long-term interferon administration might be required, raising an issue of tolerance in patients. Treatment with IFN-λ is a potential alternative approach to IFN-α; treatment of hepatitis C with this cytokine seems to cause fewer adverse effects than IFN-α and, therefore, might be more suitable for long-term treatment of HDV.
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Nur SM, Al Amin M, Alam R, Hasan MA, Hossain MA, Mannan A. An in silico approach to design potential siRNA molecules for ICP22 (US1) gene silencing of different strains of human herpes simplex 1. J Young Pharm 2013; 5:46-9. [PMID: 24023453 DOI: 10.1016/j.jyp.2013.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/16/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The herpes simplex virus (HSV-1) is a virus that manifests itself in viral infection with painful, watery blisters in the skin or on the genitals as well as mucous membrane such as the mouth or lips. During an outbreak, the disease is contagious particularly and is irredeemable with present technology. Genetic studies of HSV-1 have shown that ICP22 (US1) gene is an immediate early gene and is responsible for genome replication and also has contribution in viral infection. METHOD For disease diagnosis, ICP22 (US1) gene may be suitable target. Viral activity can be controlled through RNA interference technology, a significant method for the post-transcriptional gene silencing. However, in different viral isolates there is a genetic variability; it is very challenging to design possible siRNA molecules which can silence the respective target genes. The work was done by using various computational tools as similarity search, target alignment, secondary structure prediction and RNA interaction evaluation. RESULT In our study two effective siRNA molecules for ICP22 (US1) gene silencing of seven different strains of HSV-1 were rationally designed and authenticated using computational methods, which might lead to knockdown the viral activity. CONCLUSION siRNA molecules were foreseen against ICP22 (US1) gene of different strains of HSV-1 as effective aspirant using computational methods. Thus, the approach may deliver a vision for the chemical synthesis of antiviral RNA molecule for treatment of HSV-1, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh
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