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Palit P, Chowdhury FT, Baruah N, Sarkar B, Mou SN, Kamal M, Siddiqua TJ, Noor Z, Ahmed T. A Comprehensive Computational Investigation into the Conserved Virulent Proteins of Shigella species Unveils Potential Small-Interfering RNA Candidates as a New Therapeutic Strategy against Shigellosis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061936. [PMID: 35335300 PMCID: PMC8950558 DOI: 10.3390/molecules27061936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/19/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Shigella species account for the second-leading cause of deaths due to diarrheal diseases among children of less than 5 years of age. The emergence of multi-drug-resistant Shigella isolates and the lack of availability of Shigella vaccines have led to the pertinence in the efforts made for the development of new therapeutic strategies against shigellosis. Consequently, designing small-interfering RNA (siRNA) candidates against such infectious agents represents a novel approach to propose new therapeutic candidates to curb the rampant rise of anti-microbial resistance in such pathogens. In this study, we analyzed 264 conserved sequences from 15 different conserved virulence genes of Shigella sp., through extensive rational validation using a plethora of first-generation and second-generation computational algorithms for siRNA designing. Fifty-eight siRNA candidates were obtained by using the first-generation algorithms, out of which only 38 siRNA candidates complied with the second-generation rules of siRNA designing. Further computational validation showed that 16 siRNA candidates were found to have a substantial functional efficiency, out of which 11 siRNA candidates were found to be non-immunogenic. Finally, three siRNA candidates exhibited a sterically feasible three-dimensional structure as exhibited by parameters of nucleic acid geometry such as: the probability of wrong sugar puckers, bad backbone confirmations, bad bonds, and bad angles being within the accepted threshold for stable tertiary structure. Although the findings of our study require further wet-lab validation and optimization for therapeutic use in the treatment of shigellosis, the computationally validated siRNA candidates are expected to suppress the expression of the virulence genes, namely: IpgD (siRNA 9) and OspB (siRNA 15 and siRNA 17) and thus act as a prospective tool in the RNA interference (RNAi) pathway. However, the findings of our study require further wet-lab validation and optimization for regular therapeutic use for treatment of shigellosis.
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Affiliation(s)
- Parag Palit
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (P.P.); (M.K.); (T.J.S.); (T.A.)
| | - Farhana Tasnim Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (F.T.C.); (B.S.); (S.N.M.)
| | - Namrata Baruah
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India;
| | - Bonoshree Sarkar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (F.T.C.); (B.S.); (S.N.M.)
| | - Sadia Noor Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh; (F.T.C.); (B.S.); (S.N.M.)
| | - Mehnaz Kamal
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (P.P.); (M.K.); (T.J.S.); (T.A.)
| | - Towfida Jahan Siddiqua
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (P.P.); (M.K.); (T.J.S.); (T.A.)
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (P.P.); (M.K.); (T.J.S.); (T.A.)
- Correspondence:
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (P.P.); (M.K.); (T.J.S.); (T.A.)
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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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Panda K, Alagarasu K, Cherian SS, Parashar D. Prediction of potential small interfering RNA molecules for silencing of the spike gene of SARS-CoV-2. Indian J Med Res 2021; 153:182-189. [PMID: 33818475 PMCID: PMC8184069 DOI: 10.4103/ijmr.ijmr_2855_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Kingshuk Panda
- Chikungunya-Dengue Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Kalichamy Alagarasu
- Chikungunya-Dengue Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sarah S Cherian
- Bioinformatics Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Deepti Parashar
- Chikungunya-Dengue Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
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Islam MO, Palit P, Shawon J, Hasan MK, Mahmud A, Mahfuz M, Ahmed T, Mondal D. Exploring novel therapeutic strategies against vivax malaria through an integrated computational investigation to inhibit the merozoite surface protein−1 of Plasmodium vivax. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Mohanty PS, Sharma S, Naaz F, Kumar D, Raikwar A, Patil SA. Inhibition of Mycobacterium tuberculosis tRNA-Ligases Using siRNA-Based Gene Silencing Method: A Computational Approach. J Comput Biol 2019; 27:91-99. [PMID: 31433209 DOI: 10.1089/cmb.2019.0156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is a major public health problem in several countries. Development of first-line and second-line drug resistance strains of Mycobacterium tuberculosis further complicated the management of the disease. Despite available drugs to treat TB, 1.6 million people died from the disease in 2017. In this study, we designed 10 siRNAs against 8 tRNA ligases of M. tuberculosis and validated their usefulness for inhibition of protein synthesis by using computational approach. We found that the predicted siRNAs efficiently form seed duplex complex against their respective mRNA targets. Other different computational approaches were also undertaken to assess the stability, accessibility, and strength of seed duplex complex of designed siRNA and targeted mRNA. On the basis of the computational approach, we reciprocated that the technique will help in opening a new window in the field of TB control program and could be taken for further clinical studies to find their appropriateness for TB eradication.
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Affiliation(s)
- Partha Sarathi Mohanty
- Department of Epidemiology and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Sandeep Sharma
- Department of Epidemiology and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Farah Naaz
- Department of Epidemiology and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Dilip Kumar
- Department of Epidemiology and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Archana Raikwar
- Department of Epidemiology and National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Shripad A Patil
- Department of Immunology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
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He F, Han Y, Gong J, Song J, Wang H, Li Y. Predicting siRNA efficacy based on multiple selective siRNA representations and their combination at score level. Sci Rep 2017; 7:44836. [PMID: 28317874 PMCID: PMC5357899 DOI: 10.1038/srep44836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 12/31/2022] Open
Abstract
Small interfering RNAs (siRNAs) may induce to targeted gene knockdown, and the gene silencing effectiveness relies on the efficacy of the siRNA. Therefore, the task of this paper is to construct an effective siRNA prediction method. In our work, we try to describe siRNA from both quantitative and qualitative aspects. For quantitative analyses, we form four groups of effective features, including nucleotide frequencies, thermodynamic stability profile, thermodynamic of siRNA-mRNA interaction, and mRNA related features, as a new mixed representation, in which thermodynamic of siRNA-mRNA interaction is introduced to siRNA efficacy prediction for the first time to our best knowledge. And then an F-score based feature selection is employed to investigate the contribution of each feature and remove the weak relevant features. Meanwhile, we encode the siRNA sequence and existed empirical design rules as a qualitative siRNA representation. These two kinds of siRNA representations are combined to predict siRNA efficacy by supported Vector Regression (SVR) at score level. The experimental results indicate that our method may select the features with powerful discriminative ability and make the two kinds of siRNA representations work at full capacity. The prediction results also demonstrate that our method can outperform other popular siRNA efficacy prediction algorithms.
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Affiliation(s)
- Fei He
- Northeast Normal University, School of Computer Science and Information Technology, Changchun, 130117, China
- Northeast Normal University, School of Environment, Changchun, 130117, China
- Northeast Normal University, Institute of Computational Biology, Changchun, 130117, China
| | - Ye Han
- Jilin University, College of Computer Science and Technology, Changchun, 130012, China
- Jilin University, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Changchun, 130012, China
| | - Jianting Gong
- Northeast Normal University, School of Computer Science and Information Technology, Changchun, 130117, China
- Northeast Normal University, Institute of Computational Biology, Changchun, 130117, China
| | - Jiazhi Song
- Northeast Normal University, School of Computer Science and Information Technology, Changchun, 130117, China
- Northeast Normal University, Institute of Computational Biology, Changchun, 130117, China
| | - Han Wang
- Northeast Normal University, School of Computer Science and Information Technology, Changchun, 130117, China
- Northeast Normal University, Institute of Computational Biology, Changchun, 130117, China
| | - Yanwen Li
- Northeast Normal University, School of Computer Science and Information Technology, Changchun, 130117, China
- Northeast Normal University, Institute of Computational Biology, Changchun, 130117, China
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Utilizing Selected Di- and Trinucleotides of siRNA to Predict RNAi Activity. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:5043984. [PMID: 28243313 PMCID: PMC5294759 DOI: 10.1155/2017/5043984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/15/2016] [Indexed: 02/04/2023]
Abstract
Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named “siRNApred” with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorithm. Experimental data demonstrated that the binding site of the Argonaute protein correlates with siRNA activity. “siRNApred” is effective for selecting active siRNAs, and the prediction results demonstrate that our method can outperform other current siRNA activity prediction methods in terms of prediction accuracy.
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of Potential RNAi (miRNA and siRNA) Molecules for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Gene Silencing by Computational Method. Interdiscip Sci 2015. [PMID: 26223545 PMCID: PMC7090891 DOI: 10.1007/s12539-015-0266-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF1ab replicase polyprotein may be used as a suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence-specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In the current study, four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, 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
| | - Md Anayet Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.
| | - Mohammad Al Amin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Mehjabeen Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Tahmina Sharmin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
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Freire JEDC, Medeiros SCD, Lopes Neto AV, Monteiro Júnior JE, Sousa AJS, Rocha AJ, Menezes LMBD. Bioethical conflicts of gene therapy: a brief critical review. Rev Assoc Med Bras (1992) 2015; 60:520-4. [PMID: 25650850 DOI: 10.1590/1806-9282.60.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/03/2014] [Indexed: 11/22/2022] Open
Abstract
Methods and techniques employed in gene therapy are reviewed in parallel with pertinent ethical conflicts. Clinical interventions based on gene therapy techniques preferentially use vectors for the transportation of therapeutic genes, however little is known about the potential risks and damages to the patient. Thus, attending carefully to the clinical complications arising as well as to security is essential. Despite the scientific and technological advances, there are still many uncertainties about the side effects of gene therapy. Moreover, there is a need, above all, to understand the principles of bioethics as both science and ethics, in accordance with its socioecological responsibility, in order to prioritize the health and welfare of man and nature, using properly natural resources and technology. Therefore, it is hard to determine objective results and to which extent the insertion of genes can affect the organism, as well as the ethical implication.
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Affiliation(s)
| | | | - Antônio Viana Lopes Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Antônio José Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25373633 DOI: 10.1007/s12539-014-0208-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, 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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11
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25519155 DOI: 10.1007/s12539-014-0233-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, 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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