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Banik M, Paudel KR, Majumder R, Idrees S. Prediction of virus-host interactions and identification of hot spot residues of DENV-2 and SH3 domain interactions. Arch Microbiol 2024; 206:162. [PMID: 38483579 PMCID: PMC10940428 DOI: 10.1007/s00203-024-03892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Dengue virus, particularly serotype 2 (DENV-2), poses a significant global health threat, and understanding the molecular basis of its interactions with host cell proteins is imperative for developing targeted therapeutic strategies. This study elucidated the interactions between proline-enriched motifs and Src homology 3 (SH3) domain. The SH3 domain is pivotal in mediating protein-protein interactions, particularly by recognizing and binding to proline-rich regions in partner proteins. Through a computational pipeline, we analyzed the interactions and binding modes of proline-enriched motifs with SH3 domains, identified new potential DENV-2 interactions with the SH3 domain, and revealed potential hot spot residues, underscoring their significance in the viral life cycle. This comprehensive analysis provides crucial insights into the molecular basis of DENV-2 infection, highlighting conserved and serotype-specific interactions. The identified hot spot residues offer potential targets for therapeutic intervention, laying the foundation for developing antiviral strategies against Dengue virus infection. These findings contribute to the broader understanding of viral-host interactions and provide a roadmap for future research on Dengue virus pathogenesis and treatment.
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Affiliation(s)
- Mithila Banik
- Department of Bioinformatics and Biotechnology, Asian University for Women, Chattogram, Bangladesh
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Rajib Majumder
- Applied Bioscience, Macquarie University, Sydney, NSW, Australia
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, NSW, Australia.
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Sartaj Sohrab S, Aly El-Kafrawy S, Mirza Z, Hassan AM, Alsaqaf F, Ibraheem Azhar E. Delivery of siRNAs against MERS-CoV in Vero and HEK-293 cells: A comparative evaluation of transfection reagents. J King Saud Univ Sci 2023; 35:102540. [PMID: 36624781 PMCID: PMC9814285 DOI: 10.1016/j.jksus.2023.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 05/28/2023]
Abstract
Background A new coronavirus was identified in Jeddah, Saudi Arabia in 2012 and designated as Middle East Respiratory Syndrome Coronavirus (MERS-CoV). To date, this virus has been reported in 27 countries. The virus transmission to humans has already been reported from camels. Currently, there is no vaccine or antiviral therapy available against this virus. Methods The siRNAs were in silico predicted, designed, and chemically synthesized by using the MERS-CoV-orf1ab region as a target. The antiviral activity was experimentally evaluated by delivering the siRNAs with Lipofectamine™ 2000 and JetPRIMER as transfection reagents in both Vero cell and HEK-293-T cell lines at two different concentrations (10.0 nM and 5.0 nM). The Ct value of quantitative Real-Time PCR (qRT-PCR) was used to calculate and determine the reduction of viral RNA level in both cell supernatant and cell lysate isolated from both cell lines. Results The sequence alignment resulted in the selection of highly conserved regions. The orf1ab region was used to predict and design the siRNAs and a total of twenty-one siRNAs were finally selected from four hundred and twenty-six siRNAs generated by online software. Inhibition of viral replication and significant reduction of viral RNA was observed against selected siRNAs in both cell lines at both concentrations. Based on the Ct value, the siRNAs # 11, 12, 18, and 20 were observed to be the best performing in both cell lines at both concentrations. Conclusion Based on the results and data analysis, it is concluded that the use of two different transfection reagents was significantly effective. But the Lipofectamine™ 2000 was found to be a better transfection reagent than the JetPRIMER for the delivery of siRNAs in both cell lines.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Aly El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Sohrab SS, El-Kafrawy SA, Mirza Z, Hassan AM, Alsaqaf F, Azhar EI. Computational Design and Experimental Evaluation of MERS-CoV siRNAs in Selected Cell Lines. Diagnostics (Basel) 2023; 13. [PMID: 36611443 DOI: 10.3390/diagnostics13010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 01/04/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is caused by a well-known coronavirus first identified in a hospitalized patient in the Kingdom of Saudi Arabia. MERS-CoV is a serious pathogen affecting both human and camel health globally, with camels being known carriers of viruses that spread to humans. In this work, MERS-CoV genomic sequences were retrieved and analyzed by multiple sequence alignment to design and predict siRNAs with online software. The siRNAs were designed from the orf1ab region of the virus genome because of its high sequence conservation and vital role in virus replication. The designed siRNAs were used for experimental evaluation in selected cell lines: Vero cells, HEK-293-T, and Huh-7. Virus inhibition was assessed according to the cycle threshold value during a quantitative real-time polymerase chain reaction. Out of 462 potential siRNAs, we filtered out 21 based on specific selection criteria without off-target effect. The selected siRNAs did not show any cellular toxicity in the tested cell lines at various concentrations. Based on our results, it was obvious that the combined use of siRNAs exhibited a reduction in MERS-CoV replication in the Vero, HEK-293-T, and Huh-7 cell lines, with the highest efficacy displayed in the Vero cells.
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Rubio-Miranda JÁ, Cázares-Raga FE, Coy-Arechavaleta AS, Viettri M, Cortes-Martínez L, Lagunes-Guillén A, Chavez-Munguía B, Ludert JE, Hernández-Hernández FDLC. Septin 2 interacts with dengue virus replication complex proteins and participates in virus replication in mosquito cells. Virology 2022; 570:67-80. [DOI: 10.1016/j.virol.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022]
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Rodriguez-Salazar CA, Recalde-Reyes DP, Bedoya JP, Padilla-Sanabria L, Castaño-Osorio JC, Giraldo MI. In Vitro Inhibition of Replication of Dengue Virus Serotypes 1-4 by siRNAs Bound to Non-Toxic Liposomes. Viruses 2022; 14:339. [PMID: 35215929 PMCID: PMC8875542 DOI: 10.3390/v14020339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus is a ssRNA+ flavivirus, which produces the dengue disease in humans. Currently, no specific treatment exists. siRNAs regulate gene expression and have been used systematically to silence viral genomes; however, they require controlled release. Liposomes show favorable results encapsulating siRNA for gene silencing. The objective herein was to design and evaluate in vitro siRNAs bound to liposomes that inhibit DENV replication. siRNAs were designed against DENV1-4 from conserved regions using siDirect2.0 and Web-BLOCK-iT™ RNAiDesigner; the initial in vitro evaluation was carried out through transfection into HepG2 cells. siRNA with silencing capacity was encapsulated in liposomes composed of D-Lin-MC3-DMA, DSPC, Chol. Cytotoxicity, hemolysis, pro-inflammatory cytokine release and antiviral activity were evaluated using plaque assay and RT-qPCR. A working concentration of siRNA was established at 40 nM. siRNA1, siRNA2, siRNA3.1, and siRNA4 were encapsulated in liposomes, and their siRNA delivery through liposomes led to a statistically significant decrease in viral titers, yielded no cytotoxicity or hemolysis and did not stimulate release of pro-inflammatory cytokines. Finally, liposomes were designed with siRNA against DENV, which proved to be safe in vitro.
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Affiliation(s)
- Carlos Andrés Rodriguez-Salazar
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Delia Piedad Recalde-Reyes
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander Von Humboldt, Armenia 630003, Colombia
| | - Juan Pablo Bedoya
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Leonardo Padilla-Sanabria
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Jhon Carlos Castaño-Osorio
- Center of Biomedical Research, Faculty of Health Sciences, Universidad del Quindío, Armenia 630003, Colombia; (D.P.R.-R.); (J.P.B.); (L.P.-S.); (J.C.C.-O.)
| | - Maria Isabel Giraldo
- Department of Microbiology, Immunology University of Texas Medical Branch, Galveston, TX 77555, USA
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Basawarajappa SG, Rangaiah A, Venugopal SJ, Varun CN, Nagaraj V, Padukone S, Shankar SM. Clinical and Molecular facets of Dengue Virus infection from Bengaluru, South India. Nepal J Epidemiol 2021; 11:1053-1062. [PMID: 34733567 PMCID: PMC8560139 DOI: 10.3126/nje.v11i3.37712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022] Open
Abstract
Background Dengue virus (DENV) continues to be an epidemic with high mortality rates. The clinical features, especially in the early phase of infection, are nonspecific and there is no single marker that can be reliably deployed for diagnostics. Further, serotype and genotype diversity is not clearly understood. This study was conceived to understand the performance characteristics of various diagnostic markers; serotype and genotype distribution is thus a vital requirement. Methods A subset of blood samples was obtained for all the clinically suspected Dengue cases during the period January to December 2017. The samples were tested for IgM and IgG antibodies and NS1 antigen by both ELISA and rapid tests. Real-time PCR, Conventional PCR and sequencing was performed based on the serology results. Correlation of the data with demographic and clinical details was used to analyze the performance characteristics of various tests. Results Clinical signs and symptoms could not predict dengue positivity due to lack of specific symptoms. The performance of IgM rapid test was found to be lower than the ELISA method (53.5% agreement). The NS1 rapid and NS1 ELISA tests were comparable (89.2% agreement). Majority of the infections were caused due to DEN-2 serotype and phylogenetic analysis revealed all the sequenced DEN-2 serotypes belong to Genotype IV. Three sequences were deposited into NCBI GenBank (GenBank accession number MW583116, MW579054 and MW579053). Conclusion Our comprehensive data suggests that NS1 ELISA and PCR are best used in the early phase of dengue infection (< 5 days post-onset of fever), whereas IgM antibody detection is reliable only in the late phase. We also highlight the unreliable performance of rapid tests.
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Affiliation(s)
- Shantala Gowdara Basawarajappa
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Ambica Rangaiah
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Shwetha Jinnahalli Venugopal
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Chakrakodi N Varun
- State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Vijay Nagaraj
- Institute of Animal Health and Veterinary Biologicals, Hebbal, Bengaluru-560024
| | - Shashiraja Padukone
- State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Sathyanarayan Muthur Shankar
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India.,State Level VRDL, Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, Karnataka, India
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Nanaware N, Banerjee A, Mullick Bagchi S, Bagchi P, Mukherjee A. Dengue Virus Infection: A Tale of Viral Exploitations and Host Responses. Viruses 2021; 13:v13101967. [PMID: 34696397 PMCID: PMC8541669 DOI: 10.3390/v13101967] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Dengue is a mosquito-borne viral disease (arboviral) caused by the Dengue virus. It is one of the prominent public health problems in tropical and subtropical regions with no effective vaccines. Every year around 400 million people get infected by the Dengue virus, with a mortality rate of about 20% among the patients with severe dengue. The Dengue virus belongs to the Flaviviridae family, and it is an enveloped virus with positive-sense single-stranded RNA as the genetic material. Studies of the infection cycle of this virus revealed potential host targets important for the virus replication cycle. Here in this review article, we will be discussing different stages of the Dengue virus infection cycle inside mammalian host cells and how host proteins are exploited by the virus in the course of infection as well as how the host counteracts the virus by eliciting different antiviral responses.
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Affiliation(s)
- Nikita Nanaware
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, MH, India; (N.N.); (A.B.)
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, MH, India; (N.N.); (A.B.)
| | | | - Parikshit Bagchi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Correspondence: or (P.B.); or (A.M.)
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, MH, India; (N.N.); (A.B.)
- Correspondence: or (P.B.); or (A.M.)
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Prakash O, Khan DN, Singh T, Shukla S, Prakash S, Amita J. Effect of siRNA targeting dengue virus genes on replication of dengue virus: an in vitro experimental study. Virusdisease 2021;:1-8. [PMID: 34485626 DOI: 10.1007/s13337-021-00700-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/20/2021] [Indexed: 11/25/2022] Open
Abstract
Dengue is a notorious viral infection, which affects a large segment of world populations in absence of vaccines and anti-viral treatment. The current study evaluates role of effective siRNA in dengue virus replication. Eight siRNA were synthesized against five different genes (Capsid, CprM, NS1, NS3 and NS5) of all serotypes of dengue virus. All serotype of DV were transfected with all synthesized siRNA in vitro, using BHK-21 cell lines. Culture fluid from test and control was tested by Real time PCR for CT value comparison in siRNA treated cell line (test) and untreated cell line (controls). Percent knockdown (%KD) was calculated by ∆∆CT methods to know the difference in test and control CT value. It was found that siRNA targeted against capsid gene worked best and showed inhibition of all four DV serotypes. DV-1, DV-2, DV-3 and DV-4 showed 93.8%, 99.3%, 87.5% and 93.8% knock down (%KD) respectively by siRNA targeted against capsid gene. Additionally, Si2 (target CprM gene 60-899) and Si 6 (target NS1 gene 3007-3025) were also showing inhibition of replication. Most serotypes of DV (with few exceptions) were not inhibited by siRNA targeted against NS-1, NS-3, and NS-5 genes. Animal studies using siRNAs are warranted to establish their therapeutic role.
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El-Kafrawy SA, Sohrab SS, Mirza Z, Hassan AM, Alsaqaf F, Azhar EI. In Vitro Inhibitory Analysis of Rationally Designed siRNAs against MERS-CoV Replication in Huh7 Cells. Molecules 2021; 26:2610. [PMID: 33947034 DOI: 10.3390/molecules26092610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
MERS-CoV was identified for the first time in Jeddah, Saudi Arabia in 2012 in a hospitalized patient. This virus subsequently spread to 27 countries with a total of 939 deaths and 2586 confirmed cases and now has become a serious concern globally. Camels are well known for the transmission of the virus to the human population. In this report, we have discussed the prediction, designing, and evaluation of potential siRNA targeting the ORF1ab gene for the inhibition of MERS-CoV replication. The online software, siDirect 2.0 was used to predict and design the siRNAs, their secondary structure and their target accessibility. ORF1ab gene folding was performed by RNAxs and RNAfold software. A total of twenty-one siRNAs were selected from 462 siRNAs according to their scoring and specificity. siRNAs were evaluated in vitro for their cytotoxicity and antiviral efficacy in Huh7 cell line. No significant cytotoxicity was observed for all siRNAs in Huh7 cells. The in vitro study showed the inhibition of viral replication by three siRNAs. The data generated in this study provide preliminary and encouraging information to evaluate the siRNAs separately as well as in combination against MERS-CoV replication in other cell lines. The prediction of siRNAs using online software resulted in the filtration and selection of potential siRNAs with high accuracy and strength. This computational approach resulted in three effective siRNAs that can be taken further to in vivo animal studies and can be used to develop safe and effective antiviral therapies for other prevalent disease-causing viruses.
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Panda K, Alagarasu K, Parashar D. Oligonucleotide-Based Approaches to Inhibit Dengue Virus Replication. Molecules 2021; 26:956. [PMID: 33670247 PMCID: PMC7918374 DOI: 10.3390/molecules26040956] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Dengue fever is one of the most common viral infections affecting humans. It is an expanding public health problem, particularly in tropical and subtropical regions. No effective vaccine or antiviral therapies against Dengue virus (DENV) infection are available. Therefore, there is a strong need to develop safe and effective therapeutic strategies that can reduce the burden and duration of hospitalizations due to this life-threatening disease. Oligonucleotide-based strategies are considered as an attractive means of inhibiting viral replication since oligonucleotides can be designed to interact with any viral RNA, provided its sequence is known. The resultant targeted destruction of viral RNA interferes with viral replication without inducing any adverse effects on cellular processes. In this review, we elaborate the ribozymes, RNA interference, CRISPR, aptamer and morpholino strategies for the inhibition of DENV replication and discuss the challenges involved in utilizing such approaches.
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Affiliation(s)
- Kingshuk Panda
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Kalichamy Alagarasu
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Deepti Parashar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
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Sohrab SS, Aly El-Kafrawy S, Mirza Z, Hassan AM, Alsaqaf F, Azhar EI. In silico prediction and experimental validation of siRNAs targeting ORF1ab of MERS-CoV in Vero cell line. Saudi J Biol Sci 2021; 28:1348-1355. [PMID: 33519276 PMCID: PMC7833792 DOI: 10.1016/j.sjbs.2020.11.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus is well known to cause respiratory syndrome and this virus was identified and isolated for the first time from Jeddah, Saudi Arabia in 2012 from infected patient. In this report, we have conducted the in-silico prediction, designing and evaluation of siRNAs targeting Middle East Respiratory Syndrome Coronavirus orf1ab gene to inhibit the virus replication. By using bioinformatics software, total twenty-one functional, off-target reduced siRNA were selected from four hundred and sixty-two siRNAs based on their greater potency and specificity. We have evaluated only seven siRNAs to analyze their performance and efficacy as antivirals by reverse transfection approach in Vero cells. There was no cytotoxicity of siRNAs at various concentrations was observed in Vero cells. Based on the real-time PCR results, better inhibition of viral replication was observed in the siRNA-1 and 4 as compared to other siRNAs. The results generated from this work provided suitable information about the efficacy of siRNAs which encouraged us to further evaluate the remaining siRNAs to determine their inhibitory effect on the virus replication. We concluded that the insilico prediction and designing resulted in the screening of potential siRNAs with better efficiency, and strength. This can be used to develop oligonucleotide-based antiviral therapeutics against MERS-CoV in the near future.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Aly El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No-80216, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Sohrab SS, El-Kafrawy SA, Mirza Z, Hassan AM, Alsaqaf F, Azhar EI. Designing and evaluation of MERS-CoV siRNAs in HEK-293 cell line. J Infect Public Health 2020; 14:238-243. [PMID: 33493920 PMCID: PMC7771261 DOI: 10.1016/j.jiph.2020.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Background The MERS-CoV was identified for the first time from Jeddah, Saudi Arabia in 2012 from a hospitalized patient. This virus has now been spread to 27 countries with a total of 858 deaths and 2494 confirmed cases and has become a serious concern for the human population. Camels are well known for the transmission of the virus to the human population. Methods In this report, we have discussed the designing, prediction, and evaluation of potential siRNAs against the orf1ab gene of MERS-CoV. The online software was used to predict and design the siRNAs and finally, total twenty-one siRNA were filtered out from four hundred and sixty-two sIRNAs as per their scoring and specificity criteria. We have used only ten siRNAs to evaluate their cytotoxicity and efficacy by reverse transfection approach in HEK-293-T cell lines. Results Based on the results and data generated; no cytotoxicity was observed for any siRNAs at various concentrations in HEK-293-T cells. The ct value of real-time PCR showed the inhibition of viral replication in siRNA-1, 2, 4, 6, and 9. The data generated provided the preliminary information and encouraged us to evaluate the remaining siRNAs separately as well as in combination to analyses the replication of MERS-CoV inhibition in other cell lines. Conclusion Based on the results obtained; it is concluded that the prediction of siRNAs using online software resulted in the filtration of potential siRNAs with high accuracy and strength. This technology can be used to design and develop antiviral therapy not only for MERS-CoV but also against other viruses.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box, No-80216, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sherif Aly El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box, No-80216, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box, No-80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box, No-80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box, No-80216, Jeddah 21589, Saudi Arabia; Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Ali F, Chorsiya A, Anjum V, Khasimbi S, Ali A. A systematic review on phytochemicals for the treatment of dengue. Phytother Res 2020; 35:1782-1816. [PMID: 33118251 DOI: 10.1002/ptr.6917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/23/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023]
Abstract
Dengue fever is prevalent in subtopic regions, producing mortality and morbidity worldwide, which have been of major concern to different governments and World Health Organization. The search of new anti-dengue agents from phytochemicals was assumed to be highly emergent in past. The phytochemicals have been used in wide distribution of vector ailments such as malaria. The demand of the phytochemicals is based on the medicines which are mostly considered to be safer, less harmful than synthetic drugs and nontoxic. This review mentions majorly about the phytochemicals potentially inhibiting dengue fever around the world. The phytochemicals have been isolated from different species, have potential for the treatment of dengue. Different crude extracts and essential oils obtained from different species showed a broad activity against different phytochemicals. The current studies showed that natural products represent a rich source of medicines toward the dengue fever. Furthermore, ethnobotanical surveys and laboratory investigation established identified natural plants species in the development of drug discovery to control the dengue fever.
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Affiliation(s)
- Faraat Ali
- Department of Inspection and Licensing, Laboratory Services, Botswana Medicines Regulatory Authority, Gaborone, Botswana
| | - Anushma Chorsiya
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Varisha Anjum
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmacy, Jamia Hamdard, New Delhi, India
| | - Shaik Khasimbi
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), New Delhi, India
| | - Asad Ali
- Department of Chemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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Abstract
RNA interference (RNAi) provides the means for alternative antiviral therapy. Delivery of RNAi in the form of short interfering RNA (siRNA), short hairpin RNA (shRNA) and micro-RNA (miRNA) have demonstrated efficacy in gene silencing for therapeutic applications against viral diseases. Bioinformatics has played an important role in the design of efficient RNAi sequences targeting various pathogenic viruses. However, stability and delivery of RNAi molecules have presented serious obstacles for reaching therapeutic efficacy. For this reason, RNA modifications and formulation of nanoparticles have proven useful for non-viral delivery of RNAi molecules. On the other hand, utilization of viral vectors and particularly self-replicating RNA virus vectors can be considered as an attractive alternative. In this review, examples of antiviral therapy applying RNAi-based approaches in various animal models will be described. Due to the current coronavirus pandemic, a special emphasis will be dedicated to targeting Coronavirus Disease-19 (COVID-19).
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Ramyasoma HPBKD, Dassanayake RS, Hapugoda M, Capurro ML, Silva Gunawardene YIN. Multiple dengue virus serotypes resistant transgenic Aedes aegypti fitness evaluated under laboratory conditions. RNA Biol 2020; 17:918-929. [PMID: 32138589 DOI: 10.1080/15476286.2020.1735210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dengue viruses (DENV) are the wildest transmitted arbovirus members of the family Flaviviridae, genus Flavivirus. Dengue viruses are composed of four serotypes, DENV1, 2, 3, and 4, and these viruses can cause dengue fever and dengue haemorrhagic fever or dengue shock syndrome, when infecting humans. RNA interference (RNAi) is a self-defence mechanism, which can be used to prevent invasions of RNA viruses to the host. Genetically engineering a host with an RNAi molecule that targets a single virus serotype may develop escape mutants, and can cause unusual dominance over other serotypes. Therefore, the simultaneous targeting of multiple serotypes is necessary to block DENV transmission. Here, we report the development of transgenic Aedes aegypti based on a bioinformatically designed multiple miRshRNA (microRNA-based shRNA) DNA sequence under the control of a blood-meal induced promoter, Carboxypeptidase A, to induce RNAi for DENV in Aedes aegypti, and demonstrate the expression of a synthetic multiple shRNA polycistronic cluster having RNA interference sequences to target DENV genomes. The transgenic mosquitoes have lower rates of infection, dissemination, and transmission for DENV2 and DENV4 compared to wild mosquitoes, with a significant reduction of dengue copy number and antigen levels in the midgut. These levels of DENV were low enough to make transgenic mosquitoes stop the DENV transmission from infected host to a susceptible host and refractory to DENV2 and DENV4 infection. Such multiple resistance in Ae. aegypti has not been documented previously. Laboratory fitness measurement of transgenic Ae. aegypti showed results comparable to other reported transgenic mosquitoes.
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Affiliation(s)
| | | | - Menaka Hapugoda
- Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya , Kelaniya, Sri Lanka
| | - Margareth L Capurro
- Department of Parasitology (ICB), University of São Paulo , São Paulo, Brazil
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16
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Higuera A, Ramírez JD. Molecular epidemiology of dengue, yellow fever, Zika and Chikungunya arboviruses: An update. Acta Trop 2019; 190:99-111. [PMID: 30444971 DOI: 10.1016/j.actatropica.2018.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/10/2018] [Accepted: 11/10/2018] [Indexed: 02/06/2023]
Abstract
Arboviruses are a group of viruses transmitted by arthropods. They are characterized by a wide geographic distribution, which is associated with the presence of the vector, and cause asymptomatic infections or febrile diseases in humans in both enzootic and urban cycles. Recent reports of human infections caused by viruses such as dengue, Zika, and chikungunya have raised concern regarding public health, and have led to the re-evaluation of surveillance mechanisms and measures to control the transmission of these arboviruses. Viruses such as Mayaro and Usutu are not currently responsible for a high number of symptomatic infections in humans, but should remain under epidemiological surveillance to avoid the emergence of new epidemics, as happened with Zika virus, that are associated with new or more severe symptoms. Additionally, significant variation has been observed in these viruses, giving rise to different lineages. Until recently, the emergence of new lineages has primarily been related to geographical distribution and dispersion, allowing us to ascertain the possible origins and direction of expansion of each virus type, and to make predictions regarding regions where active infections in humans are likely to occur. Therefore, this review is focused on untangling the molecular epidemiology of Dengue, Yellow fever, Zika and Chikungunya due to their recent epidemics in Latinamerica but provides an update on the geographical distribution globally of these viral variants, and outlines the need for further understanding of the genotypes/lineages assignment.
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17
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Yousaf M, Junaid K, Iqbal MS, Aslam I, Ahmad S, Aqeel M, Ashfaq UA, Khaliq S, Ghani MU, Waqar N. Analysis of dengue virus burden and serotypes pattern in Faisalabad, 2016–2017. Future Virol 2018. [DOI: 10.2217/fvl-2017-0155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue is the fastest growing mosquito-borne viral infection and has become a public epidemic in Pakistan. This cross-sectional study was carried out to explore the prevalence and characterization of dengue virus serotypes in Faisalabad, Pakistan during 2016–2017. Aim: To determine most prevalent dengue serotype in Faisalabad, Pakistan. Methodology: Cross-sectional study of stored serum specimens for dengue virus genotype by multiplex real time (RT)-PCR, antidengue IgM, IgG and NS1.Results: Viral RNA detection of 42 patients revealed positive results in 125 (34.4%) samples. DENV-3 (76%) was the predominant genotype followed by DENV-2 (17%) and 7% of DENV1. None of the samples were positive for DENV-4. Conclusion: DENV-3 is the most prevalent serotype of dengue virus observed in Faisalabad, Pakistan.
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Affiliation(s)
- Muhammad Yousaf
- University Institute of Medical Laboratory Technology, University of Lahore, Lahore, Pakistan
| | - Kashaf Junaid
- University Institute of Medical Laboratory Technology, University of Lahore, Lahore, Pakistan
| | - Muhammad Sarfaraz Iqbal
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Imran Aslam
- University Institute of Medical Laboratory Technology, University of Lahore, Lahore, Pakistan
| | - Sheraz Ahmad
- University Institute of Medical Laboratory Technology, University of Lahore, Lahore, Pakistan
| | - Muhammad Aqeel
- University Institute of Medical Laboratory Technology, University of Lahore, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Saba Khaliq
- Department of Physiology, University of Health Sciences, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nayyar Waqar
- Al Kabeer International Diagnostic & Research Laboratory, Faisalabad, Pakistan
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Galabov AS, Mukova L, Abashev YP, Wassilewa L, Tzvetkov P, Minkov V, Barinskiy IF, Rice CM, Ouzounov S, Sidzhakova D. Cycluridine: A novel antiviral effective against flaviviruses. Antivir Chem Chemother 2017; 25:58-67. [PMID: 28768435 PMCID: PMC5890530 DOI: 10.1177/2040206617723442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This review describes the contemporary state of research for antivirals effective against flaviviruses, especially focusing on inhibitors of the pestivirus causative agent of bovine viral diarrhoea virus. We highlight cycluridine, an originally synthesized Mannich’s base [a tetrahydro-2(1H)-pyrimidinones derivative], as a highly effective antiviral possessing a strong inhibitory effect on bovine viral diarrhoea virus replication. Cycluridine was active against replication of a wide variety of bovine viral diarrhoea virus strains in cell cultures. The drug-sensitive period in the bovine viral diarrhoea virus replication cycle included the latent period and the exponential phase; a 90-min delay in the peak of viral RNA synthesis was observed. Cycluridine administered orally manifested a pronounced protective effect in calves with natural mucosal disease/viral diarrhoea and calves experimentally infected with bovine viral diarrhoea virus. Its magnitude of activity and selectivity places cycluridine in the lead among all known substances with anti- bovine viral diarrhoea virus activity. Additionally, cycluridine applied subcutaneously showed anti-tick-born encephalitis virus activity, manifesting a marked protective effect in mice infected with tick-born encephalitis virus. Cycluridine could be a prospective antiviral in veterinary and medical practice for the treatment of bovine viral diarrhoea virus and other flavivirus infections.
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Affiliation(s)
- Angel S Galabov
- 1 The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lucia Mukova
- 1 The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Yuriy P Abashev
- 1 The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lilia Wassilewa
- 1 The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Igor F Barinskiy
- 4 D.I. Ivanovsky Institute of Virology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Charles M Rice
- 5 Medical Faculty, University of Saint Louis, Missouri, USA
| | - Sergey Ouzounov
- 1 The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Dorotea Sidzhakova
- 6 Faculty of Chemistry and Pharmacy, St. Kliment Ohridski University of Sofia, Bulgaria
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19
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Islan GA, Durán M, Cacicedo ML, Nakazato G, Kobayashi RKT, Martinez DST, Castro GR, Durán N. Nanopharmaceuticals as a solution to neglected diseases: Is it possible? Acta Trop 2017; 170:16-42. [PMID: 28232069 DOI: 10.1016/j.actatropica.2017.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 12/05/2016] [Accepted: 02/10/2017] [Indexed: 12/22/2022]
Abstract
The study of neglected diseases has not received much attention, especially from public and private institutions over the last years, in terms of strong support for developing treatment for these diseases. Support in the form of substantial amounts of private and public investment is greatly needed in this area. Due to the lack of novel drugs for these diseases, nanobiotechnology has appeared as an important new breakthrough for the treatment of neglected diseases. Recently, very few reviews focusing on filiarasis, leishmaniasis, leprosy, malaria, onchocerciasis, schistosomiasis, trypanosomiasis, and tuberculosis, and dengue virus have been published. New developments in nanocarriers have made promising advances in the treatment of several kinds of diseases with less toxicity, high efficacy and improved bioavailability of drugs with extended release and fewer applications. This review deals with the current status of nanobiotechnology in the treatment of neglected diseases and highlights how it provides key tools for exploring new perspectives in the treatment of a wide range of diseases.
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Affiliation(s)
- German A Islan
- Laboratorio de Nanobiomateriales, CINDEFI, Depto. de Quimica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET (CCT La Plata), 1900, La Plata, Argentina
| | - Marcela Durán
- Urogenital Carcinogenesis: Urogenitaland Immunotherapy Laboratory, Institute of Biology, University of Campinas, Campinas, SP, Brazil,; NanoBioss, Chemistry Institute, University of Campinas, SP, Brazil
| | - Maximiliano L Cacicedo
- Laboratorio de Nanobiomateriales, CINDEFI, Depto. de Quimica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET (CCT La Plata), 1900, La Plata, Argentina
| | - Gerson Nakazato
- Department of Microbiology, Biology Sciences Center, Londrina State University (UEL), Londrina, Brazil
| | - Renata K T Kobayashi
- Department of Microbiology, Biology Sciences Center, Londrina State University (UEL), Londrina, Brazil
| | - Diego S T Martinez
- NanoBioss, Chemistry Institute, University of Campinas, SP, Brazil; Brazilian Nanotechnology National Laboratory (LNNano-CNPEM), Campinas, SP, Brazil
| | - Guillermo R Castro
- Laboratorio de Nanobiomateriales, CINDEFI, Depto. de Quimica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET (CCT La Plata), 1900, La Plata, Argentina.
| | - Nelson Durán
- NanoBioss, Chemistry Institute, University of Campinas, SP, Brazil; Brazilian Nanotechnology National Laboratory (LNNano-CNPEM), Campinas, SP, Brazil; Biological Chemistry Laboratory, Institute of Chemistry, University of Campinas, Campinas, SP. Brazil.
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20
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Abstract
Medicinal plants are the main natural pools for the discovery and development of new drugs. In the modern era of computer-aided drug designing (CADD), there is need of prompt efforts to design and construct useful database management system that allows proper data storage, retrieval and management with user-friendly interface. An inclusive database having information about classification, activity and ready-to-dock library of medicinal plant's phytochemicals is therefore required to assist the researchers in the field of CADD. The present work was designed to merge activities of phytochemicals from medicinal plants, their targets and literature references into a single comprehensive database named as Medicinal Plants Database for Drug Designing (MPD3). The newly designed online and downloadable MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. The designed database is deemed to be very useful for the researchers who are engaged in medicinal plants research, CADD and drug discovery/development with ease of operation and increased efficiency. The designed MPD3 is a comprehensive database which provides most of the information related to the medicinal plants at a single platform. MPD3 is freely available at: http://bioinform.info .
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Affiliation(s)
- Arooj Mumtaz
- a Department of Bioinformatics and Biotechnology , Government College, University Faisalabad (GCUF) , Faisalabad , Pakistan.,b Department of Bioinformatics and Computational Biology , Virtual University of Pakistan , Lahore , Pakistan
| | - Usman Ali Ashfaq
- a Department of Bioinformatics and Biotechnology , Government College, University Faisalabad (GCUF) , Faisalabad , Pakistan
| | - Muhammad Tahir Ul Qamar
- a Department of Bioinformatics and Biotechnology , Government College, University Faisalabad (GCUF) , Faisalabad , Pakistan.,c Center of Agricultural Biochemistry and Biotechnology (CABB) , University of Agriculture (UAF) , Faisalabad , Pakistan
| | - Farooq Anwar
- d Department of Pharmaceutical Chemistry , College of Pharmacy, Prince Sattam bin Abdulaziz University , Al-Kharj , Saudi Arabia.,e Department of Chemistry , University of Sargodha (UOS) , Sargodha , Pakistan
| | - Faisal Gulzar
- f Department of Pharmcology , University of Sargodha (UOS) , Sargodha , Pakistan
| | - Muhammad Amjad Ali
- c Center of Agricultural Biochemistry and Biotechnology (CABB) , University of Agriculture (UAF) , Faisalabad , Pakistan.,g Department of Plant Pathology , University of Agriculture (UAF) , Faisalabad , Pakistan
| | - Nazamid Saari
- h Faculty of Food Science and Technology , University Putra Malaysia, UPM , Serdang , Malaysia
| | - Muhammad Tariq Pervez
- b Department of Bioinformatics and Computational Biology , Virtual University of Pakistan , Lahore , Pakistan
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21
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Shi X, Zhang X, Chang Y, Jiang B, Deng R, Wang A, Zhang G. Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells. BMC Vet Res 2016; 12:90. [PMID: 27268206 PMCID: PMC4895886 DOI: 10.1186/s12917-016-0717-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/01/2016] [Indexed: 01/06/2023] Open
Abstract
Background Porcine reproductive and respiratory syndrome virus (PRRSV) induces one of most important devastating disease of swine worldwide, and the current methods poorly control it. Previous studies have indicated that the nonstructural protein 11 (nsp11) of PRRSV may be an important protein for the immune escape of PRRSV. Results Here, we firstly explored the effect of over-expression of nsp11 on PRRSV infection and found that over-expression of nsp11 enhanced the PRRSV titers while the small interfering RNA (siRNAs) specifically targeting nsp11 could reduce the PRRSV titers in MARC-145 cells. Conclusion In conclusion, PRRSV nsp11 promotes PRRSV infection in MARC-145 cells and siRNAs targeting nsp11 may be a potential therapeutic strategy to control PRRSV in future.
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Affiliation(s)
- Xibao Shi
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China. .,Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
| | - Xiaozhuan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Yongzhe Chang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Bo Jiang
- Office of Science & Technology, Chongqing Police College, Chongqing, 401331, China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Aiping Wang
- Department of Bioengineering, Zhengzhou University, Zhengzhou, Henan, 450000, 450002, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China. .,College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
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Abstract
Chikungunya virus (CHIKV) is a mosquito-borne emerging pathogen that presents a major health impact in humans. The virus causes acute febrile illness accompanied by joint pains and, in many cases, persistent arthralgia lasting for weeks to years. There are currently no licensed antiviral agents available against CHIKV. A few lead compounds and natural products have recently shown promising results and could emerge as effective treatments for CHIKV. Further, with the emerging knowledge of the biology of CHIKV, RNAi-based gene silencing approaches also hold great promise for the treatment of CHIKV. This review summarizes the applicability of RNAi agents, siRNA, shRNA and miRNA central to RNAi as therapeutic approaches against CHIKV.
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Affiliation(s)
- Deepti Parashar
- National Institute of Virology, 20-A, Dr Ambedkar Road, Pune 411001, Maharashtra, India
| | - Sarah Cherian
- National Institute of Virology, 20-A, Dr Ambedkar Road, Pune 411001, Maharashtra, India
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23
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Abstract
Zika virus was initially discovered in east Africa about 70 years ago and remained a neglected arboviral disease in Africa and Southeast Asia. The virus first came into the limelight in 2007 when it caused an outbreak in Micronesia. In the ensuing decade, it spread widely in other Pacific islands, after which its incursion into Brazil in 2015 led to a widespread epidemic in Latin America. In most infected patients the disease is relatively benign. Serious complications include Guillain-Barré syndrome and congenital infection which may lead to microcephaly and maculopathy. Aedes mosquitoes are the main vectors, in particular, Ae. aegypti. Ae. albopictus is another potential vector. Since the competent mosquito vectors are highly prevalent in most tropical and subtropical countries, introduction of the virus to these areas could readily result in endemic transmission of the disease. The priorities of control include reinforcing education of travellers to and residents of endemic areas, preventing further local transmission by vectors, and an integrated vector management programme. The container habitats of Ae. aegypti and Ae. albopictus means engagement of the community and citizens is of utmost importance to the success of vector control.
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Affiliation(s)
- Samson Sai-Yin Wong
- Department of Microbiology, Research Centre for Infection and Immunology, Faculty of Medicine, The University of Hong Kong, Hong Kong.
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24
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Tahir U, Khan UH, Zubair MS, Bahar-E-Mustafa. Wolbachia pipientis: A potential candidate for combating and eradicating dengue epidemics in Pakistan. ASIAN PAC J TROP MED 2015; 8:989-998. [PMID: 26706669 DOI: 10.1016/j.apjtm.2015.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022] Open
Abstract
Dengue virus syndrome is an emerging global health challenge which is endemic in tropical countries like Pakistan. In recent years dengue incidences have increased considerably in different areas of Pakistan with more sever impacts on urban and peri-urban populations. This review is an effort to highlight the changing epidemiology of dengue fever, role of Government of Pakistan in disease management and control using preventive and community based approaches in the region. Moreover, there is an emphasis on application of Wolbachia as novel, inexpensive and environmentally benign candidate for control and eradication of dengue transmitting vectors.
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Affiliation(s)
- Uruj Tahir
- Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, Pakistan.
| | - Umair Hassan Khan
- Department of Microbiology, University of Agriculture Faisalabad, Sub-Campus Toba Tek Singh, Pakistan
| | | | - Bahar-E-Mustafa
- Department of Microbiology, University of Agriculture Faisalabad, Sub-Campus Toba Tek Singh, Pakistan
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Alam I, Hassan S, Alam I, Gul R, Ali F, Ali I, Ullah S, Khan IA, Awan A. PAIgG and PAIgM levels in secondary dengue virus infections lead to thrombocytopenia in patients from KP, Pakistan. Asian Pac J Trop Biomed 2015. [DOI: 10.1016/j.apjtb.2015.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Sessions OM, Wilm A, Kamaraj US, Choy MM, Chow A, Chong Y, Ong XM, Nagarajan N, Cook AR, Ooi EE. Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints. PLoS Negl Trop Dis 2015; 9:e0004044. [PMID: 26327586 DOI: 10.1371/journal.pntd.0004044] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Dengue viruses (DENV) cause debilitating and potentially life-threatening acute disease throughout the tropical world. While drug development efforts are underway, there are concerns that resistant strains will emerge rapidly. Indeed, antiviral drugs that target even conserved regions in other RNA viruses lose efficacy over time as the virus mutates. Here, we sought to determine if there are regions in the DENV genome that are not only evolutionarily conserved but genetically constrained in their ability to mutate and could hence serve as better antiviral targets. High-throughput sequencing of DENV-1 genome directly from twelve, paired dengue patients’ sera and then passaging these sera into the two primary mosquito vectors showed consistent and distinct sequence changes during infection. In particular, two residues in the NS5 protein coding sequence appear to be specifically acquired during infection in Ae. aegypti but not Ae. albopictus. Importantly, we identified a region within the NS3 protein coding sequence that is refractory to mutation during human and mosquito infection. Collectively, these findings provide fresh insights into antiviral targets and could serve as an approach to defining evolutionarily constrained regions for therapeutic targeting in other RNA viruses. Dengue viruses cause debilitating and potentially life-threatening acute disease throughout the tropical world. While drug development efforts are underway, there are concerns that drug-resistant strains will emerge rapidly. Indeed, many antiviral drugs for other RNA viruses lose efficacy over time as the virus mutates. Here, we sought to determine if there are regions in the dengue virus genome that are constrained in their ability to mutate and could therefore serve as better targets for antiviral drugs. Deep sequencing of the dengue virus 1 genome directly from the blood of twelve dengue patients and from mosquitoes given this blood showed consistent and distinct mutation patterns during infection. Importantly, we identified regions within the viral genome that are resistant to mutation during human and mosquito infection. Collectively, these findings provide fresh insights into potential antiviral targets and could serve as an approach to defining better regions for therapeutic targeting in other RNA viruses.
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Shi X, Chang Y, Zhang X, Wang L, Li C, Jiang K, Chen J, Wang C, Deng R, Fan J, Zhang G. Small interfering RNA targeting nonstructural protein1 α (nsp1α) of porcine reproductive and respiratory syndrome virus (PRRSV) can reduce the replication of PRRSV in MARC-145 cells. Res Vet Sci 2015; 99:215-7. [PMID: 25683113 PMCID: PMC7111734 DOI: 10.1016/j.rvsc.2015.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 11/15/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically devastating and pandemic diseases of swine, which is poorly controlled by current methods. The inhibition of specific genes by small interfering RNA (siRNA) has been proven to be a potential therapeutic strategy against viral infection. Previous studies have indicated that the nonstructural protein 1α (nsp1α) of PRRSV may take an important role in virulence of PRRSV. The present work was involved to explore the effect of siRNA targeting nsp1α on the replication of PRRSV in MARC-145 cells, and the results showed that over-expression of nsp1α enhanced the replication of PRRSV and that siRNAs specifically targeting nsp1α significantly inhibited the replication of PRRSV in MARC-145 cells. In conclusion, this work indicated that nsp1α may be a viral pathogenicity factor of PRRSV and that siRNAs specifically targeting nsp1α may be a new strategy to control PRRSV in the future.
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Affiliation(s)
- Xibao Shi
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Yongzhe Chang
- College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xiaozhuan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; College of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Li Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Chunxi Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Kai Jiang
- College of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Jing Chen
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Chao Wang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Jianming Fan
- The Laboratory of Toxicology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Gaiping Zhang
- College of Veterinary Medicine and Animal Science, Henan Agricultural University, Zhengzhou, Henan 450002, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China.
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da Silva AS, Raposo JV, Pereira TC, Pinto MA, de Paula VS. Effects of RNA interference therapy against herpes simplex virus type 1 encephalitis. Antivir Ther 2015; 21:225-35. [DOI: 10.3851/imp3016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
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Idrees S, Ashfaq UA. Discovery and design of cyclic peptides as dengue virus inhibitors through structure-based molecular docking. ASIAN PAC J TROP MED 2014; 7:513-6. [PMID: 25063278 DOI: 10.1016/S1995-7645(14)60085-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/15/2014] [Accepted: 06/15/2014] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To find potential peptide inhibitors against the NS2B/NS3 protease of DENV which in turn, can inhibit the viral replication inside host cell. METHODS Cyclic peptides were designed having combination of positively charged amino acids using ChemSketch software and were converted to 3D structures. DENV NS3 protein structure was retrieved from Protein Data Bank (PDB) using PDB Id: 2FOM. DENV NS3 and cylic peptides were docked using MOE software after structural optimization. RESULTS Through molecular docking it was revealed that most of the peptides bound deeply in the binding pocket of DENV NS2B/NS3 protease an had interactions with catalytic triad. Peptide 2 successfully blocked the catalytic triad of NS2B/NS3 protease. Peptide 1, 4 and 6 also had potential interactions with active residues of the NS2B/NS3 protease while all other peptides were in close contact with the active sites of NS2B/NS3 protease thus, these peptides can serve as a potential drug candidate to stop viral replication. CONCLUSIONS Thus, it can be concluded from the study that these peptides could serve as important inhibitors to inhibit the viral replication and need further in-vitro investigations to confirm their efficacy.
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Qamar MTU, Mumtaz A, Naseem R, Ali A, Fatima T, Jabbar T, Ahmad Z, Ashfaq UA. Molecular Docking Based Screening of Plant Flavonoids as Dengue NS1 Inhibitors. Bioinformation 2014; 10:460-5. [PMID: 25187688 PMCID: PMC4135296 DOI: 10.6026/97320630010460] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022] Open
Abstract
Dengue infection has turned into a serious health concern globally due to its high morbidity rate and a high possibility of increase
in its mortality rate on the account of unavailability of any proper treatment for severe dengue infection. The situation demands an
urgent development of efficient and practicable treatment to deal with Dengue virus (DENV). Flavonoids, a class of
phytochemicals present in medicinal plants, possess anti-viral activity and can be strong drug candidates against viruses. NS1
glycoprotein of Dengue virus is involved in its RNA replication and can be a strong target for screening of drugs against this virus.
Current study focuses on the identification of flavonoids which can block Asn-130 glycosylation site of Dengue virus NS1 to inhibit
viral replication as glycosylation of NS1 is required for its biological functioning. Molecular docking approach was used in this
study and the results revealed that flavonoids have strong potential interactions with active site of NS1. Six flavonoids
(Deoxycalyxin A; 3,5,7,3',4'-pentahydroxyflavonol-3-O-beta-D-galactopyranoside; (3R)-3',8-Dihydroxyvestitol; Sanggenon O;
Epigallocatechin gallate; Chamaejasmin) blocked the Asn-130 glycosylation site of NS1 and could be able to inhibit the viral
replication. It can be concluded from this study that these flavonoids could serve as antiviral drugs for dengue infections. Further
in-vitro analyses are required to confirm their efficacy and to evaluate their drug potency.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Arooj Mumtaz
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Rabbia Naseem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Amna Ali
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tabeer Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Tehreem Jabbar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Zubair Ahmad
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Punjab, Pakistan
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Paul AM, Shi Y, Acharya D, Douglas JR, Cooley A, Anderson JF, Huang F, Bai F. Delivery of antiviral small interfering RNA with gold nanoparticles inhibits dengue virus infection in vitro. J Gen Virol 2014; 95:1712-1722. [PMID: 24828333 DOI: 10.1099/vir.0.066084-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dengue virus (DENV) infection in humans can cause flu-like illness, life-threatening haemorrhagic fever or even death. There is no specific anti-DENV therapeutic or approved vaccine currently available, partially due to the possibility of antibody-dependent enhancement reaction. Small interfering RNAs (siRNAs) that target specific viral genes are considered a promising therapeutic alternative against DENV infection. However, in vivo, siRNAs are vulnerable to degradation by serum nucleases and rapid renal excretion due to their small size and anionic character. To enhance siRNA delivery and stability, we complexed anti-DENV siRNAs with biocompatible gold nanoparticles (AuNPs) and tested them in vitro. We found that cationic AuNP-siRNA complexes could enter Vero cells and significantly reduce DENV serotype 2 (DENV-2) replication and infectious virion release under both pre- and post-infection conditions. In addition, RNase-treated AuNP-siRNA complexes could still inhibit DENV-2 replication, suggesting that AuNPs maintained siRNA stability. Collectively, these results demonstrated that AuNPs were able to efficiently deliver siRNAs and control infection in vitro, indicating a novel anti-DENV strategy.
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Affiliation(s)
- Amber M Paul
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Yongliang Shi
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Dhiraj Acharya
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Jessica R Douglas
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Amanda Cooley
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - John F Anderson
- Department of Entomology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Fengwei Bai
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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Qamar TU, Mumtaz A, Ashfaq UA, Azhar S, Fatima T, Hassan M, Hussain SS, Akram W, Idrees S. Computer Aided Screening of Phytochemicals from Garcinia against the Dengue NS2B/NS3 Protease. Bioinformation 2014; 10:115-8. [PMID: 24748749 PMCID: PMC3974236 DOI: 10.6026/97320630010115] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 01/31/2014] [Indexed: 11/23/2022] Open
Abstract
Dengue virus NS2/NS3 protease because of its ability to cleave viral proteins is considered as an attractive target to screen antiviral agents. Medicinal plants contain a variety of phytochemicals that can be used as drug against different diseases and infections. Therefore, this study was designed to uncover possible phytochemical of different classes (Aromatic, Carbohydrates, Lignin, Saponins, Steroids, Tannins, Terpenoids, Xanthones) that could be used as inhibitors against the NS2B/NS3 protease of DENV. With the help of molecular docking, Garcinia phytochemicals found to be bound deeply inside the active site of DENV NS2B/NS3 protease among all tested phytochemicals and had interactions with catalytic triad (His51, Asp75, Ser135). Thus, it can be concluded from the study that these Gracinia phytochemicals could serve as important inhibitors to inhibit the viral replication inside the host cell. Further in-vitro investigations require confirming their efficacy.
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Affiliation(s)
- Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Arooj Mumtaz
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Samia Azhar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Tabeer Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Muhammad Hassan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Syed Sajid Hussain
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Waheed Akram
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
| | - Sobia Idrees
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), 38000, Pakistan; Tahir ul Qamar
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Mia MS, Begum RA, Er AC, Abidin RDZRZ, Pereira JJ. Trends of dengue infections in Malaysia, 2000-2010. ASIAN PAC J TROP MED 2014; 6:462-6. [PMID: 23711707 DOI: 10.1016/s1995-7645(13)60075-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 04/15/2013] [Accepted: 05/15/2013] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To analyze trends of dengue incidences and deaths in Malaysia from 2000 to 2010 as well as the predominant dengue virus serotypes during the last decade. METHODS We used the national data on annual reported cases, deaths, incidence rate, mortality rate, and case fatality rate of dengue fever (DF) and dengue hemorrhagic fever (DHF) as well as dengue virus serotypes prevalent in Malaysia during the last decade. Trend/ regression lines were fitted to investigate the trend of dengue incidences and deaths due to the disease for a 11-year period (2000-2010). For the distribution of national incidence rate, mortality rate, and case fatality rate of DF and DHF, descriptive statistics using mean and 95% confidence intervals (CI 39) for means, and range were applied. RESULTS The number of dengue cases and number of deaths have increased, on average, by 14% and 8% per year respectively. The average annual incidence rate of DF per 100 000 populations was higher as compared to that of DHF. Conversely, the yearly mean mortality rate of DHF per 100 000 populations was greater than that of DF. The simultaneous circulation of all four dengue serotypes has been found in Malaysia. But a particular dengue virus serotype predominates for at least two years before it becomes replaced by another serotype. CONCLUSIONS The dengue situation in Malaysia has worsened with an increasing number of reported cases and deaths during the last decade. The increasing trend of dengue highlights the need for a more systematic surveillance and reporting of the disease.
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Affiliation(s)
- Md Shahin Mia
- Institute for Environment and Development, Universiti Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor D. E., Malaysia
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Abstract
The dengue virus (DENV) genome encodes 10 different genes including the NS3 gene, which has a protease and helicase domain used in virus replication. This domain is a potential target for antiviral agents against dengue. Due to a high mutation rate, DENV is classified into four major serotypes (DENV1–DENV4). This study was designed to perform conservancy analysis of all four serotypes by drawing a consensus sequence for each serotype and then drawing a global consensus sequence to study conserved residues in all four serotypes. A total of 127 NS3 sequences belonging to all four serotypes were retrieved and aligned using multiple alignment feature of CLC Workbench and were subjected to phylogenetic tree construction. Conservancy analysis of NS3 revealed conserved peptides with active site residues that can be important in developing antiviral agents against dengue virus. Among conserved residues, residues G142, Ser144, and G145 (catalytic pocket residues), A219, D220, and D221 (divalent cations binding residues), and His56, Asp79, Ser144, 146 were highly conserved among all the serotypes. Residues from L138 to L149 and from L226 to L245 were also considerably conserved in all serotypes, while lysine141 mutated to serine in serotype 3. A total of 14 peptides from the conserved regions of DENV NS3 protein were identified, which may be helpful to develop peptide inhibitors. The DENV NS3 phylogenetic tree showed the evolutionary relationship among all four serotypes, and all serotypes of dengue were found to have evolved from the dengue 4 serotype. Because of its high variability, DENV has become a global health concern. It is important to study residues that are present in protease, helicase, the catalytic pocket Mg2+ binding site, and the AAA domain. This study revealed peptides with active site residues that are highly conserved among all four serotypes. These regions of the NS3 sequence may be helpful in developing antiviral agents.
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Affiliation(s)
- Ambreen Ayub
- Department of Bioinformatics and Biotechnology, Government College University , Faisalabad, Pakistan
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Idrees S, Ashfaq UA, Idrees N. Development of global consensus sequence of HCV glycoproteins involved in viral entry. Theor Biol Med Model 2013; 10:24. [PMID: 23575038 PMCID: PMC3639888 DOI: 10.1186/1742-4682-10-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/07/2013] [Indexed: 01/11/2023] Open
Abstract
Background HCV affects >170 million people worldwide and is a leading cause of liver diseases such as hepatocellular carcinoma. Each year, Pakistan reports hundreds of cases and now it has become a serious health issue. HCV has two transmembrane glycoproteins (E1 and E2) that are involved in virus entry through viral attachment, but because of their hypervariable nature they have become difficult targets for vaccine development. Methods A total of 150 protein sequences of E1 and E2 belonging to genotypes 3a and 1a were retrieved from the NCBI protein database and were subjected to conservation and variation analysis using the multiple sequence alignment feature of the CLC workbench. A consensus sequence of each genotype of E1 and E2 was obtained and these consensus sequences were further analyzed to construct a global consensus sequence, which was used to design potentially conserved peptides. Results From the sequence conservation analysis, highly conserved residues were identified and were used to design peptides. Only two peptides were found to be conserved in the E1 protein of genotypes 3a and 1a and a total of nine conserved peptides were designed for the HCV E2 protein of those genotypes. These designed peptides could serve as useful targets in developing new inhibitory compounds. Conclusion This study was designed to perform conservation and variability analysis of HCV glycoproteins and to find potentially conserved peptides among genotypes 3a and 1a (the most prevalent genotypes in Pakistan) that could serve as useful targets in the development of novel inhibitory compounds, thus reducing the threat of HCV infection in Pakistan.
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Affiliation(s)
- Sobia Idrees
- Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan.
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