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Nawaz R, Arif MA, Ahmad Z, Ahad A, Shahid M, Hassan Z, Husnain A, Aslam A, Raza MS, Mehmood U, Idrees M. An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes. BMC Infect Dis 2023; 23:872. [PMID: 38087193 PMCID: PMC10718025 DOI: 10.1186/s12879-023-08870-0] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell entry, immunoevasion, and pathological progression. METHODS This in silico study is focused on designing sequence specific siRNA molecules as a tool for silencing the non-structural and accessory genes of the virus. The gene sequences of NSP3, 4, and 6 along with ORF3a, 6, 7a, 8, and 10 were retrieved for conservation, phylogenetic, and sequence logo analyses. siRNA candidates were predicted using siDirect 2.0 targeting these genes. The GC content, melting temperatures, and various validation scores were calculated. Secondary structures of the guide strands and siRNA-target duplexes were predicted. Finally, tertiary structures were predicted and subjected to structural validations. RESULTS This study revealed that NSP3, 4, and 6 and accessory genes ORF3a, 6, 7a, 8, and 10 have high levels of conservation across globally circulating SARS-CoV-2 strains. A total of 71 siRNA molecules were predicted against the selected genes. Following rigorous screening including binary validations and minimum free energies, final siRNAs with high therapeutic potential were identified, including 7, 2, and 1 against NSP3, NSP4, and NSP6, as well as 3, 1, 2, and 1 targeting ORF3a, ORF7a, ORF8, and ORF10, respectively. CONCLUSION Our novel in silico pipeline integrates effective methods from previous studies to predict and validate siRNA molecules, having the potential to inhibit viral replication pathway in vitro. In total, this study identified 17 highly specific siRNA molecules targeting NSP3, 4, and 6 and accessory genes ORF3a, 7a, 8, and 10 of SARS-CoV-2, which might be used as an additional antiviral treatment option especially in the cases of life-threatening urgencies.
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Affiliation(s)
- Rabia Nawaz
- Department of Biological Sciences, Superior University, Lahore, Pakistan.
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Muhammad Ali Arif
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Zainab Ahmad
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ammara Ahad
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zohal Hassan
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ali Husnain
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ali Aslam
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Saad Raza
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Uqba Mehmood
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Idrees
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Vice chancellor, University of Peshawar, Peshawar, Pakistan
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Reza MN, Mahmud S, Ferdous N, Ahammad I, Hossain MU, Al Amin M, Mohiuddin AKM. Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer. Cancer Med 2023; 12:22407-22419. [PMID: 38037736 PMCID: PMC10757103 DOI: 10.1002/cam4.6772] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/05/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Helicobacter pylori is a gastric pathogen that is responsible for causing chronic inflammation and increasing the risk of gastric cancer development. It is capable of persisting for decades in the harsh gastric environment because of the inability of the host to eradicate the infection. Several treatment strategies have been developed against this bacterium using different antibiotics. But the effectiveness of treating H. pylori has significantly decreased due to widespread antibiotic resistance, including an increased risk of gastric cancer. The small interfering RNAs (siRNA), which is capable of sequence-specific gene-silencing can be used as a new therapeutic approach for the treatment of a variety of such malignancies. In the current study, we rationally designed two siRNA molecules to silence the cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA) genes of H. pylori for their significant involvement in developing cancer. METHODS We selected a common region of all the available transcripts from different countries of CagA and VacA to design the siRNA molecules. The final siRNA candidate was selected based on the results from machine learning algorithms, off-target similarity, and various thermodynamic properties. RESULT Further, we utilized molecular docking and all atom molecular dynamics (MD) simulations to assess the binding interactions of the designed siRNAs with the major components of the RNA-induced silencing complex (RISC) and results revealed the ability of the designed siRNAs to interact with the proteins of RISC complex in comparable to those of the experimentally reported siRNAs. CONCLUSION These designed siRNAs should effectively silence the CagA and VacA genes of H. pylori during siRNA mediated treatment in gastric cancer.
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Affiliation(s)
- Mahjerin Nasrin Reza
- Department of Biotechnology and Genetic Engineering, Life Science FacultyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Life Science FacultyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Nadim Ferdous
- Department of Biotechnology and Genetic Engineering, Life Science FacultyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - Ishtiaque Ahammad
- Bioinformatics DivisionNational Institute of BiotechnologyAshuliaBangladesh
| | | | - Md. Al Amin
- Department of Biotechnology and Genetic Engineering, Life Science FacultyMawlana Bhashani Science and Technology UniversityTangailBangladesh
| | - A. K. M. Mohiuddin
- Department of Biotechnology and Genetic Engineering, Life Science FacultyMawlana Bhashani Science and Technology UniversityTangailBangladesh
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Ramalingam PS, Arumugam S. Computational design and validation of effective siRNAs to silence oncogenic KRAS. 3 Biotech 2023; 13:350. [PMID: 37780803 PMCID: PMC10541393 DOI: 10.1007/s13205-023-03767-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Oncogenic KRAS mutations drive cancer progression in lung, colon, breast, and pancreatic ductal adenocarcinomas. Apart from the current strategies, such as KRAS upstream inhibitors, downstream effector inhibitors, interaction inhibitors, cell cycle inhibitors, and direct KRAS inhibitors, against KRAS-mutated cancers, the therapeutic small interfering RNAs (siRNAs) represent a promising alternative strategy that directly binds with the target mRNA and inhibits protein translation via mRNA degradation. Here, in the present study, we utilized various in silico approaches to design potential siRNA candidates against KRAS mRNA. We have predicted nearly 17 siRNAs against the KRAS mRNA, and further through various criteria, such as U, R, and A rules, GC%, secondary structure formation, mRNA-siRNA duplex stability, Tm (Cp), Tm (Conc), and inhibition efficiency, they have been filtered into 4 potential siRNAs namely siRNA8, siRNA11, siRNA12, and siRNA17. Further, the molecular docking analysis revealed that the siRNA8, siRNA11, siRNA12, and siRNA17 showed higher negative binding energies, such as - 379.13 kcal/mol, - 360.19 kcal/mol, - 288.47 kcal/mol, and - 329.76 kcal/mol, toward the human Argonaute2 protein (hAgo2) respectively. In addition, the normal mode analysis of the hAgo2-siRNAs complexes indicates the structural changes and deformation of the hAgo2 protein upon the binding of siRNA molecules in the dynamic environment which suggests that these siRNAs could be effective. Finally, we conclude that these 4 siRNAs have therapeutic potential against KRAS mRNA and also have to be studied in vitro and in vivo to evaluate their specificity toward mutant KRAS (not degrading wild-type KRAS). Also, the current challenges in the use of siRNA therapeutics could be overcome by the emerging siRNA delivery methods, such as Antibody-siRNA conjugates (ARCs) and Gelatin-Antibody Delivery System (GADS), in the near future and these siRNAs could be employed as potential therapeutic agents against KRAS-mutated cancers. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03767-w.
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Affiliation(s)
| | - Sivakumar Arumugam
- Protein Engineering Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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Kang H, Ga YJ, Kim SH, Cho YH, Kim JW, Kim C, Yeh JY. Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges. J Biomed Sci 2023; 30:88. [PMID: 37845731 PMCID: PMC10577957 DOI: 10.1186/s12929-023-00981-9] [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: 06/05/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023] Open
Abstract
RNA has emerged as a revolutionary and important tool in the battle against emerging infectious diseases, with roles extending beyond its applications in vaccines, in which it is used in the response to the COVID-19 pandemic. Since their development in the 1990s, RNA interference (RNAi) therapeutics have demonstrated potential in reducing the expression of disease-associated genes. Nucleic acid-based therapeutics, including RNAi therapies, that degrade viral genomes and rapidly adapt to viral mutations, have emerged as alternative treatments. RNAi is a robust technique frequently employed to selectively suppress gene expression in a sequence-specific manner. The swift adaptability of nucleic acid-based therapeutics such as RNAi therapies endows them with a significant advantage over other antiviral medications. For example, small interfering RNAs (siRNAs) are produced on the basis of sequence complementarity to target and degrade viral RNA, a novel approach to combat viral infections. The precision of siRNAs in targeting and degrading viral RNA has led to the development of siRNA-based treatments for diverse diseases. However, despite the promising therapeutic benefits of siRNAs, several problems, including impaired long-term protein expression, siRNA instability, off-target effects, immunological responses, and drug resistance, have been considerable obstacles to the use of siRNA-based antiviral therapies. This review provides an encompassing summary of the siRNA-based therapeutic approaches against viruses while also addressing the obstacles that need to be overcome for their effective application. Furthermore, we present potential solutions to mitigate major challenges.
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Affiliation(s)
- Hara Kang
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Yun Ji Ga
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Soo Hyun Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Young Hoon Cho
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung Won Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Chaeyeon Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Research Institute for New Drug Development, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- KU Center for Animal Blood Medical Science, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, South Korea.
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Biala G, Kedzierska E, Kruk-Slomka M, Orzelska-Gorka J, Hmaidan S, Skrok A, Kaminski J, Havrankova E, Nadaska D, Malik I. Research in the Field of Drug Design and Development. Pharmaceuticals (Basel) 2023; 16:1283. [PMID: 37765091 PMCID: PMC10536713 DOI: 10.3390/ph16091283] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The processes used by academic and industrial scientists to discover new drugs have recently experienced a true renaissance, with many new and exciting techniques being developed over the past 5-10 years alone. Drug design and discovery, and the search for new safe and well-tolerated compounds, as well as the ineffectiveness of existing therapies, and society's insufficient knowledge concerning the prophylactics and pharmacotherapy of the most common diseases today, comprise a serious challenge. This can influence not only the quality of human life, but also the health of whole societies, which became evident during the COVID-19 pandemic. In general, the process of drug development consists of three main stages: drug discovery, preclinical development using cell-based and animal models/tests, clinical trials on humans and, finally, forward moving toward the step of obtaining regulatory approval, in order to market the potential drug. In this review, we will attempt to outline the first three most important consecutive phases in drug design and development, based on the experience of three cooperating and complementary academic centers of the Visegrád group; i.e., Medical University of Lublin, Poland, Masaryk University of Brno, Czech Republic, and Comenius University Bratislava, Slovak Republic.
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Affiliation(s)
- Grazyna Biala
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Ewa Kedzierska
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Marta Kruk-Slomka
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Jolanta Orzelska-Gorka
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Sara Hmaidan
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Aleksandra Skrok
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Jakub Kaminski
- Chair and Department of Pharmacology with Pharmacodynamics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland; (E.K.); (M.K.-S.); (J.O.-G.)
| | - Eva Havrankova
- Department of Chemical Drugs, Faculty of Pharmacy, Masaryk University of Brno, 601 77 Brno, Czech Republic;
| | - Dominika Nadaska
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia (I.M.)
| | - Ivan Malik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University Bratislava, 832 32 Bratislava, Slovakia (I.M.)
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Fopase R, Panda C, Rajendran AP, Uludag H, Pandey LM. Potential of siRNA in COVID-19 therapy: Emphasis on in silico design and nanoparticles based delivery. Front Bioeng Biotechnol 2023; 11:1112755. [PMID: 36814718 PMCID: PMC9939533 DOI: 10.3389/fbioe.2023.1112755] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Small interfering RNA (siRNA)-mediated mRNA degradation approach have imparted its eminence against several difficult-to-treat genetic disorders and other allied diseases. Viral outbreaks and resulting pandemics have repeatedly threatened public health and questioned human preparedness at the forefront of drug design and biomedical readiness. During the recent pandemic caused by the SARS-CoV-2, mRNA-based vaccination strategies have paved the way for a new era of RNA therapeutics. RNA Interference (RNAi) based approach using small interfering RNA may complement clinical management of the COVID-19. RNA Interference approach will primarily work by restricting the synthesis of the proteins required for viral replication, thereby hampering viral cellular entry and trafficking by targeting host as well as protein factors. Despite promising benefits, the stability of small interfering RNA in the physiological environment is of grave concern as well as site-directed targeted delivery and evasion of the immune system require immediate attention. In this regard, nanotechnology offers viable solutions for these challenges. The review highlights the potential of small interfering RNAs targeted toward specific regions of the viral genome and the features of nanoformulations necessary for the entrapment and delivery of small interfering RNAs. In silico design of small interfering RNA for different variants of SARS-CoV-2 has been discussed. Various nanoparticles as promising carriers of small interfering RNAs along with their salient properties, including surface functionalization, are summarized. This review will help tackle the real-world challenges encountered by the in vivo delivery of small interfering RNAs, ensuring a safe, stable, and readily available drug candidate for efficient management of SARS-CoV-2 in the future.
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Affiliation(s)
- Rushikesh Fopase
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Chinmaya Panda
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Amarnath P. Rajendran
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Hasan Uludag
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada,Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
| | - Lalit M. Pandey
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
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Dhotre K, Banerjee A, Dass D, Nema V, Mukherjee A. An In-silico Approach to Design and Validate siRNA against Monkeypox Virus. Curr Pharm Des 2023; 29:3060-3072. [PMID: 38062661 DOI: 10.2174/0113816128275065231103063935] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION The monkeypox virus has emerged as an uncommon zoonotic infection. The recent outbreak of MPXV in Europe and abroad in 2022 presented a major threat to individuals at risk. At present, no specific MPXV vaccinations or medications are available. METHODS In this study, we predicted the most effective siRNA against the conserved region of the MPXV and validated the activity by performing molecular docking studies. RESULTS Ultimately, the most efficient siRNA molecule was shortlisted against the envelope protein gene (B6R) based on its toxicity, effectivity, thermodynamic stability, molecular interaction, and molecular dynamics simulations (MD) with the Human Argonaute 2 protein. CONCLUSION Thus, the strategy may offer a platform for the development of potential antiviral RNA therapeutics that target MPXV at the genomic level.
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Affiliation(s)
- Kishore Dhotre
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Debashree Dass
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Vijay Nema
- Molecular Biology, National AIDS Research Institute, Pune 411026, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
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Kalita T, Dezfouli SA, Pandey LM, Uludag H. siRNA Functionalized Lipid Nanoparticles (LNPs) in Management of Diseases. Pharmaceutics 2022; 14. [PMID: 36432711 DOI: 10.3390/pharmaceutics14112520] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
RNAi (RNA interference)-based technology is emerging as a versatile tool which has been widely utilized in the treatment of various diseases. siRNA can alter gene expression by binding to the target mRNA and thereby inhibiting its translation. This remarkable potential of siRNA makes it a useful candidate, and it has been successively used in the treatment of diseases, including cancer. However, certain properties of siRNA such as its large size and susceptibility to degradation by RNases are major drawbacks of using this technology at the broader scale. To overcome these challenges, there is a requirement for versatile tools for safe and efficient delivery of siRNA to its target site. Lipid nanoparticles (LNPs) have been extensively explored to this end, and this paper reviews different types of LNPs, namely liposomes, solid lipid NPs, nanostructured lipid carriers, and nanoemulsions, to highlight this delivery mode. The materials and methods of preparation of the LNPs have been described here, and pertinent physicochemical properties such as particle size, surface charge, surface modifications, and PEGylation in enhancing the delivery performance (stability and specificity) have been summarized. We have discussed in detail various challenges facing LNPs and various strategies to overcome biological barriers to undertake the safe delivery of siRNA to a target site. We additionally highlighted representative therapeutic applications of LNP formulations with siRNA that may offer unique therapeutic benefits in such wide areas as acute myeloid leukaemia, breast cancer, liver disease, hepatitis B and COVID-19 as recent examples.
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Dong X, Zheng W. Cheminformatics Modeling of Gene Silencing for Both Natural and Chemically Modified siRNAs. Molecules 2022; 27:6412. [PMID: 36234948 PMCID: PMC9570765 DOI: 10.3390/molecules27196412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/17/2022] Open
Abstract
In designing effective siRNAs for a specific mRNA target, it is critically important to have predictive models for the potency of siRNAs. None of the published methods characterized the chemical structures of individual nucleotides constituting a siRNA molecule; therefore, they cannot predict the potency of gene silencing by chemically modified siRNAs (cm-siRNA). We propose a new approach that can predict the potency of gene silencing by cm-siRNAs, which characterizes each nucleotide (NT) using 12 BCUT cheminformatics descriptors describing its charge distribution, hydrophobic and polar properties. Thus, a 21-NT siRNA molecule is described by 252 descriptors resulting from concatenating all the BCUT values of its composing nucleotides. Partial Least Square is employed to develop statistical models. The Huesken data (2431 natural siRNA molecules) were used to perform model building and evaluation for natural siRNAs. Our results were comparable with or superior to those from Huesken’s algorithm. The Bramsen dataset (48 cm-siRNAs) was used to build and test the models for cm-siRNAs. The predictive r2 of the resulting models reached 0.65 (or Pearson r values of 0.82). Thus, this new method can be used to successfully model gene silencing potency by both natural and chemically modified siRNA molecules.
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Ning L, Liu M, Gou Y, Yang Y, He B, Huang J. Development and application of ribonucleic acid therapy strategies against COVID-19. Int J Biol Sci 2022; 18:5070-5085. [PMID: 35982905 PMCID: PMC9379410 DOI: 10.7150/ijbs.72706] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 03/08/2022] [Accepted: 07/16/2022] [Indexed: 11/17/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2), remaining a global health crisis since its outbreak until now. Advanced biotechnology and research findings have revealed many suitable viral and host targets for a wide range of therapeutic strategies. The emerging ribonucleic acid therapy can modulate gene expression by post-transcriptional gene silencing (PTGS) based on Watson-Crick base pairing. RNA therapies, including antisense oligonucleotides (ASO), ribozymes, RNA interference (RNAi), aptamers, etc., were used to treat SARS-CoV whose genome is similar to SARV-CoV-2, and the past experience also applies for the treatment of COVID-19. Several studies against SARS-CoV-2 based on RNA therapeutic strategy have been reported, and a dozen of relevant preclinical or clinical trials are in process globally. RNA therapy has been a very active and important part of COVID-19 treatment. In this review, we focus on the progress of ribonucleic acid therapeutic strategies development and application, discuss corresponding problems and challenges, and suggest new strategies and solutions.
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Affiliation(s)
- Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Sichuan, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Mujiexin Liu
- Ineye Hospital of Chengdu University of TCM, Sichuan, China
| | - Yushu Gou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Yue Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
| | - Bifang He
- Medical College, Guizhou University, Guizhou, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan, China
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Mahfuz A, Khan MA, Sajib EH, Deb A, Mahmud S, Hasan M, Saha O, Islam A, Rahaman MM. Designing potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation. Infect Genet Evol 2022; 102:105310. [PMID: 35636695 DOI: 10.1016/j.meegid.2022.105310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening, this virus has been causing regular outbreaks in various countries, particularly in Bangladesh, India, and Malaysia. Unfortunately, no efficient vaccine or drug is available now to combat this baneful virus. NiV employs its nucleocapsid protein for genetic material packaging, which is crucial for viral replication inside the host cells. The small interfering RNAs (siRNAs) can play a central role in inhibiting the expression of disease-causing viral genes by hybridization and subsequent inactivation of the complementary target viral mRNAs through the RNA interference (RNAi) pathway. Therefore, potential siRNAs as molecular therapeutics against the nucleocapsid protein gene of NiV were designed in this study. First, ten prospective siRNAs were identified using the conserved nucleocapsid gene sequences among all available NiV strains collected from various countries. After that, off-target binding, GC (guanine-cytosine) content, secondary structure, binding affinity with the target, melting temperature, efficacy analysis, and binding capacity with the human argonaute protein 2 (AGO2) of these siRNAs were evaluated to predict their suitability. These designed siRNA molecules bear promise in silencing the NiV gene encoding the nucleocapsid protein and thus can alleviate the severity of this dangerous virus. Further in vivo experiments are recommended before using these designed siRNAs as alternative and effective molecular therapeutic agents against NiV.
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Affiliation(s)
- Amub Mahfuz
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
| | - Emran Hossain Sajib
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Anamika Deb
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh; EcoHealth Alliance, New York, NY 10018, USA
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Sartaj Sohrab S, Aly El-Kafrawy S, Ibraheem Azhar E. In silico prediction and experimental evaluation of potential siRNAs against SARS-CoV-2 inhibition in Vero E6 cells. Journal of King Saud University - Science 2022; 34:102049. [PMID: 35493709 PMCID: PMC9040457 DOI: 10.1016/j.jksus.2022.102049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/13/2021] [Accepted: 04/18/2022] [Indexed: 11/21/2022]
Abstract
Objective The acute cases of pneumonia (COVID-19) were first reported from China in December 2019, and the pathogen was identified as SARS-CoV-2. Currently, many vaccines have been developed against this virus by using multiple genes, applying different platforms, and used for the vaccinations of the human population. Spike protein genes play an important role in host cell attachment and viral entry and have been extensively used for the development of vaccine and antiviral therapeutics. Short interfering RNA is also known as silencing RNA and contribute a significant role to regulate the expression of a specific gene. By using this technology, virus inhibition has been demonstrated against many viral diseases. Methods In this work, we have reported the Insilico prediction, designing, and experimental validation of siRNAs antiviral potency against SARS-CoV-2-S-RBD. The siDirect 2.0 was selected for siRNAs prediction, and secondary structure was predicted by RNAfold while the HNADOCK was used for molecular docking analysis and specific binding of siRNAs to the selected target. We have used and evaluated four siRNAs for cellular toxicity and determination of antiviral efficiency based on the Ct value of q-real-time PCR in Vero E6 cells. Results Based on the experimental evaluation and analysis of results from generated data, we observed that there is no cytotoxicity for any tested siRNAs in Vero E6 cells. Total four siRNA were filtered out from twenty-one siRNAs following the strict selection and scoring criteria. The better antiviral efficiency was observed in 3rd siRNAs based on the Ct value of q-real-time PCR. The results that emerged from this study encouraged us to validate the efficiency of these siRNAs in multiple cells by using alone and in a combination of two or more siRNAs to inhibit the SARS-CoV-2 proliferation. Conclusion The Insilico prediction, molecular docking analysis provided the selection of better siRNAs. Based on the experimental evaluation only 3rd siRNA was found to be more effective than others and showed better antiviral efficiency. These siRNAs should also be evaluated in other cell lines either separately or in combination against SARS-CoV-2 to determine their antiviral efficiency.
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Sohrab SS, El-Kafrawy SA, Azhar EI. Effect of insilico predicted and designed potential siRNAs on inhibition of SARS-CoV-2 in HEK-293 cells. Journal of King Saud University - Science 2022; 34:101965. [PMID: 35313445 PMCID: PMC8925144 DOI: 10.1016/j.jksus.2022.101965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022]
Abstract
Objectives The COVID-19 was identified for the first time from the sea food market, Wuhan city, China in 2019 and the pathogenic organism was identified as SARS-CoV-2. Currently, this virus has spread to 223 countries and territories and known as a serious issue for the global human community. Many vaccines have been developed and used for immunization. Methods We have reported the insilico prediction, designing, secondary structure prediction, molecular docking analysis, and in vitro assessment of siRNAs against SARS-CoV-2. The online bioinformatic approach was used for siRNAs selection and designing. The selected siRNAs were evaluated for antiviral efficacy by using Lipofectamine 2000 as delivery agent to HEK-293 cells. The MTT assay was used for cytotoxicity determination. The antiviral efficacy of potential siRNAs was determined based on the Ct value of q-RT-PCR and the data analysis was done by Prism-GraphPad software. Results The analyzed data resulted in the selection of only three siRNAs out of twenty-six siRNAs generated by online software. The secondary structure prediction and molecular docking analysis of siRNAs revealed the efficient binding to the target. There was no cellular toxicity observed in the HEK-293 cells at any tested concentrations of siRNAs. The purification of RNA was completed from inoculated cells and subjected to q-RT-PCR. The highest Ct value was observed in siRNA 3 than the others. The results offered valuable evidence and invigorated us to assess the potency of siRNAs by using alone or in combination in other human cells. Conclusion The data generated from this study indicates the significance of in silico prediction and narrow down the potential siRNA' against SARS-CoV-2, and molecular docking investigation offered the effective siRNAs binding with the target. Finally, it is concluded that the online bioinformatics approach provided the prediction and selection of siRNAs with better antiviral efficacy. The siRNA-3 was observed to be the best for reduction of viral RNA in cells.
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14
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Becker J, Stanifer ML, Leist SR, Stolp B, Maiakovska O, West A, Wiedtke E, Börner K, Ghanem A, Ambiel I, Tse LV, Fackler OT, Baric RS, Boulant S, Grimm D. Ex vivo and in vivo suppression of SARS-CoV-2 with combinatorial AAV/RNAi expression vectors. Mol Ther 2022; 30:2005-2023. [PMID: 35038579 PMCID: PMC8758558 DOI: 10.1016/j.ymthe.2022.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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: 09/24/2021] [Revised: 11/11/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022] Open
Abstract
Despite rapid development and deployment of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), clinically relevant modalities to curb the pandemic by directly attacking the virus on a genetic level remain highly desirable and are urgently needed. Here we comprehensively illustrate the capacity of adeno-associated virus (AAV) vectors co-expressing a cocktail of three short hairpin RNAs (shRNAs; RNAi triggers) directed against the SARS-CoV-2 RdRp and N genes as versatile and effective antiviral agents. In cultured monkey cells and human gut organoids, our most potent vector, SAVIOR (SARS virus repressor), suppressed SARS-CoV-2 infection to background levels. Strikingly, in control experiments using single shRNAs, multiple SARS-CoV-2 escape mutants quickly emerged from infected cells within 24-48 h. Importantly, such adverse viral adaptation was fully prevented with the triple-shRNA AAV vector even during long-term cultivation. In addition, AAV-SAVIOR efficiently purged SARS-CoV-2 in a new model of chronically infected human intestinal cells. Finally, intranasal AAV-SAVIOR delivery using an AAV9 capsid moderately diminished viral loads and/or alleviated disease symptoms in hACE2-transgenic or wild-type mice infected with human or mouse SARS-CoV-2 strains, respectively. Our combinatorial and customizable AAV/RNAi vector complements ongoing global efforts to control the coronavirus disease 2019 (COVID-19) pandemic and holds great potential for clinical translation as an original and flexible preventive or therapeutic antiviral measure.
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Affiliation(s)
- Jonas Becker
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Megan Lynn Stanifer
- Department of Infectious Diseases/Molecular Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Sarah Rebecca Leist
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Bettina Stolp
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Olena Maiakovska
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ande West
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Ellen Wiedtke
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany
| | - Ali Ghanem
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Ina Ambiel
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Longping Victor Tse
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Oliver Till Fackler
- Department of Infectious Diseases/Integrative Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ralph Steven Baric
- Department of Epidemiology, University of North Carolina, 3304 Michael Hooker Research Building, Chapel Hill, NC 27599, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32611, USA; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, BioQuant BQ0030, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, 69120 Heidelberg, Germany; Department of Infectious Diseases/Virology, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, 69120 Heidelberg, Germany.
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15
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Ayyagari VS. Design of siRNA molecules for silencing of membrane glycoprotein, nucleocapsid phosphoprotein, and surface glycoprotein genes of SARS-CoV2. J Genet Eng Biotechnol 2022; 20:65. [PMID: 35482116 DOI: 10.1186/s43141-022-00346-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/13/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022]
Abstract
The global COVID-19 pandemic caused by SARS-CoV2 infected millions of people and resulted in more than 4 million deaths worldwide. Apart from vaccines and drugs, RNA silencing is a novel approach for treating COVID-19. In the present study, siRNAs were designed for the conserved regions targeting three structural genes, M, N, and S, from forty whole-genome sequences of SARS-CoV2 using four different software, RNAxs, siDirect, i-Score Designer, and OligoWalk. Only siRNAs which were predicted in common by all the four servers were considered for further shortlisting. A multistep filtering approach has been adopted in the present study for the final selection of siRNAs by the usage of different online tools, viz., siRNA scales, MaxExpect, DuplexFold, and SMEpred. All these web-based tools consider several important parameters for designing functional siRNAs, e.g., target-site accessibility, duplex stability, position-specific nucleotide preference, inhibitory score, thermodynamic parameters, GC content, and efficacy in cleaving the target. In addition, a few parameters like GC content and dG value of the entire siRNA were also considered for shortlisting of the siRNAs. Antisense strands were subjected to check for any off-target similarities using BLAST. Molecular docking was carried out to study the interactions of guide strands with AGO2 protein. A total of six functional siRNAs (two for each gene) have been finally selected for targeting M, N, and S genes of SARS-CoV2. The siRNAs have not shown any off-target effects, interacted with the domain(s) of AGO2 protein, and were efficacious in cleaving the target mRNA. However, the siRNAs designed in the present study need to be tested in vitro and in vivo in the future.
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16
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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 2022; 27:molecules27061936. [PMID: 35335300 PMCID: PMC8950558 DOI: 10.3390/molecules27061936] [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] [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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Saba AA, Adiba M, Chakraborty S, Nabi AN. Prediction of putative potential siRNAs for inhibiting SARS-CoV-2 strains, including variants of concern and interest. Future Microbiol 2022; 17:449-463. [PMID: 35285248 PMCID: PMC8958991 DOI: 10.2217/fmb-2021-0130] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To predict siRNAs as a therapeutic intervention for highly infectious new variants of SARS-CoV-2. Methods: Conserved coding sequence regions of 11 SARS-CoV-2 proteins were used to construct siRNAs through sampling of metadata comprising 214,256 sequences. Results: Predicted siRNAs S1: 5′-UCAUUGAGAAAUGUUUACGCA-3′ and S2: 5′-AAAGACAUCAGCAUACUCCUG-3′ against RdRp of SARS-CoV-2 satisfied all the stringent filtering processes and showed good binding characteristics. The designed siRNAs are expected to inhibit viral replication and transcription of various coronavirus strains encompassing variants of concern and interest. Conclusion: The predicted siRNAs are expected to be potent against SARS-CoV-2, and following in vitro and in vivo validations may be considered as potential therapeutic measures.
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Affiliation(s)
- Abdullah Al Saba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Maisha Adiba
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, Systems Cell-Signalling Laboratory, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ahm Nurun Nabi
- Department of Biochemistry and Molecular Biology, Laboratory of Population Genetics, University of Dhaka, Dhaka, 1000, Bangladesh
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Meraz M, Vernon-Carter E, Rodriguez E, Alvarez-Ramirez J. A fractal scaling analysis of the SARS-CoV-2 genome sequence. Biomed Signal Process Control 2022; 73:103433. [PMID: 36567677 PMCID: PMC9760973 DOI: 10.1016/j.bspc.2021.103433] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/04/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022]
Abstract
An approach based on fractal scaling analysis to characterize the organization of the SARS-CoV-2 genome sequence was used. The method is based on the detrended fluctuation analysis (DFA) implemented on a sliding window scheme to detect variations of long-range correlations over the genome sequence regions. The nucleotides sequence is mapped in a numerical sequence by using four different assignation rules: amino-keto, purine-pyrimidine, hydrogen-bond and hydrophobicity patterns. The originally reported sequence from Wuhan isolates (Wuhan Hu-1) was considered as a reference to contrast the structure of the 2002-2004 SARS-CoV-1 strain. Long-range correlations, quantified in terms of a scaling exponent, depended on both the mapping rule and the sequence region. Deviations from randomness were attributed to serial correlations or anti-correlations, which can be ascribed to ordered regions of the genome sequence. It was found that the Wuhan Hu-1 sequence was more random than the SARS-CoV-1 sequence, which suggests that the SARS-CoV-2 possesses a more efficient genomic structure for replication and infection. In general, the virus isolated in the early 2020 months showed slight correlation differences with the Wuhan Hu-1 sequence. However, early isolates from India and Italy presented visible differences that led to a more ordered sequence organization. It is apparent that the increased sequence order, particularly in the spike region, endowed some early variants with a more efficient mechanism to spreading, replicating and infecting. Overall, the results showed that the DFA provides a suitable framework to assess long-term correlations hidden in the internal organization of the SARS-CoV-2 genome sequence.
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Affiliation(s)
- M. Meraz
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Iztapalapa, CDMX 09340, Mexico
| | - E.J. Vernon-Carter
- Departamento de Ingenieria de Procesos e Hidraulica, Universidad Autónoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Iztapalapa, CDMX 09340, Mexico
| | - E. Rodriguez
- Departamento de Ingenieria Eléctrica y Computacion, Universidad Autónoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Iztapalapa, CDMX 09340, Mexico
| | - J. Alvarez-Ramirez
- Departamento de Ingenieria de Procesos e Hidraulica, Universidad Autónoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Iztapalapa, CDMX 09340, Mexico,Corresponding author
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Zhang Y, Almazi JG, Ong HX, Johansen MD, Ledger S, Traini D, Hansbro PM, Kelleher AD, Ahlenstiel CL. Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract. Int J Mol Sci 2022; 23:2408. [PMID: 35269550 PMCID: PMC8909959 DOI: 10.3390/ijms23052408] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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: 02/03/2022] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Since December 2019, a pandemic of COVID-19 disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread across the globe. At present, the Food and Drug Administration (FDA) has issued emergency approval for the use of some antiviral drugs. However, these drugs still have limitations in the specific treatment of COVID-19, and as such, new treatment strategies urgently need to be developed. RNA-interference-based gene therapy provides a tractable target for antiviral treatment. Ensuring cell-specific targeted delivery is important to the success of gene therapy. The use of nanoparticles (NPs) as carriers for the delivery of small interfering RNA (siRNAs) to specific tissues or organs of the human body could play a crucial role in the specific therapy of severe respiratory infections, such as COVID-19. In this review, we describe a variety of novel nanocarriers, such as lipid NPs, star polymer NPs, and glycogen NPs, and summarize the pre-clinical/clinical progress of these nanoparticle platforms in siRNA delivery. We also discuss the application of various NP-capsulated siRNA as therapeutics for SARS-CoV-2 infection, the challenges with targeting these therapeutics to local delivery in the lung, and various inhalation devices used for therapeutic administration. We also discuss currently available animal models that are used for preclinical assessment of RNA-interference-based gene therapy. Advances in this field have the potential for antiviral treatments of COVID-19 disease and could be adapted to treat a range of respiratory diseases.
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Affiliation(s)
- Yuan Zhang
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Juhura G. Almazi
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Hui Xin Ong
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Scott Ledger
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
| | - Daniela Traini
- Respiratory Technology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia; (J.G.A.); (H.X.O.); (D.T.)
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Ryde, NSW 2109, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW 2050, Australia; (M.D.J.); (P.M.H.)
| | - Anthony D. Kelleher
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia; (Y.Z.); (S.L.); (A.D.K.)
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Hussein M, Andrade dos Ramos Z, Berkhout B, Herrera-Carrillo E. In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack. Viruses 2022; 14:v14020385. [PMID: 35215977 PMCID: PMC8880226 DOI: 10.3390/v14020385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The SARS-CoV-2 pandemic has urged the development of protective vaccines and the search for specific antiviral drugs. The modern molecular biology tools provides alternative methods, such as CRISPR-Cas and RNA interference, that can be adapted as antiviral approaches, and contribute to this search. The unique CRISPR-Cas13d system, with the small crRNA guide molecule, mediates a sequence-specific attack on RNA, and can be developed as an anti-coronavirus strategy. We analyzed the SARS-CoV-2 genome to localize the hypothetically best crRNA-annealing sites of 23 nucleotides based on our extensive expertise with sequence-specific antiviral strategies. We considered target sites of which the sequence is well-conserved among SARS-CoV-2 isolates. As we should prepare for a potential future outbreak of related viruses, we screened for targets that are conserved between SARS-CoV-2 and SARS-CoV. To further broaden the search, we screened for targets that are conserved between SARS-CoV-2 and the more distantly related MERS-CoV, as well as the four other human coronaviruses (OC43, 229E, NL63, HKU1). Finally, we performed a search for pan-corona target sequences that are conserved among all these coronaviruses, including the new Omicron variant, that are able to replicate in humans. This survey may contribute to the design of effective, safe, and escape-proof antiviral strategies to prepare for future pandemics.
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Affiliation(s)
| | | | - Ben Berkhout
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
| | - Elena Herrera-Carrillo
- Correspondence: (B.B.); (E.H.-C.); Tel.: +31-20-566-4822 (B.B.); +31-20-566-4865 (E.H.-C.)
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21
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Yasmin T, Adiba M, Saba AA, Nabi AHMN. In Silico Design of siRNAs for Silencing CLEC5A Receptor as a Potential Therapeutic Approach Against Dengue and Japanese Encephalitis Virus Infection in Human. Bioinform Biol Insights 2022; 16:11779322221142122. [DOI: 10.1177/11779322221142122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 12/14/2022] Open
Abstract
Dengue and Japanese encephalitis virus (JEV) are mosquito-borne RNA viruses that can cause severe illness leading to death in the tropics and subtropics. Both of these viruses interact directly with the C-type lectin domain family 5, member A receptor (CLEC5A) on human macrophages which stimulates the release of proinflammatory cytokines. Since blockade of this interaction has been shown to suppress the secretion of cytokines, CLEC5A is considered a potential target for the development of new treatments to reduce virus-induced brain damage. Developing a vaccine against dengue is challenging because this virus can cause disease through 4 different serotypes. Therefore, the vaccine must immunize against all 4 serotypes to be effective, while unvaccinated people still contract JEV and suffer from its complications. Small interfering RNAs (siRNAs) play an important role in regulating gene expression by causing the degradation of target mRNAs. In this study, we attempted to rationally design potential siRNA molecules using various software, targeting the CLEC5A gene. In total, 3 siRNAs were found to be potential candidates for CLEC5A silencing. They showed good target accessibility, optimum guanine-cytosine (GC) content, the least chance of off-target effects, positive energy of folding, and strong interaction with Argonaute2 protein as denoted by a negative docking energy score. In addition, molecular dynamics simulation of the siRNA-Ago2-docked complexes showed the stability of the complexes over 1.5 nanoseconds. These predicted siRNAs might effectively downregulate the expression of the CLEC5A receptor and thus prove vital in the treatment of dengue and JEV infections.
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Affiliation(s)
- Tahirah Yasmin
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Maisha Adiba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - AHM Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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22
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Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res 2021; 50:333-349. [PMID: 34928377 PMCID: PMC8754636 DOI: 10.1093/nar/gkab1248] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/10/2021] [Accepted: 12/05/2021] [Indexed: 01/08/2023] Open
Abstract
A promising approach to tackle the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. So far it is unclear, which viral replication steps can be efficiently inhibited with siRNAs. Here, we report that siRNAs can target genomic RNA (gRNA) of SARS-CoV-2 after cell entry, and thereby terminate replication before start of transcription and prevent virus-induced cell death. Coronaviruses replicate via negative sense RNA intermediates using a unique discontinuous transcription process. As a result, each viral RNA contains identical sequences at the 5′ and 3′ end. Surprisingly, siRNAs were not active against intermediate negative sense transcripts. Targeting common sequences shared by all viral transcripts allowed simultaneous suppression of gRNA and subgenomic (sg)RNAs by a single siRNA. The most effective suppression of viral replication and spread, however, was achieved by siRNAs that targeted open reading frame 1 (ORF1) which only exists in gRNA. In contrast, siRNAs that targeted the common regions of transcripts were outcompeted by the highly abundant sgRNAs leading to an impaired antiviral efficacy. Verifying the translational relevance of these findings, we show that a chemically modified siRNA that targets a highly conserved region of ORF1, inhibited SARS-CoV-2 replication ex vivo in explants of the human lung. Our work encourages the development of siRNA-based therapies for COVID-19 and suggests that early therapy start, or prophylactic application, together with specifically targeting gRNA, might be key for high antiviral efficacy.
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Affiliation(s)
- Shubhankar Ambike
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Stoyan Velkov
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Domizia Baldassi
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany
| | - Suliman Qadir Afridi
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Diana Porras-Gonzalez
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Xin Wei
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Philipp Hagen
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mircea Gabriel Stoleriu
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Pulmonary Hospital; Marchioninistraße 15, 81377 Munich and Robert-Koch-Allee 2, 82131 Gauting, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstraße 5, 81377 Munich, Germany.,Institute of Lung Biology and Disease (ILBD) and Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Chunkyu Ko
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,Infectious Diseases Therapeutic Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), 34114 Daejeon, Republic of Korea
| | - Thomas Michler
- Institute of Virology, School of Medicine, Technische Universität München / Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany.,German Center for Infection Research (DZIF), Munich partner site, Germany
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23
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Khanali J, Azangou-Khyavy M, Asaadi Y, Jamalkhah M, Kiani J. Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs. Front Microbiol 2021; 12:758948. [PMID: 34858370 PMCID: PMC8630580 DOI: 10.3389/fmicb.2021.758948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [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: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023] Open
Abstract
Despite significant efforts, there are currently no approved treatments for COVID-19. However, biotechnological approaches appear to be promising in the treatment of the disease. Accordingly, nucleic acid-based treatments including aptamers and siRNAs are candidates that might be effective in COVID-19 treatment. Aptamers can hamper entry and replication stages of the SARS-CoV-2 infection, while siRNAs can cleave the viral genomic and subgenomic RNAs to inhibit the viral life cycle and reduce viral loads. As a conjugated molecule, aptamer–siRNA chimeras have proven to be dual-functioning antiviral therapy, acting both as virus-neutralizing and replication-interfering agents as well as being a siRNA targeted delivery approach. Previous successful applications of these compounds against various stages of the pathogenesis of diseases and viral infections, besides their advantages over other alternatives, might provide sufficient rationale for the application of these nucleic acid-based drugs against the SARS-CoV-2. However, none of them are devoid of limitations. Here, the literature was reviewed to assess the plausibility of using aptamers, siRNAs, and aptamer–siRNA chimeras against the SARS-CoV-2 based on their previously established effectiveness, and discussing challenges lie in applying these molecules.
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Affiliation(s)
- Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Monire Jamalkhah
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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24
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Nashiry MA, Sumi SS, Sharif Shohan MU, Alyami SA, Azad AKM, Moni MA. Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders. Brief Bioinform 2021; 22:bbab126. [PMID: 33993223 PMCID: PMC8194728 DOI: 10.1093/bib/bbab126] [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: 01/01/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), although most commonly demonstrates respiratory symptoms, but there is a growing set of evidence reporting its correlation with the digestive tract and faeces. Interestingly, recent studies have shown the association of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection with gastrointestinal symptoms in infected patients but any sign of respiratory issues. Moreover, some studies have also shown that the presence of live SARS-CoV-2 virus in the faeces of patients with COVID-19. Therefore, the pathophysiology of digestive symptoms associated with COVID-19 has raised a critical need for comprehensive investigative efforts. To address this issue we have developed a bioinformatics pipeline involving a system biological framework to identify the effects of SARS-CoV-2 messenger RNA expression on deciphering its association with digestive symptoms in COVID-19 positive patients. Using two RNA-seq datasets derived from COVID-19 positive patients with celiac (CEL), Crohn's (CRO) and ulcerative colitis (ULC) as digestive disorders, we have found a significant overlap between the sets of differentially expressed genes from SARS-CoV-2 exposed tissue and digestive tract disordered tissues, reporting 7, 22 and 13 such overlapping genes, respectively. Moreover, gene set enrichment analysis, comprehensive analyses of protein-protein interaction network, gene regulatory network, protein-chemical agent interaction network revealed some critical association between SARS-CoV-2 infection and the presence of digestive disorders. The infectome, diseasome and comorbidity analyses also discover the influences of the identified signature genes in other risk factors of SARS-CoV-2 infection to human health. We hope the findings from this pathogenetic analysis may reveal important insights in deciphering the complex interplay between COVID-19 and digestive disorders and underpins its significance in therapeutic development strategy to combat against COVID-19 pandemic.
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Affiliation(s)
- Md Asif Nashiry
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Shauli Sarmin Sumi
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Salem A Alyami
- Department of Mathematics and Statistics, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13318, Saudi Arabia
| | - A K M Azad
- iThree Institute, Faculty of Science, University Technology of Sydney, Australia
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
- Healthy Ageing Theme, The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
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25
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Saify Nabiabad H, Amini M, Demirdas S. Specific delivering of RNAi using Spike's aptamer-functionalized lipid nanoparticles for targeting SARS-CoV-2: A strong anti-Covid drug in a clinical case study. Chem Biol Drug Des 2021; 99:233-246. [PMID: 34714580 PMCID: PMC8653378 DOI: 10.1111/cbdd.13978] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/03/2021] [Revised: 09/24/2021] [Accepted: 10/24/2021] [Indexed: 12/15/2022]
Abstract
Coronavirus (SARS-CoV-2) as a global pandemic has attracted the attention of many scientific centers to find the right treatment. We expressed and purified the recombinant receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein, and specific RBD aptamers were designed using SELEX method. RNAi targeting nucleocapsid phosphoprotein was synthesized and human lung cells were inoculated with aptamer-functionalized lipid nanoparticles (LNPs) containing RNAi. The results demonstrated that RBD aptamer having KD values of 0.290 nm possessed good affinity. Based on molecular docking and efficacy prediction analysis, siRNA molecule was showed the best action. LNPs were appropriately functionalized by aptamer and contained RNAi molecules. Antiviral assay using q-PCR and ELISA demonstrated that LNP functionalized with 35 µm Apt and containing 30 nm RNAi/ml of cell culture had the best antiviral activity compared to other concentrations. Applied aptamer in the nanocarrier has two important functions. First, it can deliver the drug (RNAi) to the surface of epithelial cells. Second, by binding to the SARS-CoV-2 spike protein, it inhibits the virus entrance into cells. Our data reveal an interaction between the aptamer and the virus, and RNAi targeted the virus RNA. CT scan and the clinical laboratory tests in a clinical case study, a 36-year old man who presented with severe SARS-CoV-2, demonstrated that inhalation of 10 mg Apt-LNPs-RNAi nebulized/day for six days resulted in an improvement in consolidation and ground-glass opacity in lungs on the sixth day of treatment. Our findings suggest the treatment of SARS-CoV-2 infection through inhalation of Aptamer-LNPs-RNAi.
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Affiliation(s)
| | - Massoume Amini
- Department of Biotechnology, Bu-Ali Sina University, Hamadan, Iran
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
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26
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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] [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: 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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27
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Lai C, Liu X, Yan Q, Lv H, Zhou L, Hu L, Cai Y, Wang G, Chen Y, Chai R, Liu Z, Xu Y, Huang W, Xiao F, Hu L, Li Y, Huang J, Zhou Q, Li L, Peng T, Zhang H, Zhang Z, Chen L, Chen C, Ji T. Low Innate Immunity and Lagged Adaptive Immune Response in the Re-Tested Viral RNA Positivity of a COVID-19 Patient. Front Immunol 2021; 12:664619. [PMID: 34305895 PMCID: PMC8295488 DOI: 10.3389/fimmu.2021.664619] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/31/2021] [Indexed: 11/21/2022] Open
Abstract
Recent studies have highlighted observations regarding re-tested positivity (RP) of SARS-CoV-2 RNA in discharged COVID-19 patients, however, the immune mechanisms underlying SARS-CoV-2 RNA RP in immunocompetent patients remain elusive. Herein, we describe the case of an immunocompetent COVID-19 patient with moderate symptoms who was twice re-tested as positive for SARS-CoV-2 RNA, and the period between first and third viral RNA positivity was 95 days, longer than previously reported (18–25 days). The chest computed tomography findings, plasma anti-SARS-CoV-2 antibody, neutralizing antibodies (NAbs) titer, and whole blood transcriptic characteristics in the viral RNA RP patient and other COVID-19 patients were analyzed. During the SARS-CoV-2 RNA RP period, new lung lesions were observed. The COVID-19 patient with viral RNA RP had delayed seroconversion of anti-spike/receptor-binding domain (RBD) IgA antibody and NAbs and were accompanied with disappearance of the lung lesions. Further experimental data validated that NAbs titer was significantly associated with anti-RBD IgA and IgG, and anti-spike IgG. The RP patient had lower interferon-, T cells- and B cell-related genes expression than non-RP patients with mild-to-moderate symptoms, and displayed lower cytokines and chemokines gene expression than severe patients. Interestingly, the RP patient had low expression of antigen presentation-related genes and low B cell counts which might have contributed to the delayed anti-RBD specific antibody and low CD8+ cell response. Collectively, delayed antigen presentation-related gene expression was found related to delayed adaptive immune response and contributed to the SARS-CoV-2 RNA RP in this described immunocompetent patient.
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Affiliation(s)
- Changchun Lai
- Clinical Laboratory Medicine Department, Maoming People's Hospital, Maoming, China.,Department of Emergency, Maoming People's Hospital, Maoming, China.,Clinical Laboratory Medicine Department, Xinyi People's Hospital, Xinyi, China
| | - Xinglong Liu
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qihong Yan
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hualiang Lv
- Pulmonary and Critical Care Medicine Department, Maoming People's Hospital, Maoming, China
| | - Lei Zhou
- Pathology Laboratory Department, Maoming People's Hospital, Maoming, China
| | - Longbo Hu
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yong Cai
- CT Department, Maoming People's Hospital, Maoming, China
| | - Guoqiang Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yufeng Chen
- Clinical Laboratory Medicine Department, Maoming People's Hospital, Maoming, China
| | - Renjie Chai
- Cardiovascular Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenwei Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuhua Xu
- Vaccine Research and Development Department, Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Wendong Huang
- Scientific Research Center, Maoming People's Hospital, Maoming, China
| | - Fei Xiao
- Clinical Laboratory Medicine Department, Maoming People's Hospital, Maoming, China
| | - Linhui Hu
- Clinical Research Center, Maoming People's Hospital, Maoming, China
| | - Yaocai Li
- Infection Department, Maoming People's Hospital, Maoming, China
| | - Jianhong Huang
- Medical Department, Maoming People's Hospital, Maoming, China
| | - Qiang Zhou
- Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Luqian Li
- Clinical Laboratory Medicine Department, Maoming People's Hospital, Maoming, China
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Haiye Zhang
- Clinical Laboratory Medicine Department, Xinyi People's Hospital, Xinyi, China
| | - Zhenhui Zhang
- Critical Care Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- Bioland Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunbo Chen
- Department of Emergency, Maoming People's Hospital, Maoming, China.,Scientific Research Center, Maoming People's Hospital, Maoming, China
| | - Tianxing Ji
- Clinical Laboratory Medicine Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Chowdhury UF, Saba AA, Sufi AS, Khan AM, Sharmin I, Sultana A, Islam MO. Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein. Heliyon 2021; 7:e07320. [PMID: 34195427 PMCID: PMC8239728 DOI: 10.1016/j.heliyon.2021.e07320] [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: 12/25/2020] [Revised: 05/13/2021] [Accepted: 06/11/2021] [Indexed: 12/04/2022] Open
Abstract
Waddlia chondrophila is an emerging pathogen that has been implicated in numerous unpropitious pregnancy events in humans and ruminants. Taking into account its association with abortigenic events, possible modes of transmission, and future risk, immediate clinical measures are required to prevent widespread damage caused by this organism and hence this study. Here, a subtractive proteomics approach was employed to identify druggable proteins of W. chondrophila. Considering the essential genes, antibiotic resistance proteins, and virulence factors, 676 unique important proteins were initially identified for this bacterium. Afterward, NCBI BLASTp performed against human proteome identified 223 proteins that were further pushed into KEGG Automatic Annotation Server (KAAS) for automatic annotation. Using the information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database 14 Waddlia specific metabolic pathways were identified with respect to humans. Analyzing the data from KAAS and KEGG databases, forty-eight metabolic pathway-dependent, and seventy metabolic pathway independent proteins were identified. Standalone BLAST search against DrugBank FDA approved drug targets revealed eight proteins that are finally considered druggable proteins. Prediction of three-dimensional structures was done for the eight proteins through homology modeling and the Ramachandran plot model showed six models as a valid prediction. Finally, virtual screening against MurB protein was performed using FDA approved drugs to employ the drug repositioning strategy. Three drugs showed promising docking results that can be used for therapeutic purposes against W. chondrophila following the clinical validation of the study.
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Affiliation(s)
| | - Abdullah Al Saba
- Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Abu Sufian Sufi
- Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ishrat Sharmin
- Sarkari Karmachari Hospital, Fulbaria, Dhaka, Bangladesh
| | - Aziza Sultana
- Sarkari Karmachari Hospital, Fulbaria, Dhaka, Bangladesh
| | - Md Ohedul Islam
- Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
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Bappy SS, Shibly AZ, Sultana S, Mohiuddin AKM, Kabir Y. Designing potential siRNA molecule for the nucleocapsid(N) gene silencing of different SARS-CoV-2 strains of Bangladesh: Computational approach. Comput Biol Chem 2021; 92:107486. [PMID: 33984653 PMCID: PMC8099544 DOI: 10.1016/j.compbiolchem.2021.107486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/24/2020] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is a single-stranded RNA (+) virus first identified in China and then became an ongoing global outbreak. In most cases, it is fatal in humans due to respiratory malfunction. Extensive researches are going to find an effective therapeutic technique for the treatment of SARS-CoV-2 infected individuals. In this study, we attempted to design a siRNA molecule to silence the most suitable nucleocapsid(N) gene of SARS-CoV-2, which play a major role during viral pathogenesis, replication, encapsidation and RNA packaging. At first, 270 complete N gene sequences of different strains in Bangladesh of these viruses were retrieved from the NCBI database. Different computational methods were used to design siRNA molecules. A siRNA molecule was built against these strains using the SiDirect 2.0 server. Using Mfold and the OligoCalc server, the siRNA molecule was tested for its secondary structure and GC material. The Clustal Omega tool was employed to evaluate any off-target harmony of the planned siRNA molecule. Herein, we proposed a duplex siRNA molecule that does not fit any off-target sequences for the gene silencing of SARS-CoV-2. To treat SARS-CoV-2 infections, currently, any effective therapy is not available. Our engineered siRNA molecule could give an alternative therapeutic approach against various sequenced SARS-CoV-2 strains in Bangladesh.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh; Research and Development, Incepta Vaccine Ltd, Zirabo, Savar, Dhaka, 1341, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - A K M Mohiuddin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
| | - Yearul Kabir
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh.
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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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Jamalkhah M, Asaadi Y, Azangou-Khyavy M, Khanali J, Soleimani M, Kiani J, Arefian E. MSC-derived exosomes carrying a cocktail of exogenous interfering RNAs an unprecedented therapy in era of COVID-19 outbreak. J Transl Med 2021; 19:164. [PMID: 33888147 PMCID: PMC8061879 DOI: 10.1186/s12967-021-02840-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The onset of the SARS-CoV-2 pandemic has resulted in ever-increasing casualties worldwide, and after 15 months, standard therapeutic regimens are yet to be discovered. MAIN BODY Due to the regenerative and immunomodulatory function of MSCs, they can serve as a suitable therapeutic option in alleviating major COVID-19 complications like acute respiratory distress syndrome. However, the superior properties of their cognate exosomes as a cell-free product make them preferable in the clinic. Herein, we discuss the current clinical status of these novel therapeutic strategies in COVID-19 treatment. We then delve into the potential of interfering RNAs incorporation as COVID-19 gene therapy and introduce targets involved in SARS-CoV-2 pathogenesis. Further, we present miRNAs and siRNAs candidates with promising results in targeting the mentioned targets. CONCLUSION Finally, we present a therapeutic platform of mesenchymal stem cell-derived exosomes equipped with exogenous iRNAs, that can be employed as a novel therapeutic modality in COVID-19 management aiming to prevent further viral spread within the lung, hinder the virus life cycle and pathogenesis such as immune suppression, and ultimately, enhance the antiviral immune response.
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Affiliation(s)
- Monire Jamalkhah
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Soleimani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chatterjee D, Chowdhury UF, Shohan MUS, Mohasin M, Kabir Y. In-silico predictions of deleterious SNPs in human ephrin type-A receptor 3 (EPHA3) gene. Informatics in Medicine Unlocked 2021. [DOI: 10.1016/j.imu.2021.100728] [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] [Indexed: 11/25/2022] Open
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