1
|
Tekintaş Y, Temel A. Antisense oligonucleotides: a promising therapeutic option against infectious diseases. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:1-39. [PMID: 37395450 DOI: 10.1080/15257770.2023.2228841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
Infectious diseases have been one of the biggest health problems of humanity for centuries. Nucleic acid-based therapeutics have received attention in recent years with their effectiveness in the treatment of various infectious diseases and vaccine development studies. This review aims to provide a comprehensive understanding of the basic properties underlying the mechanism of antisense oligonucleotides (ASOs), their applications, and their challenges. The efficient delivery of ASOs is the greatest challenge for their therapeutic success, but this problem is overcome with new-generation antisense molecules developed with chemical modifications. The types, carrier molecules, and gene regions targeted by sequences have been summarized in detail. Research and development of antisense therapy is still in its infancy; however, gene silencing therapies appear to have the potential for faster and longer-lasting activity than conventional treatment strategies. On the other hand, realizing the potential of antisense therapy will require a large initial economic investment to ascertain the pharmacological properties and learn how to optimize them. The ability of ASOs to be rapidly designed and synthesized to target different microbes can reduce drug discovery time from 6 years to 1 year. Since ASOs are not particularly affected by resistance mechanisms, they come to the fore in the fight against antimicrobial resistance. The design-based flexibility of ASOs has enabled it to be used for different types of microorganisms/genes and successful in vitro and in vivo results have been revealed. The current review summarized a comprehensive understanding of ASO therapy in combating bacterial and viral infections.
Collapse
Affiliation(s)
- Yamaç Tekintaş
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| | - Aybala Temel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| |
Collapse
|
2
|
Vamva E, Griffiths A, Vink CA, Lever AML, Kenyon JC. A novel role for gag as a cis-acting element regulating RNA structure, dimerization and packaging in HIV-1 lentiviral vectors. Nucleic Acids Res 2021; 50:430-448. [PMID: 34928383 PMCID: PMC8754630 DOI: 10.1093/nar/gkab1206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 11/22/2022] Open
Abstract
Clinical usage of lentiviral vectors is now established and increasing but remains constrained by vector titer with RNA packaging being a limiting factor. Lentiviral vector RNA is packaged through specific recognition of the packaging signal on the RNA by the viral structural protein Gag. We investigated structurally informed modifications of the 5′ leader and gag RNA sequences in which the extended packaging signal lies, to attempt to enhance the packaging process by facilitating vector RNA dimerization, a process closely linked to packaging. We used in-gel SHAPE to study the structures of these mutants in an attempt to derive structure-function correlations that could inform optimized vector RNA design. In-gel SHAPE of both dimeric and monomeric species of RNA revealed a previously unreported direct interaction between the U5 region of the HIV-1 leader and the downstream gag sequences. Our data suggest a structural equilibrium exists in the dimeric viral RNA between a metastable structure that includes a U5–gag interaction and a more stable structure with a U5–AUG duplex. Our data provide clarification for the previously unexplained requirement for the 5′ region of gag in enhancing genomic RNA packaging and provide a basis for design of optimized HIV-1 based vectors.
Collapse
Affiliation(s)
- Eirini Vamva
- University of Cambridge Department of Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Alex Griffiths
- University of Cambridge Department of Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Conrad A Vink
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Andrew M L Lever
- University of Cambridge Department of Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Department of Medicine, Yong Loo Lin School of Medicine 119228, Singapore
| | - Julia C Kenyon
- University of Cambridge Department of Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, 117545, Singapore.,Homerton College, Hills Road, Cambridge CB2 8PH, UK
| |
Collapse
|
3
|
Packard BZ, Wrightson JA, Komoriya A. An Oligonucleotide Delivery Platform to Enable Assessment of Intracellular Transcripts in Live Cells by Flow Cytometry. Cytometry A 2020; 97:945-954. [PMID: 32588516 DOI: 10.1002/cyto.a.24174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 11/09/2022]
Abstract
The measurement of mRNA transcripts in live cells has been limited by inefficient delivery vehicles for oligonucleotides. Using a delivery platform which utilizes fluorophores capable of forming intramolecular H-type excitonic dimers, we show that antisense oligonucleotides (ASOs) can be delivered across the plasma membrane directly into the cytosol without receptor mediation. With HIV infection of CD4+ lymphocytes as a model system, we quantitate the level of viral infection present in live single cells with flow cytometry by measuring the hybridization of ASOs to viral sequences; we then compare this measurement with a standard HIV analysis, that is, binding of an antibody against the HIV cell surface protein gp120. The nucleic acids delivery platform described herein also enables inhibition of HIV infection by addition of ASO constructs targeting sequences in the virus' highly conserved 5'-untranslated region. Our analysis quantitates the level of inhibition by comparing both the MFI values and the mean fluorescence intensity as calculated by integration under each curve. Thus, a means for measuring intracellular transcripts at the live single cell level and the potential for delivery of a new class of antiviral agents is described. © 2020 International Society for Advancement of Cytometry.
Collapse
|
4
|
Takahashi M, Li H, Zhou J, Chomchan P, Aishwarya V, Damha MJ, Rossi JJ. Dual Mechanisms of Action of Self-Delivering, Anti-HIV-1 FANA Oligonucleotides as a Potential New Approach to HIV Therapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:615-625. [PMID: 31394430 PMCID: PMC6695270 DOI: 10.1016/j.omtn.2019.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022]
Abstract
Currently, the most effective and durable therapeutic option for HIV-1 infection is combination antiretroviral therapy (cART). Although cART is powerful and can delay viral evolution of drug resistance for decades, it is associated with limitations, including an inability to eradicate the virus and a potential for adverse effects. Therefore, it is imperative to discover new HIV therapeutic modalities. In this study, we designed, characterized, and evaluated the in vitro potency of 2′-deoxy-2′-fluoroarabinonucleotide (FANA) modified antisense oligonucleotides (ASOs) targeting highly conserved regions in the HIV-1 genome. Carrier-free cellular internalization of FANA ASOs resulted in strong suppression of HIV-1 replication in HIV-1-infected human primary cells. In vitro mechanistic studies suggested that the inhibitory effect of FANA ASOs can be attributed to RNase H1 activation and steric hindrance of dimerization. Using 5′-RACE PCR and sequencing analysis, we confirmed the presence of human RNase H1-mediated target RNA cleavage products in cells treated with FANA ASOs. We observed no overt cytotoxicity or immune responses upon FANA ASO treatment. Together, our results strongly suggest that FANA ASOs hold great promise for antiretroviral therapy. The dual ability of FANA ASOs to target RNA by recruiting RNase H1 and/or sterically blocking RNA dimerization further enhances their therapeutic potential.
Collapse
Affiliation(s)
- Mayumi Takahashi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Haitang Li
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Pritsana Chomchan
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | | | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - John J Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA; Irell and Manella Graduate School of Biological Science, Beckman Institute of City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
5
|
NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome. Proc Natl Acad Sci U S A 2016; 113:13033-13038. [PMID: 27791166 DOI: 10.1073/pnas.1614785113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.
Collapse
|
6
|
Reyes-Darias JA, Sánchez-Luque FJ, Morales JC, Pérez-Rentero S, Eritja R, Berzal-Herranz A. Glucose conjugation of anti-HIV-1 oligonucleotides containing unmethylated CpG motifs reduces their immunostimulatory activity. Chembiochem 2015; 16:584-91. [PMID: 25683851 DOI: 10.1002/cbic.201402574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 02/05/2023]
Abstract
Antisense oligodeoxynucleotides (ODNs) are short synthetic DNA polymers complementary to a target RNA sequence. They are commonly designed to halt a biological event, such as translation or splicing. ODNs are potentially useful therapeutic agents for the treatment of different human diseases. Carbohydrate-ODN conjugates have been reported to improve the cell-specific delivery of ODNs through receptor mediated endocytosis. We tested the anti-HIV activity and biochemical properties of the 5'-end glucose-conjugated GEM 91 ODN targeting the initiation codon of the gag gene of HIV-1 RNA in cell-based assays. The conjugation of a glucose residue significantly reduces the immunostimulatory effect without diminishing its potent anti-HIV-1 activity. No significant effects were observed in either ODN stability in serum, in vitro degradation of antisense DNA-RNA hybrids by RNase H, cell toxicity, cellular uptake and ability to interfere with genomic HIV-1 dimerisation.
Collapse
Affiliation(s)
- José A Reyes-Darias
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Parque Tecnológico de Ciencias de la Salud, Avd. del Conocimiento s/n, Armilla, 18016 Granada (Spain); Present address: Estación Experimental del Zaidín, (EEZ-CSIC), C/ Prof. Albareda, 1, 18008 Granada, (Spain)
| | | | | | | | | | | |
Collapse
|
7
|
Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
Collapse
Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
8
|
Kolomiets IN, Zarudnaya MI, Potyahaylo AL, Hovorun DM. Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG). J Biomol Struct Dyn 2014; 33:418-33. [DOI: 10.1080/07391102.2014.884938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
9
|
Seif E, Niu M, Kleiman L. Annealing to sequences within the primer binding site loop promotes an HIV-1 RNA conformation favoring RNA dimerization and packaging. RNA (NEW YORK, N.Y.) 2013; 19:1384-1393. [PMID: 23960173 PMCID: PMC3854529 DOI: 10.1261/rna.038497.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
The 5' untranslated region (5' UTR) of HIV-1 genomic RNA (gRNA) includes structural elements that regulate reverse transcription, transcription, translation, tRNA(Lys3) annealing to the gRNA, and gRNA dimerization and packaging into viruses. It has been reported that gRNA dimerization and packaging are regulated by changes in the conformation of the 5'-UTR RNA. In this study, we show that annealing of tRNA(Lys3) or a DNA oligomer complementary to sequences within the primer binding site (PBS) loop of the 5' UTR enhances its dimerization in vitro. Structural analysis of the 5'-UTR RNA using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) shows that the annealing promotes a conformational change of the 5' UTR that has been previously reported to favor gRNA dimerization and packaging into virus. The model predicted by SHAPE analysis is supported by antisense experiments designed to test which annealed sequences will promote or inhibit gRNA dimerization. Based on reports showing that the gRNA dimerization favors its incorporation into viruses, we tested the ability of a mutant gRNA unable to anneal to tRNA(Lys3) to be incorporated into virions. We found a ∼60% decrease in mutant gRNA packaging compared with wild-type gRNA. Together, these data further support a model for viral assembly in which the initial annealing of tRNA(Lys3) to gRNA is cytoplasmic, which in turn aids in the promotion of gRNA dimerization and its incorporation into virions.
Collapse
Affiliation(s)
- Elias Seif
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Meijuan Niu
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Lawrence Kleiman
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
| |
Collapse
|