1
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Singh J, Saeedan AS, Kaithwas G, Ansari MN. Small interfering RNA: From designing to therapeutic in cancer. J Genet Eng Biotechnol 2025; 23:100484. [PMID: 40390497 PMCID: PMC11999615 DOI: 10.1016/j.jgeb.2025.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/13/2025] [Accepted: 03/23/2025] [Indexed: 05/21/2025]
Abstract
Cancer has become a significant public health concern worldwide. It is a group of diseases, often resulting from the dysregulation of multiple cellular pathways involved in differentiation, cell proliferation, cell cycle regulation, and DNA repair. These disruptions are primarily caused by genetic mutation and epigenetic alterations which lead to uncontrolled growth and tumor formation. Targeted therapy is a precise and effective strategy to overcome the shortcomings of conventional therapy. RNA interference (RNAi) is a gene-silencing mechanism that has an uncanny ability to target disease-associated genes. Small interfering RNA (siRNA) is a key component of RNAi and has shown promise in silencing oncogenes and inhibiting cancer progression. However, the therapeutic application of siRNA faces several challenges such as poor cellular uptake, short half-life, endosomal escape, immune system activation, and off-target. Strategies to address these challenges are optimized designing of siRNA, advanced delivery systems, and chemical modification to improve cellular uptake and protect from degradation. This review focuses on the therapeutic potential of siRNA in cancer treatment and discusses the action mechanism of siRNA, barriers in siRNA, and strategies to overcome them. The review shed light on the current clinical trial of siRNA-based cancer therapy, along with outcomes and limitations.
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Affiliation(s)
- Jyoti Singh
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025 Uttar Pradesh, India
| | - Abdulaziz S Saeedan
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Gaurav Kaithwas
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow 226025 Uttar Pradesh, India
| | - Mohd Nazam Ansari
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
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2
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Anand P, Zhang Y, Patil S, Kaur K. Metabolic Stability and Targeted Delivery of Oligonucleotides: Advancing RNA Therapeutics Beyond The Liver. J Med Chem 2025; 68:6870-6896. [PMID: 39772535 PMCID: PMC11998008 DOI: 10.1021/acs.jmedchem.4c02528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 12/11/2024] [Accepted: 12/26/2024] [Indexed: 01/11/2025]
Abstract
Oligonucleotides have emerged as a formidable new class of nucleic acid therapeutics. Fully modified oligonucleotides exhibit enhanced metabolic stability and display successful clinical applicability for targets formerly considered "undruggable". Accumulating studies show that conjugation to targeting modalities of stabilized oligonucleotides, especially small interfering RNAs (siRNAs), has enabled robust delivery to intended cells/tissues. However, the major challenge in the field has been the stability and targeted delivery of oligonucleotides (siRNAs and antisense oligonucleotides (ASOs)) to extrahepatic tissues. In this Perspective, we review chemistry innovations and emerging delivery approaches that have revolutionized oligonucleotide drug discovery and development. We explore findings from both academia and industry that highlight the potential of oligonucleotides for indications involving different extrahepatic organs─including skeletal muscles, brain, lungs, skin, heart, adipose tissue, and eyes. In all, continued advances in chemistry coupled with conjugation-based approaches or novel administration routes will further advance the delivery of oligonucleotides to extrahepatic tissues.
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Affiliation(s)
- Puneet Anand
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591, United States
| | - Yu Zhang
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591, United States
| | - Spoorthi Patil
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591, United States
| | - Keerat Kaur
- Regeneron Genetic Medicines, Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591, United States
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3
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Dhara D, Mulard LA, Hollenstein M. Natural, modified and conjugated carbohydrates in nucleic acids. Chem Soc Rev 2025; 54:2948-2983. [PMID: 39936337 DOI: 10.1039/d4cs00799a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025]
Abstract
Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.
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Affiliation(s)
- Debashis Dhara
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, Université Paris Cité, CNRS UMR 352328, rue du Docteur Roux, 75724 Paris Cedex 15, France.
- Department of Structural Biology and Chemistry, Laboratory for Chemistry of Biomolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Laurence A Mulard
- Department of Structural Biology and Chemistry, Laboratory for Chemistry of Biomolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, Université Paris Cité, CNRS UMR 352328, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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4
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Ramírez-Cortés F, Ménová P. Hepatocyte targeting via the asialoglycoprotein receptor. RSC Med Chem 2025; 16:525-544. [PMID: 39628900 PMCID: PMC11609720 DOI: 10.1039/d4md00652f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 11/19/2024] [Indexed: 12/06/2024] Open
Abstract
This review highlights the potential of asialoglycoprotein receptor (ASGPR)-mediated targeting in advancing liver-specific treatments and underscores the ongoing progress in the field. First, we provide a comprehensive examination of the nature of ASGPR ligands, both natural and synthetic. Next, we explore various drug delivery strategies leveraging ASGPR, with a particular emphasis on the delivery of therapeutic nucleic acids such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs). An in-depth analysis of the current status of RNA interference (RNAi) and ASO-based therapeutics is included, detailing approved therapies and those in various stages of clinical development (phases 1 to 3). Afterwards, we give an overview of other ASGPR-targeted conjugates, such as those with peptide nucleic acids or aptamers. Finally, targeted protein degradation of extracellular proteins through ASGPR is briefly discussed.
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Affiliation(s)
| | - Petra Ménová
- University of Chemistry and Technology, Prague Technická 5 16628 Prague 6 Czech Republic
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5
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Endo Y, Itoh K, Kan-No H, Wakamatsu H, Natori Y, Saito Y, Kaise A, Nogi Y, Saito-Tarashima N, Minakawa N, Yoshimura Y. Synthesis and Resolution of 4'-Substituted Nucleosides with Potential Antiviral and Antisense Strategies. J Org Chem 2025; 90:2008-2021. [PMID: 39865870 DOI: 10.1021/acs.joc.4c02761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Nucleoside derivatives having a 4'-substituent show promise as potential antiviral agents as well as nucleoside units for constructing nucleic acid medicines. To develop new nucleosides, it is crucial to achieve feasible access to the intended derivatives, encompassing both enantiomers. Toward this end, we started synthesizing an achiral 4-hydroxymethyldihydrofuran as a sugar precursor, which we subjected to the oxidative glycosylation reaction using hypervalent iodine. The resulting racemate of a 4'-hydroxymethylated thymidine derivative underwent kinetic resolution using lipase, yielding both d- and l-isomers with high optical purity. The d-4'-hydroxymethylstavudine derivative was then converted into the corresponding phosphoramidite derivative, from which an oligonucleotide was synthesized.
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Affiliation(s)
- Yukino Endo
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Kyohei Itoh
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Hiroya Kan-No
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Hideaki Wakamatsu
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Yoshihiro Natori
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Yukako Saito
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Asako Kaise
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
| | - Yuhei Nogi
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Yuichi Yoshimura
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Komatsushima 4-4-1, Aoba-ku, Sendai 981-8558, Japan
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6
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Andersson P, Burel SA, Estrella H, Foy J, Hagedorn PH, Harper TA, Henry SP, Hoflack JC, Holgersen EM, Levin AA, Morrison E, Pavlicek A, Penso-Dolfin L, Saxena U. Assessing Hybridization-Dependent Off-Target Risk for Therapeutic Oligonucleotides: Updated Industry Recommendations. Nucleic Acid Ther 2025; 35:16-33. [PMID: 39912803 DOI: 10.1089/nat.2024.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2025] Open
Abstract
Hybridization-dependent off-target (OffT) effects, occurring when oligonucleotides bind via Watson-Crick-Franklin hybridization to unintended RNA transcripts, remain a critical safety concern for oligonucleotide therapeutics (ONTs). Despite the importance of OffT assessment of clinical trial ONT candidates, formal guidelines are lacking, with only brief mentions in Japanese regulatory documents (2020) and US Food and Drug Administration (FDA) recommendations for hepatitis B virus treatments (2022). This article presents updated industry recommendations for assessing OffTs of ONTs, building upon the 2012 Oligonucleotide Safety Working Group (OSWG) recommendations and accounting for recent technological advancements. A new OSWG subcommittee, comprising industry experts in RNase H-dependent and steric blocking antisense oligonucleotides and small interfering RNAs, has developed a comprehensive framework for OffT assessment. The proposed workflow encompasses five key steps: (1) OffT identification through in silico complementarity prediction and transcriptomics analysis, (2) focus on cell types with relevant ONT activity, (3) in vitro verification and margin assessment, (4) risk assessment based on the OffT biological role, and (5) management of unavoidable OffTs. The authors provide detailed considerations for various ONT classes, emphasizing the importance of ONT-specific factors such as chemistry, delivery systems, and tissue distribution in OffT evaluation. The article also explores the potential of machine learning models to enhance OffT prediction and discusses strategies for experimental verification and risk assessment. These updated recommendations aim to improve the safety profile of ONTs entering clinical trials and to manage unavoidable OffTs. The authors hope that these recommendations will serve as a valuable resource for ONT development and for the forthcoming finalization of the FDA draft guidance and the International Council for Harmonization S13 guidance on Nonclinical Safety Assessment of Oligonucleotide-Based Therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jean-Christophe Hoflack
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | | | | | | | - Utsav Saxena
- Dicerna Pharmaceuticals, a Novo Nordisk Company, Lexington, Massachusetts, USA
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7
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Mohamed AA, Wang PY, Bartel DP, Vos SM. The structural basis for RNA slicing by human Argonaute2. Cell Rep 2025; 44:115166. [PMID: 39932188 PMCID: PMC11893014 DOI: 10.1016/j.celrep.2024.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 11/20/2024] [Accepted: 12/16/2024] [Indexed: 02/13/2025] Open
Abstract
Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene silencing through RNA interference (RNAi), which is essential for many eukaryotes and the basis for new clinical therapies. Despite this importance, structural information on eukaryotic AGOs in a fully paired, slicing-competent conformation-hypothesized to be intrinsically unstable-has been lacking. Here, we present the cryogenic electron microscopy structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable this conformation. Critically, the N domain of AGO rotates to allow the RNA full access to the central channel and forms contacts that license rapid slicing. Moreover, a conserved loop in the PIWI domain secures the RNA near the active site to enhance slicing rate and specificity. These results explain how AGO accommodates targets possessing pairing specificity typically observed in biological and clinical slicing substrates.
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Affiliation(s)
- Abdallah A Mohamed
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Peter Y Wang
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA
| | - David P Bartel
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA.
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA.
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8
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Ruchi R, Raman GM, Kumar V, Bahal R. Evolution of antisense oligonucleotides: navigating nucleic acid chemistry and delivery challenges. Expert Opin Drug Discov 2025; 20:63-80. [PMID: 39653607 PMCID: PMC11823135 DOI: 10.1080/17460441.2024.2440095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 12/05/2024] [Indexed: 12/18/2024]
Abstract
INTRODUCTION Antisense oligonucleotide (ASO) was established as a viable therapeutic option for genetic disorders. ASOs can target RNAs implicated in various diseases, including upregulated mRNA and pre-mRNA undergoing abnormal alternative splicing events. Therapeutic applications of ASOs have been proven with the Food and Drug Administration approval of several drugs in recent years. Earlier enzymatic stability and delivery remains a big challenge for ASOs. Introducing new chemical modifications and new formulations resolving the issues related to the nuclease stability and delivery of the ASOs. Excitingly, ASOs-based bioconjugates that target the hepatocyte have gained much attraction. Efforts are ongoing to increase the therapeutic application of the ASOs to the extrahepatic tissue as well. AREA COVERED We have briefly discussed the mechanism of ASOs, the development of new chemistries, and delivery strategies for ASO-based drug discovery and development. The discussion focuses more on the already approved ASOs and those in the clinical development stage. EXPERT OPINION To expand the clinical application of ASOs, continuous effort is required to develop precise delivery strategies for targeting extrahepatic tissue to minimize the off-target effects.
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Affiliation(s)
- Ruchi Ruchi
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Govind Mukesh Raman
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
- Farmington High School, Farmington, CT, USA
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
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9
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Sarkar S, Gebert LFR, MacRae IJ. Structural basis for gene silencing by siRNAs in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.05.627081. [PMID: 39677650 PMCID: PMC11643337 DOI: 10.1101/2024.12.05.627081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Small interfering RNAs (siRNAs) guide mRNA cleavage by human Argonaute2 (hAgo2), leading to targeted gene silencing. Despite their laboratory and clinical impact, structural insights into human siRNA catalytic activity remain elusive. Here, we show that disrupting siRNA 3'-end binding by hAgo2 accelerates target cleavage and stabilizes its catalytic conformation, enabling detailed structural analysis. A 3.16 Å global resolution cryo-EM reconstruction reveals that distortion of the siRNA-target duplex at position 6 allows target RNA entry into the catalytic cleft and shifts Lysine-709, a previously unrecognized catalytic residue, into the active site. A pyrimidine at target nucleotide t10 positions another unrecognized catalytic residue, Arginine-710, for optimal cleavage. Expansion of the guide-target duplex major groove docks the scissile phosphate for hydrolysis and subsequent groove compression after position 16 permits target RNAs to exit the catalytic cleft. These findings reveal how hAgo2 catalyzes siRNA target hydrolysis, providing a high-resolution model for therapeutic design.
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Affiliation(s)
- Sucharita Sarkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contributed equally
| | - Luca F. R. Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- These authors contributed equally
| | - Ian J. MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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10
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Klarek M, Kowalski K. Chemistry of organometallic nucleic acid components: personal perspectives and prospects for the future. Dalton Trans 2024; 53:18420-18439. [PMID: 39526762 DOI: 10.1039/d4dt02634a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Organometallic modifications of biologically important compounds such as drugs, secondary natural products, peptides, and nucleic acids, to name just a few, represent a well-established strategy for the development of new anticancer and antimicrobial agents. Supported by these reasons, over 12 years ago, we initiated a research program into organometallic modifications of nucleic acid components. This account summarizes key results regarding the synthetic chemistry and biological activities of the obtained compounds. As synthetic chemists, our main goal over the last 12 years has been to develop new strategies that allow for the exploration of the chemical space of organometallic nucleic acid components. Accordingly, we have developed a Michael addition reaction-based methodology that enabled the synthesis of an entirely new class of glycol nucleic acid (GNA) constituents. Concerning GNA chemistry, we also reported the synthesis of the first-ever ferrocenyl GNA-RNA "mixed" dinucleoside phosphate analog. Recently, we developed a Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition reaction-based approach for the synthesis of novel 1,2,3-triazole-linked ("click") nucleosides. The high value of this approach is because it allows for the introduction of functional (e.g., luminescent and redox-active) groups that protrude from the main oligomer sequence. With respect to biological activity studies, we identified several promising anticancer and antimicrobial compounds. Furthermore, we found that simple ferrocenyl-nucleobase conjugates have potential as modulators of Aβ21-40 amyloid aggregation. The final section of this article serves as a guide for future studies, as it presents some challenging goals yet to be achieved within the rapidly growing field of nucleic acid chemistry.
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Affiliation(s)
- Mateusz Klarek
- University of Łódź, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, 91-403 Łódź, Poland.
| | - Konrad Kowalski
- University of Łódź, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, 91-403 Łódź, Poland.
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11
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Sahoo A, Gupta S, Das G, Ghosh A, Bagale SS, Sinha S, Gore KR. 2'- O-Alkyl- N 3-Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability. ACS Med Chem Lett 2024; 15:1250-1259. [PMID: 39140063 PMCID: PMC11318005 DOI: 10.1021/acsmedchemlett.4c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m3U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m3U and 2'-OEt-m3U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m3U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein.
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Affiliation(s)
- Avijit Sahoo
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Shalini Gupta
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Gourav Das
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Surajit Sinha
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R. Gore
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
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12
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Wang PY, Bartel DP. The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. Mol Cell 2024; 84:2918-2934.e11. [PMID: 39025072 PMCID: PMC11371465 DOI: 10.1016/j.molcel.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 05/03/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that, for different guide-RNA sequences, slicing rates of perfectly complementary bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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13
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Wang PY, Bartel DP. The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.15.562437. [PMID: 38766062 PMCID: PMC11100590 DOI: 10.1101/2023.10.15.562437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, slicing rates of perfectly complementary, bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y. Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David P. Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Lead contact
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Li S, Xiong F, Zhang S, Liu J, Gao G, Xie J, Wang Y. Oligonucleotide therapies for nonalcoholic steatohepatitis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102184. [PMID: 38665220 PMCID: PMC11044058 DOI: 10.1016/j.omtn.2024.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Nonalcoholic steatohepatitis (NASH) represents a severe disease subtype of nonalcoholic fatty liver disease (NAFLD) that is thought to be highly associated with systemic metabolic abnormalities. It is characterized by a series of substantial liver damage, including hepatocellular steatosis, inflammation, and fibrosis. The end stage of NASH, in some cases, may result in cirrhosis and hepatocellular carcinoma (HCC). Nowadays a large number of investigations are actively under way to test various therapeutic strategies, including emerging oligonucleotide drugs (e.g., antisense oligonucleotide, small interfering RNA, microRNA, mimic/inhibitor RNA, and small activating RNA) that have shown high potential in treating this fatal liver disease. This article systematically reviews the pathogenesis of NASH/NAFLD, the promising druggable targets proven by current studies in chemical compounds or biological drug development, and the feasibility and limitations of oligonucleotide-based therapeutic approaches under clinical or pre-clinical studies.
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Affiliation(s)
- Sixu Li
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
| | - Feng Xiong
- Department of Cardiology, The Third People’s Hospital of Chengdu, Chengdu 610031, China
| | - Songbo Zhang
- Department of Breast Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Jinghua Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
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15
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Lei L, Harp JM, Chaput JC, Wassarman K, Schlegel MK, Manoharan M, Egli M. Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6-SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Curr Protoc 2024; 4:e1088. [PMID: 38923271 DOI: 10.1002/cpz1.1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The middle (MID) domain of eukaryotic Argonaute (Ago) proteins and archaeal and bacterial homologues mediates the interaction with the 5'-terminal nucleotide of miRNA and siRNA guide strands. The MID domain of human Ago2 (hAgo2) is comprised of 139 amino acids with a molecular weight of 15.56 kDa. MID adopts a Rossman-like beta1-alpha1-beta2-alpha2-beta3-alpha3-beta4-alpha4 fold with a nucleotide specificity loop between beta3 and alpha3. Multiple crystal structures of nucleotides bound to hAgo2 MID have been reported, whereby complexes were obtained by soaking ligands into crystals of MID domain alone. This protocol describes a simplified one-step approach to grow well-diffracting crystals of hAgo2 MID-nucleotide complexes by mixing purified His6-SUMO-MID fusion protein, Ulp1 protease, and excess nucleotide in the presence of buffer and precipitant. The crystal structures of MID complexes with UMP, UTP and 2'-3' linked α-L-threofuranosyl thymidine-3'-triphosphate (tTTP) are presented. This article also describes fluorescence-based assays to measure dissociation constants (Kd) of MID-nucleotide interactions for nucleoside 5'-monophosphates and nucleoside 3',5'-bisphosphates. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Crystallization of Ago2 MID-nucleotide complexes Basic Protocol 2: Measurement of dissociation constant Kd between Ago2 MID and nucleotides.
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Affiliation(s)
- Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee
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16
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Tang Q, Khvorova A. RNAi-based drug design: considerations and future directions. Nat Rev Drug Discov 2024; 23:341-364. [PMID: 38570694 PMCID: PMC11144061 DOI: 10.1038/s41573-024-00912-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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17
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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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18
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Chernikov IV, Ponomareva UA, Meschaninova MI, Bachkova IK, Vlassov VV, Zenkova MA, Chernolovskaya EL. Cholesterol Conjugates of Small Interfering RNA: Linkers and Patterns of Modification. Molecules 2024; 29:786. [PMID: 38398538 PMCID: PMC10892548 DOI: 10.3390/molecules29040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Cholesterol siRNA conjugates attract attention because they allow the delivery of siRNA into cells without the use of transfection agents. In this study, we compared the efficacy and duration of silencing induced by cholesterol conjugates of selectively and totally modified siRNAs and their heteroduplexes of the same sequence and explored the impact of linker length between the 3' end of the sense strand of siRNA and cholesterol on the silencing activity of "light" and "heavy" modified siRNAs. All 3'-cholesterol conjugates were equally active under transfection, but the conjugate with a C3 linker was less active than those with longer linkers (C8 and C15) in a carrier-free mode. At the same time, they were significantly inferior in activity to the 5'-cholesterol conjugate. Shortening the sense strand carrying cholesterol by two nucleotides from the 3'-end did not have a significant effect on the activity of the conjugate. Replacing the antisense strand or both strands with fully modified ones had a significant effect on silencing as well as improving the duration in transfection-mediated and carrier-free modes. A significant 78% suppression of MDR1 gene expression in KB-8-5 xenograft tumors developed in mice promises an advantage from the use of fully modified siRNA cholesterol conjugates in combination chemotherapy.
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Affiliation(s)
- Ivan V Chernikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Ul'yana A Ponomareva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Mariya I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Irina K Bachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
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19
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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20
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Kowalski K. Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides. Bioorg Chem 2023; 141:106921. [PMID: 37871392 DOI: 10.1016/j.bioorg.2023.106921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
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Affiliation(s)
- Konrad Kowalski
- University of Lodz, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, PL-91403 Lodz, Poland.
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21
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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: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [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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22
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Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M. Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023; 62:2854-2867. [PMID: 37694722 PMCID: PMC11062489 DOI: 10.1021/acs.biochem.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several efforts are currently directed at the creation and cellular implementation of alternative genetic systems composed of pairing components that are orthogonal to the natural dA/dT and dG/dC base pairs. In an alternative approach, Watson-Crick-type pairing is conserved, but one or all of the four letters of the A, C, G, and T alphabet are substituted by modified components. Thus, all four nucleobases were altered to create halogenated deazanucleic acid (DZA): dA was replaced by 7-deaza-2'-deoxyadenosine (dzA), dG by 7-deaza-2'-deoxyguanosine (dzG), dC by 5-fluoro-2'-deoxycytidine (FdC), and dT by 5-chloro-2'-deoxyuridine (CldU). This base-pairing system was previously shown to retain function in Escherichia coli. Here, we analyze the stability, hydration, structure, and dynamics of a DZA Dickerson-Drew Dodecamer (DDD) of sequence 5'-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3'. Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing revealed a dramatic loss of hydration for the DZA-DDD relative to that for the DDD. The parent DDD 5'-d(CGCGAATTCGCG)-3' features an A-tract, a run of adenosines uninterrupted by a TpA step, and exhibits a hallmark narrow minor groove. Crystal structures─in the presence of RNase H─and MD simulations show increased conformational plasticity ("morphing") of DZA-DDD relative to that of the DDD. The narrow dzA-tract minor groove in one structure widens to resemble that in canonical B-DNA in a second structure. These changes reflect an indirect consequence of altered DZA major groove electrostatics (less negatively polarized compared to that in DNA) and hydration (reduced compared to that in DNA). Therefore, chemical modifications outside the minor groove that lead to collapse of major groove electrostatics and hydration can modulate A-tract geometry.
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Affiliation(s)
- Pradeep S Pallan
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Terry P Lybrand
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Elena Eremeeva
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Martin Egli
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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