1
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Cochran M, Arias D, Burke R, Chu D, Erdogan G, Hood M, Kovach P, Kwon HW, Chen Y, Moon M, Miller CD, Huang H, Levin A, Doppalapudi VR. Structure-Activity Relationship of Antibody-Oligonucleotide Conjugates: Evaluating Bioconjugation Strategies for Antibody-siRNA Conjugates for Drug Development. J Med Chem 2024; 67:14852-14867. [PMID: 39197831 PMCID: PMC11403602 DOI: 10.1021/acs.jmedchem.4c00802] [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: 09/01/2024]
Abstract
Antibody-oligonucleotide conjugates are a promising class of therapeutics for extrahepatic delivery of small interfering ribonucleic acids (siRNAs). These conjugates can be optimized for improved delivery and mRNA knockdown (KD) through understanding of structure-activity relationships. In this study, we systematically examined factors including antibody isotype, siRNA chemistry, linkers, conjugation chemistry, PEGylation, and drug-to-antibody ratios (DARs) for their impact on bioconjugation, pharmacokinetics (PK), siRNA delivery, and bioactivity. Conjugation site (cysteine, lysine, and Asn297 glycan) and DAR proved critical for optimal conjugate PK and siRNA delivery. SiRNA chemistry including 2' sugar modifications and positioning of phosphorothioates were found to be critical for delivery and duration of action. By utilizing cleavable and noncleavable linkers, we demonstrated the impact of linkers on PK and mRNA KD. To achieve optimal properties of antibody-siRNA conjugates, a careful selection of siRNA chemistry, DAR, conjugation sites, linkers, and antibody isotype is necessary.
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Affiliation(s)
- Michael Cochran
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Danny Arias
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Rob Burke
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - David Chu
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Gulin Erdogan
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Michael Hood
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Philip Kovach
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Hae Won Kwon
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Yanling Chen
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Michael Moon
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Christopher D Miller
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Hanhua Huang
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Arthur Levin
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
| | - Venkata Ramana Doppalapudi
- Avidity Biosciences, Inc., 10578 Science Center Drive Suite 125. San Diego, California 92121, United States
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2
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Ye Z, Chen H, Weinans H, van der Wal B, Rios JL. Novel Aptamer Strategies in Combating Bacterial Infections: From Diagnostics to Therapeutics. Pharmaceutics 2024; 16:1140. [PMID: 39339177 PMCID: PMC11435160 DOI: 10.3390/pharmaceutics16091140] [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: 07/11/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial infections and antimicrobial resistance are posing substantial difficulties to the worldwide healthcare system. The constraints of conventional diagnostic and therapeutic approaches in dealing with continuously changing infections highlight the necessity for innovative solutions. Aptamers, which are synthetic oligonucleotide ligands with a high degree of specificity and affinity, have demonstrated significant promise in the field of bacterial infection management. This review examines the use of aptamers in the diagnosis and therapy of bacterial infections. The scope of this study includes the utilization of aptasensors and imaging technologies, with a particular focus on their ability to detect conditions at an early stage. Aptamers have shown exceptional effectiveness in suppressing bacterial proliferation and halting the development of biofilms in therapeutic settings. In addition, they possess the capacity to regulate immune responses and serve as carriers in nanomaterial-based techniques, including radiation and photodynamic therapy. We also explore potential solutions to the challenges faced by aptamers, such as nuclease degradation and in vivo instability, to broaden the range of applications for aptamers to combat bacterial infections.
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Affiliation(s)
- Zijian Ye
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Huaizhi Chen
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Harrie Weinans
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Biomechanical Engineering, Faculty of Mechanical Engineering, Delft University of Technology (TU Delft), 2628 CD Delft, The Netherlands
| | - Bart van der Wal
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jaqueline Lourdes Rios
- Department of Orthopedics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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3
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Rivera Flores IV, Monopoli K, Jackson S, Echeverria D, O'Reilly D, Brown RH, Khvorova A. Near Sequence Homology Does Not Guarantee siRNA Cross-Species Efficacy. Nucleic Acid Ther 2024. [PMID: 39189114 DOI: 10.1089/nat.2024.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Abstract
Small interfering RNAs (siRNAs) represent a novel class of drugs capable of potent and sustained modulation of genes across various tissues. Preclinical development of siRNAs necessitates assessing efficacy and toxicity in animal models. While identifying therapeutic leads with cross-species activity can expedite development, it may compromise efficacy and be infeasible for certain gene targets. Here, we investigate whether deriving species-active siRNAs from potent human-targeting leads-an approach termed mismatch conversion-can yield potent compounds. We systematically altered potent siRNAs targeting human genes associated with diseases-SOD1 (ALS), JAK1 (inflammation), and HTT (HD)-to generate species-matching variants with full complementarity to their target in NHPs, mice, rats, sheep, and dogs. Variants potency and efficacy were measured in corresponding cell lines. We demonstrate that sequence, position, and number of mismatches significantly influence the ability to generate potent species-active compounds via mismatch conversion. Across tested sequences, mismatch conversion strategy ability to identify a species-active lead varied from 0% to 70%. For SOD1, lead compounds identified from species-focus screening in mouse and dog cells were more potent than leads obtained from mismatch conversion. Thus, a focused screening of therapeutic lead and model compounds may represent a more reliable strategy for the clinical advancement of siRNAs.
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Affiliation(s)
- Iris Valeria Rivera Flores
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Samuel Jackson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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4
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Allen S, O'Reilly D, Miller R, Sapp E, Summers A, Paquette J, Echeverria Moreno D, Bramato B, McHugh N, Yamada K, Aronin N, DiFiglia M, Khvorova A. mRNA Nuclear Clustering Leads to a Difference in Mutant Huntingtin mRNA and Protein Silencing by siRNAs In Vivo. Nucleic Acid Ther 2024; 34:164-172. [PMID: 39023561 PMCID: PMC11387003 DOI: 10.1089/nat.2024.0027] [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] [Indexed: 07/20/2024] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the first exon of the huntingtin gene (HTT). Oligonucleotide therapeutics, such as short interfering RNA (siRNA), reduce levels of huntingtin mRNA and protein in vivo and are considered a viable therapeutic strategy. However, the extent to which they silence huntingtin mRNA in the nucleus is not established. We synthesized siRNA cross-reactive to mouse (wild-type) Htt and human (mutant) HTT in a divalent scaffold and delivered to two mouse models of HD. In both models, divalent siRNA sustained lowering of wild-type Htt, but not mutant HTT mRNA expression in striatum and cortex. Near-complete silencing of both mutant HTT protein and wild-type HTT protein was observed in both models. Subsequent fluorescent in situ hybridization analysis shows that divalent siRNA acts predominantly on cytoplasmic mutant HTT transcripts, leaving clustered mutant HTT transcripts in the nucleus largely intact in treated HD mouse brains. The observed differences between mRNA and protein levels, exaggerated in the case of extended repeats, might apply to other repeat-associated neurological disorders.
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Affiliation(s)
- Sarah Allen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria Moreno
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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5
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Ferguson CM, Godinho BMDC, Echeverria D, Hassler M, Vangjeli L, Sousa J, McHugh N, Alterman J, Hariharan V, Krishnamurthy P, Watts J, Rogaev E, Khvorova A. A combinatorial approach for achieving CNS-selective RNAi. Nucleic Acids Res 2024; 52:5273-5284. [PMID: 38348876 PMCID: PMC11109952 DOI: 10.1093/nar/gkae100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 12/30/2023] [Accepted: 02/12/2024] [Indexed: 05/23/2024] Open
Abstract
RNA interference (RNAi) is an endogenous process that can be harnessed using chemically modified small interfering RNAs (siRNAs) to potently modulate gene expression in many tissues. The route of administration and chemical architecture are the primary drivers of oligonucleotide tissue distribution, including siRNAs. Independently of the nature and type, oligonucleotides are eliminated from the body through clearance tissues, where their unintended accumulation may result in undesired gene modulation. Divalent siRNAs (di-siRNAs) administered into the CSF induce robust gene silencing throughout the central nervous system (CNS). Upon clearance from the CSF, they are mainly filtered by the kidneys and liver, with the most functionally significant accumulation occurring in the liver. siRNA- and miRNA-induced silencing can be blocked through substrate inhibition using single-stranded, stabilized oligonucleotides called antagomirs or anti-siRNAs. Using APOE as a model target, we show that undesired di-siRNA-induced silencing in the liver can be mitigated through administration of liver targeting GalNAc-conjugated anti-siRNAs, without impacting CNS activity. Blocking unwanted hepatic APOE silencing achieves fully CNS-selective silencing, essential for potential clinical translation. While we focus on CNS/liver selectivity, coadministration of differentially targeting siRNA and anti-siRNAs can be adapted as a strategy to achieve tissue selectivity in different organ combinations.
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Affiliation(s)
- Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lorenc Vangjeli
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Julia Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | | | - Jonathan Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Eveny Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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6
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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: 0] [Impact Index Per Article: 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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7
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Allen S, O'Reilly D, Miller R, Sapp E, Summers A, Paquette J, Moreno DE, Bramato B, McHugh N, Yamada K, Aronin N, DiFiglia M, Khvorova A. mRNA nuclear clustering leads to a difference in mutant huntingtin mRNA and protein silencing by siRNAs in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590997. [PMID: 38774633 PMCID: PMC11106801 DOI: 10.1101/2024.04.24.590997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the first exon of the huntingtin gene (HTT). Oligonucleotide therapeutics, such as short interfering RNA (siRNA), reduce levels of huntingtin mRNA and protein in vivo and are considered a viable therapeutic strategy. However, the extent to which they silence HTT mRNA in the nucleus is not established. We synthesized siRNA cross-reactive to mouse (wild-type) Htt and human (mutant) HTT in a di-valent scaffold and delivered to two mouse models of HD. In both models, di-valent siRNA sustained lowering of wild-type Htt, but not mutant HTT mRNA expression in striatum and cortex. Near-complete silencing of both mutant HTT protein and wild-type Htt protein was observed in both models. Subsequent fluorescent in situ hybridization (FISH) analysis shows that di-valent siRNA acts predominantly on cytoplasmic mutant HTT transcripts, leaving clustered mutant HTT transcripts in the nucleus largely intact in treated HD mouse brains. The observed differences between mRNA and protein levels, exaggerated in the case of extended repeats, might apply to other repeat-associated neurological disorders.
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8
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Davodabadi F, Farasati Far B, Sargazi S, Fatemeh Sajjadi S, Fathi-Karkan S, Mirinejad S, Ghotekar S, Sargazi S, Rahman MM. Nanomaterials-Based Targeting of Long Non-Coding RNAs in Cancer: A Cutting-Edge Review of Current Trends. ChemMedChem 2024; 19:e202300528. [PMID: 38267373 DOI: 10.1002/cmdc.202300528] [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] [Received: 09/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
This review article spotlights the burgeoning potential of using nanotherapeutic strategies to target long non-coding RNAs (lncRNAs) in cancer cells. This updated discourse underlines the prominent role of lncRNAs in instigating cancer, facilitating its progression, and metastasis, validating lncRNAs' potential for being effective diagnostic biomarkers and therapeutic targets. The manuscript offers an in-depth examination of different strategies presently employed to modulate lncRNA expression and function for therapeutic purposes. Among these strategies, Antisense Oligonucleotides (ASOs), RNA interference (RNAi) technologies, and the innovative clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing tools garner noteworthy mention. A significant section of the review is dedicated to nanocarriers and their crucial role in drug delivery. These nanocarriers' efficiency in targeting lncRNAs in varied types of cancers is elaborated upon, validating the importance of targeted therapy. The manuscript culminates by reaffirming the promising prospects of targeting lncRNAs to enhance the accuracy of cancer diagnosis and improve treatment efficacy. Consequently, new paths are opened to more research and innovation in employing nanotherapeutic approaches against lncRNAs in cancer cells. Thus, this comprehensive manuscript serves as a valuable resource that underscores the vital role of lncRNAs and the various nano-strategies for targeting them in cancer treatment. Future research should also focus on unraveling the complex regulatory networks involving lncRNAs and identifying fundamental functional interactions to refine therapeutic strategies targeting lncRNAs in cancer.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran
| | - Bahareh Farasati Far
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyedeh Fatemeh Sajjadi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 9453155166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, 9414974877, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Suresh Ghotekar
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammed M Rahman
- Center of Excellence for Advanced Materials Research (CEAMR) & Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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9
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Hayashi J, Ochi Y, Senpuku K, Wada SI, Wada F, Harada-Shiba M, Urata H. Rational design of prodrug-type apoB-targeted siRNA for nuclease resistance improvement without compromising gene silencing potency. Bioorg Med Chem 2024; 104:117693. [PMID: 38552598 DOI: 10.1016/j.bmc.2024.117693] [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] [Received: 02/19/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Synthetic siRNA molecules without chemical modifications are easily degraded in the body, and 2'-O-modifications are frequently introduced to enhance stability. However, such chemical modifications tend to impact the gene knockdown potency of siRNA negatively. To circumvent this problem, we previously developed a prodrug-type siRNA bearing 2'-O-methyldithiomethyl (MDTM) groups, which can be converted into unmodified siRNA under the reductive environment in cells. In this study, we developed a nuclease-resistant prodrug-type 2'-O-MDTM siRNA for deployment in future animal experiments. To rationally design siRNA modified with a minimal number of 2'-O-MDTM nucleotide residues, we identified the sites susceptible to nuclease digestion and tolerant to 2'-O-methyl (2'-OMe) modification in the antisense strand of apolipoprotein B-targeted siRNA. Subsequently, we optimized the positions where the 2'-OMe and 2'-O-MDTM groups should be incorporated. siRNA bearing the 2'-O-MDTM and 2'-OMe groups at their respective optimized positions exhibited efficient knockdown potency in vitro and enhanced stability in serum.
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Affiliation(s)
- Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yosuke Ochi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kota Senpuku
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Fumito Wada
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Mariko Harada-Shiba
- National Cerebral & Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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10
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Garreau M, Weidner J, Hamilton R, Kolosionek E, Toki N, Stavenhagen K, Paris C, Bonetti A, Czechtizky W, Gnerlich F, Rydzik A. Chemical modification patterns for microRNA therapeutic mimics: a structure-activity relationship (SAR) case-study on miR-200c. Nucleic Acids Res 2024; 52:2792-2807. [PMID: 38421619 PMCID: PMC11014349 DOI: 10.1093/nar/gkae141] [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] [Received: 12/21/2022] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
microRNA (miRNA) mimics are an emerging class of oligonucleotide therapeutics, with a few compounds already in clinical stages. Synthetic miRNAs are able to restore downregulated levels of intrinsic miRNAs, allowing for parallel regulation of multiple genes involved in a particular disease. In this work, we examined the influence of chemical modifications patterns in miR-200c mimics, assessing the regulation of a selection of target messenger RNAs (mRNA) and, subsequently, of the whole transcriptome in A549 cells. We have probed 37 mimics and provided an initial set of instructions for designing miRNA mimics with potency and selectivity similar to an unmodified miRNA duplex. Additionally, we have examined the stability of selected mimics in serum. Finally, the selected two modification patterns were translated to two other miRNAs, miR-34a and miR-155. To differing degrees, these designs acted on target mRNAs in a similar manner to the unmodified mimic. Here, for the first time, we describe a structured overview of 'miRNA mimics modification templates' that are chemically stabilised and optimised for use in an in vitro set up and highlight the need of further sequence specific optimization when mimics are to be used beyond in vitro tool experiments.
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Affiliation(s)
- Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Russell Hamilton
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Naoko Toki
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Kathrin Stavenhagen
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Clément Paris
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Alessandro Bonetti
- Translational Genomics, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
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11
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Jadhav V, Vaishnaw A, Fitzgerald K, Maier MA. RNA interference in the era of nucleic acid therapeutics. Nat Biotechnol 2024; 42:394-405. [PMID: 38409587 DOI: 10.1038/s41587-023-02105-y] [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: 10/05/2022] [Accepted: 12/15/2023] [Indexed: 02/28/2024]
Abstract
Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering RNA (siRNA) drug development, including the first approval in 2018 of a liver-targeted siRNA interference (RNAi) therapeutic in lipid nanoparticles and subsequent approvals of five more RNAi drugs, which used metabolically stable siRNAs combined with N-acetylgalactosamine ligands for conjugate-based liver delivery. We also consider the remaining challenges in the field, such as delivery to muscle, brain and other extrahepatic organs. Today's RNAi therapeutics exhibit high specificity, potency and durability, and are transitioning from applications in rare diseases to widespread, chronic conditions.
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Affiliation(s)
- Vasant Jadhav
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Akshay Vaishnaw
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Kevin Fitzgerald
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Martin A Maier
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
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12
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Hoogenboezem EN, Patel SS, Lo JH, Cavnar AB, Babb LM, Francini N, Gbur EF, Patil P, Colazo JM, Michell DL, Sanchez VM, McCune JT, Ma J, DeJulius CR, Lee LH, Rosch JC, Allen RM, Stokes LD, Hill JL, Vickers KC, Cook RS, Duvall CL. Structural optimization of siRNA conjugates for albumin binding achieves effective MCL1-directed cancer therapy. Nat Commun 2024; 15:1581. [PMID: 38383524 PMCID: PMC10881965 DOI: 10.1038/s41467-024-45609-0] [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: 03/14/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The high potential of siRNAs to silence oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, divalent lipid-conjugated siRNAs are optimized for in situ binding to albumin to improve pharmacokinetics and tumor delivery. Systematic variation of the siRNA conjugate structure reveals that the location of the linker branching site dictates tendency toward albumin association versus self-assembly, while the lipid hydrophobicity and reversibility of albumin binding also contribute to siRNA intracellular delivery. The lead structure increases tumor siRNA accumulation 12-fold in orthotopic triple negative breast cancer (TNBC) tumors over the parent siRNA. This structure achieves approximately 80% silencing of the anti-apoptotic oncogene MCL1 and yields better survival outcomes in three TNBC models than an MCL-1 small molecule inhibitor. These studies provide new structure-function insights on siRNA-lipid conjugate structures that are intravenously injected, associate in situ with serum albumin, and improve pharmacokinetics and tumor treatment efficacy.
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Affiliation(s)
- Ella N Hoogenboezem
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Shrusti S Patel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Justin H Lo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ashley B Cavnar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren M Babb
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Eva F Gbur
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Prarthana Patil
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Juan M Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Danielle L Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Violeta M Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua T McCune
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jinqi Ma
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Carlisle R DeJulius
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Linus H Lee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ryan M Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry D Stokes
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jordan L Hill
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Rebecca S Cook
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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13
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Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Amrani N, Chen Z, Gaston N, Wagh A, Newby G, Xie J, Liu DR, Gao G, Wolfe S, Khvorova A, Watts J, Sontheimer E. Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo. Nucleic Acids Res 2024; 52:977-997. [PMID: 38033325 PMCID: PMC10810193 DOI: 10.1093/nar/gkad1125] [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] [Received: 03/09/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a 'protecting oligo'), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
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Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Atish Wagh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, 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
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, 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
| | - Scot A Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, 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
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, 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
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14
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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15
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Acharya A, Yadav M, Nagpure M, Kumaresan S, Guchhait SK. Molecular medicinal insights into scaffold hopping-based drug discovery success. Drug Discov Today 2024; 29:103845. [PMID: 38013043 DOI: 10.1016/j.drudis.2023.103845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
In both academia and the pharmaceutical industry, innovative hypotheses, methodologies and technologies that can shorten the drug research and development, leading to higher success rates, are vital. In this review, we demonstrate how innovative variations of the scaffold-hopping strategy have been used to create new druggable molecular spaces, drugs, clinical candidates, preclinical candidates, and bioactive agents. We also analyze molecular modulations that enabled improvements of the pharmacodynamic (PD), physiochemical, and pharmacokinetic (PK) properties (P3 properties) of the drugs resulting from these scaffold-hopping strategies.
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Affiliation(s)
- Ayan Acharya
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mukul Yadav
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mithilesh Nagpure
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sanathanalaxmi Kumaresan
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India; National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sankar K Guchhait
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India.
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16
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Collotta D, Bertocchi I, Chiapello E, Collino M. Antisense oligonucleotides: a novel Frontier in pharmacological strategy. Front Pharmacol 2023; 14:1304342. [PMID: 38044945 PMCID: PMC10690781 DOI: 10.3389/fphar.2023.1304342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are short single stranded synthetic RNA or DNA molecules, whereas double-stranded RNA nucleotide sequences are called small interfering RNA (siRNA). ASOs bind to complementary nucleic acid sequences impacting the associated functions of the targeted nucleic acids. They represent an emerging class of drugs that, through a revolutionary mechanism of action, aim to directly regulate disease-causing genes and their variants, providing an alternative tool to traditional "protein-specific" therapies. The majority of the ASOs are designed to treat orphan genetic disorders that in most of the cases are seriously disabling and still lacking an adequate therapy. In order to translate ASOs into clinical success, constant technological advances have been instrumental in overcoming several pharmacological, toxicological and formulation limitations. Accordingly, chemical structures have been recently implemented and new bio-conjugation and nanocarriers formulation strategies explored. The aim of this work is to offer an overview of the antisense technology with a comparative analysis of the oligonucleotides approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA).
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Affiliation(s)
- D. Collotta
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - I. Bertocchi
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi (NICO), University of Turin, Turin, Italy
| | - E. Chiapello
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
| | - M. Collino
- Department of Neuroscience Rita Levi Montalcini, University of Turin, Turin, Italy
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17
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Qin Y, Ma X, Tao R, Du Y, Chen T. Synthesis, Reverse Transcription, Replication, and Inter-Transcription of 2'-Modified Nucleic Acids with Evolved Thermophilic Polymerases: Efforts toward Multidimensional Expansion of the Central Dogma. ACS Synth Biol 2023; 12:2616-2631. [PMID: 37646406 DOI: 10.1021/acssynbio.3c00213] [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: 09/01/2023]
Abstract
In the past decades, various xenobiotic nucleic acids (XNAs), including 2'-modified nucleic acids, have been developed as novel genetic materials and demonstrated great potential in synthetic biology and biotechnology. Enzymatic polymerization and replication of these artificial polymers are obviously the prerequisite to make full use of them, and DNA and RNA polymerases from different families have thus been extensively engineered for these purposes. However, the performance of engineered XNA polymerases is still far from satisfactory, especially in terms of the efficiency of synthesizing XNA with bigger lengths and the capability of directly replicating XNAs or transcribing one XNA to another. In this work, we tailored a mutant of Stoffel fragment of Taq DNA polymerase, SFM4-3, by engineering a key residue pair on the surfaces of fingers and thumb domains, and successfully obtained mutants with significantly enhanced efficiency for the synthesis of fully 2'-OMe-modified DNA with bigger lengths. Remarkably, we also found that these polymerase mutants are capable of synthesizing, reverse transcribing, and even replicating RNA and different fully 2'-modified XNAs, as well as transcribing one of these nucleic acids to another, with varied efficiencies. The application of these activities for producing DNA strands end-protected by XNA duplexes was then demonstrated. These results clearly suggest that the genetic information can be stored in and transmitted among DNA, RNA, and different 2'-modified XNAs with the assistance of polymerase mutants, and the central dogma of life can be expanded to higher dimensions via the development of XNAs together with engineering their polymerases.
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Affiliation(s)
- Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Rui Tao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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18
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Matsuda S, Bala S, Liao JY, Datta D, Mikami A, Woods L, Harp JM, Gilbert JA, Bisbe A, Manoharan RM, Kim M, Theile CS, Guenther DC, Jiang Y, Agarwal S, Maganti R, Schlegel MK, Zlatev I, Charisse K, Rajeev KG, Castoreno A, Maier M, Janas MM, Egli M, Chaput JC, Manoharan M. Shorter Is Better: The α-(l)-Threofuranosyl Nucleic Acid Modification Improves Stability, Potency, Safety, and Ago2 Binding and Mitigates Off-Target Effects of Small Interfering RNAs. J Am Chem Soc 2023; 145:19691-19706. [PMID: 37638886 DOI: 10.1021/jacs.3c04744] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Chemical modifications are necessary to ensure the metabolic stability and efficacy of oligonucleotide-based therapeutics. Here, we describe analyses of the α-(l)-threofuranosyl nucleic acid (TNA) modification, which has a shorter 3'-2' internucleotide linkage than the natural DNA and RNA, in the context of small interfering RNAs (siRNAs). The TNA modification enhanced nuclease resistance more than 2'-O-methyl or 2'-fluoro ribose modifications. TNA-containing siRNAs were prepared as triantennary N-acetylgalactosamine conjugates and were tested in cultured cells and mice. With the exceptions of position 2 of the antisense strand and position 11 of the sense strand, the TNA modification did not inhibit the activity of the RNA interference machinery. In a rat toxicology study, TNA placed at position 7 of the antisense strand of the siRNA mitigated off-target effects, likely due to the decrease in the thermodynamic binding affinity relative to the 2'-O-methyl residue. Analysis of the crystal structure of an RNA octamer with a single TNA on each strand showed that the tetrose sugar adopts a C4'-exo pucker. Computational models of siRNA antisense strands containing TNA bound to Argonaute 2 suggest that TNA is well accommodated in the region kinked by the enzyme. The combined data indicate that the TNA nucleotides are promising modifications expected to increase the potency, duration of action, and safety of siRNAs.
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Affiliation(s)
- Shigeo Matsuda
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Saikat Bala
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Atsushi Mikami
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Lauren Woods
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - Jason A Gilbert
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - MaryBeth Kim
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Christopher S Theile
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Yongfeng Jiang
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Saket Agarwal
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Rajanikanth Maganti
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Mark K Schlegel
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | | | - Adam Castoreno
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Maier
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Maja M Janas
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0146, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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19
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Monopoli KR, Korkin D, Khvorova A. Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:93-109. [PMID: 37456778 PMCID: PMC10338369 DOI: 10.1016/j.omtn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Chemically modified small interfering RNAs (siRNAs) are promising therapeutics guiding sequence-specific silencing of disease genes. Identifying chemically modified siRNA sequences that effectively silence target genes remains challenging. Such determinations necessitate computational algorithms. Machine learning is a powerful predictive approach for tackling biological problems but typically requires datasets significantly larger than most available siRNA datasets. Here, we describe a framework applying machine learning to a small dataset (356 modified sequences) for siRNA efficacy prediction. To overcome noise and biological limitations in siRNA datasets, we apply a trichotomous, two-threshold, partitioning approach, producing several combinations of classification threshold pairs. We then test the effects of different thresholds on random forest machine learning model performance using a novel evaluation metric accounting for class imbalances. We identify thresholds yielding a model with high predictive power, outperforming a linear model generated from the same data, that was predictive upon experimental evaluation. Using a novel model feature extraction method, we observe target site base importances and base preferences consistent with our current understanding of the siRNA-mediated silencing mechanism, with the random forest providing higher resolution than the linear model. This framework applies to any classification challenge involving small biological datasets, providing an opportunity to develop high-performing design algorithms for oligonucleotide therapies.
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Affiliation(s)
- Kathryn R. Monopoli
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dmitry Korkin
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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20
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [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] [Received: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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21
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Chatterjee K, Lakdawala S, Quadir SS, Puri D, Mishra DK, Joshi G, Sharma S, Choudhary D. siRNA-Based Novel Therapeutic Strategies to Improve Effectiveness of Antivirals: An Insight. AAPS PharmSciTech 2023; 24:170. [PMID: 37566146 DOI: 10.1208/s12249-023-02629-1] [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] [Received: 01/31/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Since the ground-breaking discovery of RNA interference (RNAi), scientists have made significant progress in the field of small interfering RNA (siRNA) treatments. Due to severe barriers to the therapeutic application of siRNA, nanoparticle technologies for siRNA delivery have been designed. For pathological circumstances such as viral infection, toxic RNA abnormalities, malignancies, and hereditary diseases, siRNAs are potential therapeutic agents. However, systemic administration of siRNAs in vivo remains a substantial issue due to a lack of "drug-likeness" (siRNA are relatively larger than drugs and have low hydrophobicity), physiological obstacles, and possible toxicities. This write-up covers important accomplishment in the field of clinical trials and patents specially based of siRNAs using targeting viruses. Furthermore, it offers deep insight of nanoparticle applied for siRNA delivery and strategies to improve the effectiveness of antivirals.
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Affiliation(s)
- Krittika Chatterjee
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed to be University), Mumbai, 400056, India
| | - Sagheerah Lakdawala
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed to be University), Mumbai, 400056, India
| | - Sheikh Shahnawaz Quadir
- Department of Pharmaceutical Sciences, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Dinesh Puri
- School of Pharmacy, Graphic Era Hill University, Dehradun, Uttarakhand, 248001, India
| | - Dinesh Kumar Mishra
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya (A Central University), Koni, Bilaspur (C.G.), 495009, India
| | - Garima Joshi
- Department of Pharmaceutical Sciences, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Sanjay Sharma
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed to be University), Mumbai, 400056, India.
| | - Deepak Choudhary
- Department of Pharmaceutical Sciences, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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22
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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23
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Tian R, Shang Y, Wang Y, Jiang Q, Ding B. DNA Nanomaterials-Based Platforms for Cancer Immunotherapy. SMALL METHODS 2023; 7:e2201518. [PMID: 36651129 DOI: 10.1002/smtd.202201518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Indexed: 05/17/2023]
Abstract
The past few decades have witnessed the evolving paradigm for cancer therapy from nonspecific cytotoxic agents to selective, mechanism-based therapeutics, especially immunotherapy. In particular, the integration of nanomaterials with immunotherapy is proven to improve the therapeutic outcome and minimize off-target toxicity in the treatment. As a novel nanomaterial, DNA-based self-assemblies featuring uniform geometries, feasible modifications, programmability, surface addressability, versatility, and intrinsic biocompatibility, are extensively exploited for innovative and effective cancer immunotherapy. In this review, the successful employment of DNA nanoplatforms for cancer immunotherapy, including the delivery of immunogenic cell death inducers, adjuvants and vaccines, immune checkpoint blockers as well as the application in immune cell engineering and adoptive cell therapy is summarized. The remaining challenges and future perspectives regarding the pharmacokinetics/pharmacodynamics, in vivo fate and immunogenicity of DNA materials, and the design of intelligent DNA nanomedicine for individualized cancer immunotherapy are also discussed.
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Affiliation(s)
- Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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24
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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25
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Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Chen Z, Gaston N, Newby GA, Xie J, Liu DR, Gao G, Wolfe SA, Khvorova A, Watts JK, Sontheimer EJ. Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533459. [PMID: 36993169 PMCID: PMC10055305 DOI: 10.1101/2023.03.20.533459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a "protecting oligo"), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
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Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, 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, Massachusetts, 01605, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, 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, Massachusetts, 01605, USA
| | - Scot A. Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
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26
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Jones JD, Grassmyer KT, Kennedy RT, Koutmou KS, Maloney TD. Nuclease P1 Digestion for Bottom-Up RNA Sequencing of Modified siRNA Therapeutics. Anal Chem 2023; 95:4404-4411. [PMID: 36812429 DOI: 10.1021/acs.analchem.2c04902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
siRNA therapeutics provide a selective and powerful approach to reduce the expression of disease-causing genes. For regulatory approval, these modalities require sequence confirmation which is typically achieved by intact tandem mass spectrometry sequencing. However, this process produces highly complex spectra which are difficult to interpret and typically results in less than full sequence coverage. We sought to develop a bottom-up siRNA sequencing platform to ease sequencing data analysis and provide full sequence coverage. Analogous to bottom-up proteomics, this process requires chemical or enzymatic digestion to reduce the oligonucleotide length down to analyzable lengths, but siRNAs commonly contain modifications that inhibit the degradation process. We tested six digestion schemes for their feasibility to digest the 2' modified siRNAs and identified that nuclease P1 provides an effective digestion workflow. Using a partial digestion, nuclease P1 provides high 5' and 3' end sequence coverage with multiple overlapping digestion products. Additionally, this enzyme provides high-quality and highly reproducible RNA sequencing no matter the RNA phosphorothioate content, 2'-fluorination status, sequence, or length. Overall, we developed a robust enzymatic digestion scheme for bottom-up siRNA sequencing using nuclease P1, which can be implemented into existing sequence confirmation workflows.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States.,Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Kathleen T Grassmyer
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, Michigan 48109, United States
| | - Todd D Maloney
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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27
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Banerjee S, Hemmat MA, Shubham S, Gosai A, Devarakonda S, Jiang N, Geekiyanage C, Dillard JA, Maury W, Shrotriya P, Lamm MH, Nilsen-Hamilton M. Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing. Int J Mol Sci 2023; 24:4627. [PMID: 36902059 PMCID: PMC10003157 DOI: 10.3390/ijms24054627] [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: 12/31/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.
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Affiliation(s)
- Soma Banerjee
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
| | - Mahsa Askary Hemmat
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Shambhavi Shubham
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Agnivo Gosai
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Nianyu Jiang
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | | | - Jacob A. Dillard
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Wendy Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 50011, USA
| | - Pranav Shrotriya
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Monica H. Lamm
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Marit Nilsen-Hamilton
- Ames Laboratory, U.S. Department of Energy, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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28
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Hoogenboezem EN, Patel SS, Cavnar AB, Lo JH, Babb LM, Francini N, Patil P, Colazo JM, Michell DL, Sanchez VM, McCune JT, Ma J, DeJulius CR, Lee LH, Rosch JC, Allen RM, Stokes LD, Hill JL, Vickers KC, Cook RS, Duvall CL. Structural Optimization of siRNA Conjugates for Albumin Binding Achieves Effective MCL1-Targeted Cancer Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528574. [PMID: 36824780 PMCID: PMC9948981 DOI: 10.1101/2023.02.14.528574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The high potential for therapeutic application of siRNAs to silence traditionally undruggable oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, siRNAs were optimized for in situ binding to albumin through C18 lipid modifications to improve pharmacokinetics and tumor delivery. Systematic variation of siRNA conjugates revealed a lead structure with divalent C18 lipids each linked through three repeats of hexaethylene glycol connected by phosphorothioate bonds. Importantly, we discovered that locating the branch site of the divalent lipid structure proximally (adjacent to the RNA) rather than at a more distal site (after the linker segment) promotes association with albumin, while minimizing self-assembly and lipoprotein association. Comparison to higher albumin affinity (diacid) lipid variants and siRNA directly conjugated to albumin underscored the importance of conjugate hydrophobicity and reversibility of albumin binding for siRNA delivery and bioactivity in tumors. The lead conjugate increased tumor siRNA accumulation 12-fold in orthotopic mouse models of triple negative breast cancer over the parent siRNA. When applied for silencing of the anti-apoptotic oncogene MCL-1, this structure achieved approximately 80% MCL1 silencing in orthotopic breast tumors. Furthermore, application of the lead conjugate structure to target MCL1 yielded better survival outcomes in three independent, orthotopic, triple negative breast cancer models than an MCL1 small molecule inhibitor. These studies provide new structure-function insights on optimally leveraging siRNA-lipid conjugate structures that associate in situ with plasma albumin for molecular-targeted cancer therapy.
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Affiliation(s)
| | - Shrusti S. Patel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Ashley B. Cavnar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Justin H. Lo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Lauren M. Babb
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Prarthana Patil
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Juan M. Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Violeta M. Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joshua T. McCune
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Jinqi Ma
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | | | | | - Jonah C. Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN
| | - Ryan M. Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Larry D. Stokes
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Jordan L. Hill
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Rebecca S. Cook
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Craig L. Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
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29
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Rydzik AM, Riether D, Gottschling D. Synthesis of 2'-modified N6-methyladenosine phosphoramidites and their incorporation into siRNA. Bioorg Med Chem Lett 2023; 81:129126. [PMID: 36632927 DOI: 10.1016/j.bmcl.2023.129126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/01/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
A synthesis of 2'-fluoro and 2'-methoxy N6-methyladenosine phosphoramidites and their successful incorporation into oligonucleotides is reported. 2'-fluoro and 2́-methoxy modifications of sugars in siRNAs are known to aid stability and N6-methylation modifies the potency of therapeutic silencing RNAs (siRNA). We demonstrate that a combination of those modifications incorporated into the antisense strand of siRNA leads to efficient knockdown of a target gene in cells. This work broadens the available pool of chemical modifications of therapeutic siRNAs and provides tools for their efficient synthesis.
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Affiliation(s)
- Anna M Rydzik
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dirk Gottschling
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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30
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Lu ZG, Shen J, Yang J, Wang JW, Zhao RC, Zhang TL, Guo J, Zhang X. Nucleic acid drug vectors for diagnosis and treatment of brain diseases. Signal Transduct Target Ther 2023; 8:39. [PMID: 36650130 PMCID: PMC9844208 DOI: 10.1038/s41392-022-01298-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Nucleic acid drugs have the advantages of rich target selection, simple in design, good and enduring effect. They have been demonstrated to have irreplaceable superiority in brain disease treatment, while vectors are a decisive factor in therapeutic efficacy. Strict physiological barriers, such as degradation and clearance in circulation, blood-brain barrier, cellular uptake, endosome/lysosome barriers, release, obstruct the delivery of nucleic acid drugs to the brain by the vectors. Nucleic acid drugs against a single target are inefficient in treating brain diseases of complex pathogenesis. Differences between individual patients lead to severe uncertainties in brain disease treatment with nucleic acid drugs. In this Review, we briefly summarize the classification of nucleic acid drugs. Next, we discuss physiological barriers during drug delivery and universal coping strategies and introduce the application methods of these universal strategies to nucleic acid drug vectors. Subsequently, we explore nucleic acid drug-based multidrug regimens for the combination treatment of brain diseases and the construction of the corresponding vectors. In the following, we address the feasibility of patient stratification and personalized therapy through diagnostic information from medical imaging and the manner of introducing contrast agents into vectors. Finally, we take a perspective on the future feasibility and remaining challenges of vector-based integrated diagnosis and gene therapy for brain diseases.
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Affiliation(s)
- Zhi-Guo Lu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
| | - Jie Shen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jun Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Jing-Wen Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Rui-Chen Zhao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Tian-Lu Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Jing Guo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Xin Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China.
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31
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Strategies and challenges for non-viral delivery of non-coding RNAs to the heart. Trends Mol Med 2023; 29:70-91. [PMID: 36371335 DOI: 10.1016/j.molmed.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/06/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022]
Abstract
Non-coding RNAs (ncRNAs), such as miRNAs and long non-coding RNAs (lncRNAs) have been reported as regulators of cardiovascular pathophysiology. Their transient effect and diversified mechanisms of action offer a plethora of therapeutic opportunities for cardiovascular diseases (CVDs). However, physicochemical RNA features such as charge, stability, and structural organization hinder efficient on-target cellular delivery. Here, we highlight recent preclinical advances in ncRNA delivery for the cardiovascular system using non-viral approaches. We identify the unmet needs and advance possible solutions towards clinical translation. Finding the optimal delivery vehicle and administration route is vital to improve therapeutic efficacy and safety; however, given the different types of ncRNAs, this may ultimately not be frameable within a one-size-fits-all approach.
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Ota M, Takahashi H, Nogi Y, Kagotani Y, Saito-Tarashima N, Kondo J, Minakawa N. Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog. Bioorg Med Chem 2022; 76:117093. [PMID: 36434923 DOI: 10.1016/j.bmc.2022.117093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022]
Abstract
A large number of chemically modified oligonucleotides (ONs) have been developed for RNA-based technologies. In most modified RNAs, the characteristic 2'-hydroxyl (2'-OH) groups are removed to enhance both nuclease resistance and hybridization ability. However, the importance of the 2'-OH group in RNA structure and function is well known. Here, we report the synthesis and properties of 4'-selenoRNA in which all four nucleoside units retain the 2'-OH groups but contain a selenium atom instead of an oxygen atom at the 4'-position of the furanose ring. 4'-SelenoRNA has enhanced ability to form duplexes with RNA, and high endonuclease resistance despite the presence of the 2'-OH groups. X-ray crystallography analysis showed that the 4'-selenoRNA duplex adopts an A-conformation, similar to natural RNA, although one 4'-selenocytidine residue has unusual South-type sugar puckering. Furthermore, preliminary studies using 4'-seleno-modified siRNAs suggest that 4'-selenoRNA may be applicable to RNA interference technology. Collectively, our results raise the possibility of a new class of modified RNA in which 2'-OH groups do not need to be masked.
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Affiliation(s)
- Masashi Ota
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Hiromi Takahashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Yuhei Nogi
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Yuma Kagotani
- 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
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan.
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Sarli SL, Watts JK. Harnessing nucleic acid technologies for human health on earth and in space. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:113-126. [PMID: 36336357 DOI: 10.1016/j.lssr.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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Hofmeister A, Jahn-Hofmann K, Brunner B, Helms M, Metz-Weidmann C, Krack A, Kurz M, Heubel C, Scheidler S. Small Interfering RNAs Containing Dioxane- and Morpholino-Derived Nucleotide Analogues Show Improved Off-Target Profiles and Chirality-Dependent In Vivo Knock-Down. J Med Chem 2022; 65:13736-13752. [PMID: 36223135 DOI: 10.1021/acs.jmedchem.2c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To expand the applicability of recently developed dioxane- and morpholino-based nucleotide analogues, their seed region destabilizing properties in small interfering RNAs (siRNAs) were investigated in order to improve potential off-target profiles. For this purpose, the corresponding adenosine analogues were synthesized in two diastereomeric series as building blocks for the automated oligonucleotide synthesis. The obtained nucleotide precursors were integrated at position 7 of an siRNA antisense strand, targeting transthyretin messenger RNA. Evaluation of the melting temperatures revealed significant differences in the obtained duplex stabilities between the two diastereomeric series, while the influence of the central scaffold was small. All siRNAs containing these novel nucleotide structures showed improved off-target profiles in vitro compared to their parent sequence with the common 2'-OMe-modified adenosine at the same position. In contrast, in vivo potencies were highly dependent on the chirality within the six-membered nucleotide scaffolds and showed high mRNA downregulations for the (2R,6R)-configured diastereomers.
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Affiliation(s)
- Armin Hofmeister
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Bodo Brunner
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Mike Helms
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | | | - Arne Krack
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Michael Kurz
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Christoph Heubel
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
| | - Sabine Scheidler
- Sanofi R&D, Industrial Park Hoechst, Frankfurt am Main 65926, Germany
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Chemical optimization of siRNA for safe and efficient silencing of placental sFLT1. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:135-149. [PMID: 35847173 PMCID: PMC9263991 DOI: 10.1016/j.omtn.2022.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
Preeclampsia (PE) is a rising, potentially lethal complication of pregnancy. PE is driven primarily by the overexpression of placental soluble fms-like tyrosine kinase 1 (sFLT1), a validated diagnostic and prognostic marker of the disease when normalized to placental growth factor (PlGF) levels. Injecting cholesterol-conjugated, fully modified, small interfering RNAs (siRNAs) targeting sFLT1 mRNA into pregnant mice or baboons reduces placental sFLT1 and ameliorates clinical signs of PE, providing a strong foundation for the development of a PE therapeutic. siRNA delivery, potency, and safety are dictated by conjugate chemistry, siRNA duplex structure, and chemical modification pattern. Here, we systematically evaluate these parameters and demonstrate that increasing 2'-O-methyl modifications and 5' chemical stabilization and using sequence-specific duplex asymmetry and a phosphocholine-docosanoic acid conjugate enhance placental accumulation, silencing efficiency and safety of sFLT1-targeting siRNAs. The optimization strategy here provides a framework for the chemical optimization of siRNAs for PE as well as other targets and clinical indications.
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Engineered ionizable lipid siRNA conjugates enhance endosomal escape but induce toxicity in vivo. J Control Release 2022; 349:831-843. [PMID: 35917865 DOI: 10.1016/j.jconrel.2022.07.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022]
Abstract
Lipid conjugation supports delivery of small interfering RNAs (siRNAs) to extrahepatic tissues, expanding the therapeutic potential of siRNAs beyond liver indications. However, siRNA silencing efficacy in extrahepatic tissues remains inferior to that routinely achieved in liver, partially due to the low rate of endosomal escape following siRNA internalization. Improving siRNA endosomal release into cytoplasm is crucial to improving efficacy of lipid-conjugated siRNAs. Given the ability of ionizable lipids to enhance endosomal escape in a context of lipid nanoparticles (LNP), here, we provide the first report on the effect of an ionizable lipid conjugate on siRNA endosomal escape, tissue distribution, efficacy, and toxicity in vivo. After developing a synthetic route to covalently attach the ionizable lipid, DLin-MC3-DMA, to siRNAs, we demonstrate that DLin-MC3-DMA enhances endosomal escape in cell culture without compromising siRNA efficacy. In mice, DLin-MC3-DMA conjugated siRNAs exhibit a similar overall tissue distribution profile to the similarly hydrophobic cholesterol-conjugated siRNA. However, only DLin-MC3-DMA conjugated siRNAs accumulated in vascular compartments, suggesting an effect of conjugate structure on intratissue distribution. Interestingly, we observed non-specific modulation of gene expression in tissues with high accumulation of DLin-MC3-DMA siRNAs (>20 pmol/mg of tissue) while limited non-specific gene modulation has been observed in tissues with lower siRNA accumulation. These findings suggest modulating the nature of the conjugate is a promising strategy to alter siRNA intratissue and intracellular trafficking. Fine-tuning the nature of the conjugate to optimize endosomal escape while minimizing toxicity will be critical for the progression of therapeutic siRNA applications beyond the liver.
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Luo M, Lee LKC, Peng B, Choi CHJ, Tong WY, Voelcker NH. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201740. [PMID: 35851766 PMCID: PMC9475540 DOI: 10.1002/advs.202201740] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/19/2022] [Indexed: 06/01/2023]
Abstract
Central Nervous System (CNS) diseases, such as Alzheimer's diseases (AD), Parkinson's Diseases (PD), brain tumors, Huntington's disease (HD), and stroke, still remain difficult to treat by the conventional molecular drugs. In recent years, various gene therapies have come into the spotlight as versatile therapeutics providing the potential to prevent and treat these diseases. Despite the significant progress that has undoubtedly been achieved in terms of the design and modification of genetic modulators with desired potency and minimized unwanted immune responses, the efficient and safe in vivo delivery of gene therapies still poses major translational challenges. Various non-viral nanomedicines have been recently explored to circumvent this limitation. In this review, an overview of gene therapies for CNS diseases is provided and describes recent advances in the development of nanomedicines, including their unique characteristics, chemical modifications, bioconjugations, and the specific applications that those nanomedicines are harnessed to deliver gene therapies.
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Affiliation(s)
- Meihua Luo
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Australian Institute for Bioengineering and Nanotechnologythe University of QueenslandSt LuciaQLD4072Australia
| | - Leo Kit Cheung Lee
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Bo Peng
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Frontiers Science Center for Flexible ElectronicsXi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical materials & EngineeringNorthwestern Polytechnical UniversityXi'an710072China
| | - Chung Hang Jonathan Choi
- Department of Biomedical EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong
| | - Wing Yin Tong
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutics ScienceMonash UniversityParkville Campus, 381 Royal ParadeParkvilleVIC3052Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)ClaytonVIC3168Australia
- Melbourne Centre for NanofabricationVictorian Node of the Australian National Fabrication Facility151 Wellington RoadClaytonVIC3168Australia
- Materials Science and EngineeringMonash University14 Alliance LaneClaytonVIC3800Australia
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39
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Duan C, Townley H. Exploitation of High Tumour GSH Levels for Targeted siRNA Delivery in Rhabdomyosarcoma Cells. Biomolecules 2022; 12:biom12081129. [PMID: 36009022 PMCID: PMC9405954 DOI: 10.3390/biom12081129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Metastatic alveolar rhabdomyosarcoma (aRMS) is an aggressive paediatric cancer with a poor prognosis. Downregulation of critical tumour genes using targeted siRNA remains an obstacle, but association with nanoparticles could help to deliver, protect, target, and enhance penetration. siRNA towards two genes was investigated: (i) Human αB-crystallin (CRYAB) and Heat Shock Protein Family B (Small) Member 2 (HSPB2), and (ii) Keratin 17 (KRT17). A mesoporous silica based nanosystem was linked to siRNA via disulfide bonds and loaded with IR820 dye. Transfection efficiency and signalling was evaluated, and the metabolic effects and cell proliferation were monitored in 2D culture and 3D spheroid models. The bound siRNA was protected from degradation with RNase I for at least 24 h. The delivered siRNA showed significant suppression of viability; 53.21 ± 23.40% for CRYAB and HSPB2 siRNA, and 88.06 ± 17.28% for KRT17 siRNA. After 72 h this increased to >50% cell apoptosis and necrosis. Intracellular total glutathione (GSH) levels were also compared with fibroblasts, and the RMS cell lines showed a several-fold increase. IR820 cellular uptake rate and penetration depth was significantly improved by nanoparticle delivery. Targetted siRNA delivery may pave the way for less invasive and more effective treatments of aRMS.
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Affiliation(s)
- Chengchen Duan
- Nuffield Department of Women’s and Reproductive Health, Oxford University John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Helen Townley
- Nuffield Department of Women’s and Reproductive Health, Oxford University John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
- Department of Engineering Science, Oxford University, Parks Road, Oxford OX1 3PJ, UK
- Correspondence: ; Tel.: +44-1865-283792
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40
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Kajino R, Sakamoto S, Ueno Y. Synthesis, gene silencing activity, thermal stability, and serum stability of siRNA containing four ( S)-5'- C-aminopropyl-2'- O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). RSC Adv 2022; 12:11454-11476. [PMID: 35425057 PMCID: PMC9002251 DOI: 10.1039/d2ra00705c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Herein, we report the synthesis of (S)-5'-C-aminopropyl-2'-O-methyladenosine and (S)-5'-C-aminopropyl-2'-O-methylguanosine phosphoramidites and the properties of small interfering RNAs (siRNAs) containing four (S)-5'-C-aminopropyl-2'-O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). The siRNAs containing (S)-5'-C-aminopropyl-nucleosides at the 3'- and 5'-regions of the passenger strand were well tolerated for RNA interference (RNAi) activity. Conversely, the (S)-5'-C-aminopropyl modification in the central region of the passenger strand decreased the RNAi activity. Furthermore, the siRNAs containing three or four consecutive (S)-5'-C-aminopropyl-2'-O-methylnucleosides at the 3'- and 5'-regions of the passenger strand exhibited RNAi activity similar to that of the corresponding 2'-O-methyl-modified siRNAs. Finally, it was observed that (S)-5'-C-aminopropyl modifications effectively improved the serum stability of the siRNAs, compared with 2'-O-methyl modifications. Therefore, (S)-5'-C-aminopropyl-2'-O-methylnucleosides would be useful for improving the serum stability of therapeutic siRNA molecules without affecting their RNAi activities.
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Affiliation(s)
- Ryohei Kajino
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Shuichi Sakamoto
- Institute of Microbial Chemistry (BIKAKEN) Numazu Branch, Microbial Chemistry Research Foundation 18-24 Miyamoto Numazu Shizuoka 410-0301 Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Department of Life Science and Chemistry, The Graduate School of Natural Science and Technology, Gifu University Japan
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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41
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Pal S, Chandra G, Patel S, Singh S. Fluorinated Nucleosides: Synthesis, Modulation in Conformation and Therapeutic Application. CHEM REC 2022; 22:e202100335. [PMID: 35253973 DOI: 10.1002/tcr.202100335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Indexed: 12/17/2022]
Abstract
Over the last twenty years, fluorination on nucleoside has established itself as the most promising tool to use to get biologically active compounds that could sustain the clinical trial by affecting the pharmacodynamics and pharmacokinetic properties. Due to fluorine's inherent unique properties and its judicious introduction into the molecule, makes the corresponding nucleoside metabolically very stable, lipophilic, and opens a new site of intermolecular binding. Fluorination on various nucleosides has been extensively studied as a result, a series of fluorinated nucleosides come up for different therapeutic uses which are either approved by the FDA or under the advanced stage of the clinical trial. Here in this review, we are summarizing the latest development in the chemistry of fluorination on nucleoside that led to varieties of new analogs like carbocyclic, acyclic, and conformationally biased nucleoside and their biological properties, the influence of fluorine on conformation, oligonucleotide stability, and their use in therapeutics.
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Affiliation(s)
- Shantanu Pal
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
| | - Girish Chandra
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Samridhi Patel
- Department of Chemistry, School of Physical and Chemical Sciences, Central University of South Bihar, SH-7, Gaya Panchanpur Road, Gaya, Bihar, India, 824236
| | - Sakshi Singh
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar Argul, Odisha, India, 752050
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42
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Li Z, Wang X, Zhou X, Wang J, Guan Z, Yang Z. Optimization in Chemical Modification of Single-Stranded siRNA Encapsulated by Neutral Cytidinyl/Cationic Lipids. Front Chem 2022; 10:843181. [PMID: 35345539 PMCID: PMC8957067 DOI: 10.3389/fchem.2022.843181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Single-stranded siRNA (ss-siRNA) refers to the antisense strand of siRNA, which plays the role of gene silencing. Since single-stranded RNA is unstable, the present study employed a homemade neutral cytidinyl/cationic lipid delivery system and chemical modifications to improve its stability. The results showed that with the aid of mixed lipids, ss-siRNA could knock down 40% of target mRNA at 25 nM. With 2ʹ-F/2ʹ-OMe, phosphorothioate and 5ʹ-terminal phosphorylation, the optimized ss-siRNA could knock down 80% of target mRNA at 25 nM. Further knocking down AGO2, the ss-siRNAs could not effectively silence target mRNAs. Analysis of the biodistribution in vivo showed that ss-siRNA was less durable than siRNA, but spread more quickly to tissues. This study provides a safe and efficient ss-siRNA delivery and modification strategy, which lays the foundation for future works.
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43
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Yenilmez B, Wetoska N, Kelly M, Echeverria D, Min K, Lifshitz L, Alterman JF, Hassler MR, Hildebrand S, DiMarzio C, McHugh N, Vangjeli L, Sousa J, Pan M, Han X, Brehm MA, Khvorova A, Czech MP. An RNAi therapeutic targeting hepatic DGAT2 in a genetically obese mouse model of nonalcoholic steatohepatitis. Mol Ther 2022; 30:1329-1342. [PMID: 34774753 PMCID: PMC8899521 DOI: 10.1016/j.ymthe.2021.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is a severe liver disorder characterized by triglyceride accumulation, severe inflammation, and fibrosis. With the recent increase in prevalence, NASH is now the leading cause of liver transplant, with no approved therapeutics available. Although the exact molecular mechanism of NASH progression is not well understood, a widely held hypothesis is that fat accumulation is the primary driver of the disease. Therefore, diacylglycerol O-acyltransferase 2 (DGAT2), a key enzyme in triglyceride synthesis, has been explored as a NASH target. RNAi-based therapeutics is revolutionizing the treatment of liver diseases, with recent chemical advances supporting long-term gene silencing with single subcutaneous administration. Here, we identified a hyper-functional, fully chemically stabilized GalNAc-conjugated small interfering RNA (siRNA) targeting DGAT2 (Dgat2-1473) that, upon injection, elicits up to 3 months of DGAT2 silencing (>80%-90%, p < 0.0001) in wild-type and NSG-PiZ "humanized" mice. Using an obesity-driven mouse model of NASH (ob/ob-GAN), Dgat2-1473 administration prevents and reverses triglyceride accumulation (>85%, p < 0.0001) without increased accumulation of diglycerides, resulting in significant improvement of the fatty liver phenotype. However, surprisingly, the reduction in liver fat did not translate into a similar impact on inflammation and fibrosis. Thus, while Dgat2-1473 is a practical, long-lasting silencing agent for potential therapeutic attenuation of liver steatosis, combinatorial targeting of a second pathway may be necessary for therapeutic efficacy against NASH.
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Affiliation(s)
- Batuhan Yenilmez
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Nicole Wetoska
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Mark Kelly
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Dimas Echeverria
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Kyounghee Min
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Lawrence Lifshitz
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Julia F Alterman
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Matthew R Hassler
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samuel Hildebrand
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chloe DiMarzio
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Nicholas McHugh
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Lorenc Vangjeli
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Jacquelyn Sousa
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Meixia Pan
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Xianlin Han
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Michael P Czech
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street Biotech Two, Suite 100, Worcester, MA 01605, USA.
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44
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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45
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Harumoto T, Iwai H, Tanigawa M, Kubo T, Atsumi T, Tsutsumi K, Takashima M, Destito G, Soloff R, Tomizuka K, Nycholat C, Paulson J, Uehara K. Enhancement of Gene Knockdown on CD22-Expressing Cells by Chemically Modified Glycan Ligand-siRNA Conjugates. ACS Chem Biol 2022; 17:292-298. [PMID: 35020348 DOI: 10.1021/acschembio.1c00652] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Extrahepatic targeted delivery of oligonucleotides, such as small interfering RNA (siRNA) and antisense oligonucleotides (ASOs), is an attractive technology for the development of nucleic acid-based medicines. To target CD22-expressing B cells, several drug platforms have shown promise, including antibodies, antibody-drug conjugates, and nanoparticles, but to date CD22-targeted delivery of oligonucleotide therapeutics has not been reported. Here we report the uptake and enhancement of siRNA gene expression knockdown in CD22-expressing B cells using a chemically stabilized and modified CD22 glycan ligand-conjugated siRNA. This finding has the potential to broaden the use of siRNA technology, opening up novel therapeutic opportunities, and presents an innovative approach for targeted delivery of siRNAs to B cell lymphomas.
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Affiliation(s)
- Toshimasa Harumoto
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hiroto Iwai
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Mari Tanigawa
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Toshiko Kubo
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Toshiyuki Atsumi
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kyoko Tsutsumi
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Michio Takashima
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Giuseppe Destito
- Kyowa Kirin Inc., 9420 Athena Circle, La Jolla, California 92037, United States
| | - Rachel Soloff
- Kyowa Kirin Inc., 9420 Athena Circle, La Jolla, California 92037, United States
| | - Kazuma Tomizuka
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Corwin Nycholat
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Paulson
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Keiji Uehara
- Research Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi Financial City Grand Cube, 1-9-2 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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46
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Hui RWH, Mak LY, Seto WK, Yuen MF. RNA interference as a novel treatment strategy for chronic hepatitis B infection. Clin Mol Hepatol 2022; 28:408-424. [PMID: 35172540 PMCID: PMC9293617 DOI: 10.3350/cmh.2022.0012] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Chronic hepatitis B (CHB) is a major cause of liver-related morbidity and mortality. Functional cure of CHB, defined as sustainable hepatitis B surface antigen (HBsAg) seroclearance, is associated with improved clinical outcomes. However, functional cure is rarely attainable by current treatment modalities. RNA interference (RNAi) by small-interfering RNA (siRNA) and anti-sense oligonucleotide (ASO) has been studied as a novel treatment strategy for CHB. RNAi targets post-transcriptional messenger RNAs and pregenomic RNAs to reduce hepatitis B virus (HBV) antigen production and viral replication. By reducing viral antigens, host immune reconstitution against HBV may also be attained. Phase I/II trials on siRNAs have demonstrated them to be safe and well-tolerated. siRNA is effective when given in monthly doses with different total number of doses according to different trial design, and can lead to sustainable dose-dependent mean HBsAg reduction by 2–2.5 log. Incidences of HBsAg seroclearance after siRNA therapy have also been reported. ASOs have also been studied in early phase trials, and a phase Ib study using frequent dosing regimen within 4 weeks could achieve similar HBsAg reduction of 2 log from baseline. Given the established efficacy and safety of nucleos(t) ide analogues (NAs), future RNAi regimens will likely include NA backbone. While the current evidence on RNAi appears promising, it remains undetermined whether the potent HBsAg reduction by RNAi can result in a high rate of HBsAg seroclearance with durability. Data on RNAi from phase IIb/III trials are keenly anticipated.
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Affiliation(s)
- Rex Wan-Hin Hui
- Department of Medicine, The University of Hong Kong, Hong Kong
| | - Lung-Yi Mak
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Wai-Kay Seto
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Man-Fung Yuen
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
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47
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Holm A, Hansen SN, Klitgaard H, Kauppinen S. Clinical advances of RNA therapeutics for treatment of neurological and neuromuscular diseases. RNA Biol 2021; 19:594-608. [PMID: 35482908 PMCID: PMC9067473 DOI: 10.1080/15476286.2022.2066334] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
RNA therapeutics comprise a diverse group of oligonucleotide-based drugs such as antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), and short hairpin RNAs (shRNAs) that can be designed to selectively interact with drug targets currently undruggable with small molecule-based drugs or monoclonal antibodies. Furthermore, RNA-based therapeutics have the potential to modulate entire disease pathways, and thereby represent a new modality with unprecedented potential for generating disease-modifying drugs for a wide variety of human diseases, including central nervous system (CNS) disorders. Here, we describe different strategies for delivering RNA drugs to the CNS and review recent advances in clinical development of ASO drugs and siRNA-based therapeutics for the treatment of neurological diseases and neuromuscular disorders.Abbreviations 2'-MOE: 2'-O-(2-methoxyethyl); 2'-O-Me: 2'-O-methyl; 2'-F: 2'-fluoro; AD: Alzheimer's disease; ALS: Amyotrophic lateral sclerosis; ALSFRS-R: Revised Amyotrophic Lateral Sclerosis Functional Rating Scale; ARC: Antibody siRNA Conjugate; AS: Angelman Syndrome; ASGRP: Asialoglycoprotein receptor; ASO: Antisense oligonucleotide; AxD: Alexander Disease; BBB: Blood brain barrier; Bp: Basepair; CNM: Centronuclear myopathies; CNS: Central Nervous System; CPP: Cell-penetrating Peptide; CSF: Cerebrospinal fluid; DMD: Duchenne muscular dystrophy; DNA: Deoxyribonucleic acid; FAP: Familial amyloid polyneuropathy; FALS: Familial amyotrophic lateral sclerosis; FDA: The United States Food and Drug Administration; GalNAc: N-acetylgalactosamine; GoF: Gain of function; hATTR: Hereditary transthyretin amyloidosis; HD: Huntington's disease; HRQOL: health-related quality of life; ICV: Intracerebroventricular; IT: Intrathecal; LNA: Locked nucleic acid; LoF: Loss of function; mRNA: Messenger RNA; MS: Multiple Sclerosis; MSA: Multiple System Atrophy; NBE: New Biological Entity; NCE: New Chemical Entity; NHP: Nonhuman primate; nt: Nucleotide; PD: Parkinson's disease; PNP: Polyneuropathy; PNS: Peripheral nervous system; PS: Phosphorothioate; RISC: RNA-Induced Silencing Complex; RNA: Ribonucleic acid; RNAi: RNA interference; s.c.: Subcutaneous; siRNA: Small interfering RNA; SMA: Spinal muscular atrophy; SMN: Survival motor neuron; TTR: Transthyretin.
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Affiliation(s)
- Anja Holm
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15, 2450Copenhagen, Denmark
| | - Stine N. Hansen
- Neumirna Therapeutics, A.C. Meyers Vænge 15, 2450Copenhagen, Denmark
| | - Henrik Klitgaard
- Neumirna Therapeutics, A.C. Meyers Vænge 15, 2450Copenhagen, Denmark
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15, 2450Copenhagen, Denmark
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48
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Yamada K, Hildebrand S, Davis SM, Miller R, Conroy F, Sapp E, Caiazzi J, Alterman JF, Roux L, Echeverria D, Hassler MR, Pfister EL, DiFiglia M, Aronin N, Khvorova A. Structurally constrained phosphonate internucleotide linkage impacts oligonucleotide-enzyme interaction, and modulates siRNA activity and allele specificity. Nucleic Acids Res 2021; 49:12069-12088. [PMID: 34850120 PMCID: PMC8643693 DOI: 10.1093/nar/gkab1126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/09/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Oligonucleotides is an emerging class of chemically-distinct therapeutic modalities, where extensive chemical modifications are fundamental for their clinical applications. Inter-nucleotide backbones are critical to the behaviour of therapeutic oligonucleotides, but clinically explored backbone analogues are, effectively, limited to phosphorothioates. Here, we describe the synthesis and bio-functional characterization of an internucleotide (E)-vinylphosphonate (iE-VP) backbone, where bridging oxygen is substituted with carbon in a locked stereo-conformation. After optimizing synthetic pathways for iE-VP-linked dimer phosphoramidites in different sugar contexts, we systematically evaluated the impact of the iE-VP backbone on oligonucleotide interactions with a variety of cellular proteins. Furthermore, we systematically evaluated the impact of iE-VP on RNA-Induced Silencing Complex (RISC) activity, where backbone stereo-constraining has profound position-specific effects. Using Huntingtin (HTT) gene causative of Huntington's disease as an example, iE-VP at position 6 significantly enhanced the single mismatch discrimination ability of the RISC without negative impact on silencing of targeting wild type htt gene. These findings suggest that the iE-VP backbone can be used to modulate the activity and specificity of RISC. Our study provides (i) a new chemical tool to alter oligonucleotide-enzyme interactions and metabolic stability, (ii) insight into RISC dynamics and (iii) a new strategy for highly selective SNP-discriminating siRNAs.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Faith Conroy
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Edith L Pfister
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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49
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Yamada Y. Nucleic Acid Drugs-Current Status, Issues, and Expectations for Exosomes. Cancers (Basel) 2021; 13:cancers13195002. [PMID: 34638486 PMCID: PMC8508492 DOI: 10.3390/cancers13195002] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Nucleic acid drugs provide novel therapeutic modalities with characteristics that differ from those of small molecules and antibodies. In this review, I focus on the various mechanisms through which nucleic acid drugs act on, the status of their clinical development, and discuss several hurdles that need to be surmounted. In addition, by listing examples of how the progress in exosome biology can lead to the solution of problems in nucleic acid drug therapy, I hope that many more nucleic acid drugs including anticancer drugs will be developed in the future. Abstract Nucleic acid drugs are being developed as novel therapeutic modalities. They have great potential to treat human diseases such as cancers, viral infections, and genetic disorders due to unique characteristics that make it possible to approach undruggable targets using classical small molecule or protein/antibody-based biologics. In this review, I describe the advantages, classification, and clinical status of nucleic acid therapeutics. To date, more than 10 products have been launched, and many products have been tested in clinics. To promote the use of nucleic acid therapeutics such as antibodies, several hurdles need to be surmounted. The most important issue is the delivery of nucleic acids and several other challenges have been reported. Recent advanced delivery platforms are lipid nanoparticles and ligand conjugation approaches. With the progress of exosome biology, exosomes are expected to contribute to the solution of various problems associated with nucleic acid drugs.
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Affiliation(s)
- Yoji Yamada
- Research Management Office, Research Unit, R&D Division, Kyowa Kirin Co. Ltd., 1-9-2, Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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50
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Hunter WB, Wintermantel WM. Optimizing Efficient RNAi-Mediated Control of Hemipteran Pests (Psyllids, Leafhoppers, Whitefly): Modified Pyrimidines in dsRNA Triggers. PLANTS 2021; 10:plants10091782. [PMID: 34579315 PMCID: PMC8472347 DOI: 10.3390/plants10091782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
The advantages from exogenously applied RNAi biopesticides have yet to be realized in through commercialization due to inconsistent activity of the dsRNA trigger, and the activity level of RNAi suppression. This has prompted research on improving delivery methods for applying exogenous dsRNA into plants and insects for the management of pests and pathogens. Another aspect to improve RNAi activity is the incorporation of modified 2′-F pyrimidine nucleotides into the dsRNA trigger. Modified dsRNA incorporating 32–55% of the 2′-F- nucleotides produced improved RNAi activity that increased insect mortality by 12–35% greater than non-modified dsRNA triggers of the same sequence. These results were repeatable across multiple Hemiptera: the Asian citrus psyllid (Diaphorina citri, Liviidae); whitefly (Bemisia tabaci, Aleyroididae); and the glassy-winged sharpshooter (Homalodisca vitripennis, Cicadellidae). Studies using siRNA with modified 2′-F- pyrimidines in mammalian cells show they improved resistance to degradation from nucleases, plus result in greater RNAi activity, due to increase concentrations and improved binding affinity to the mRNA target. Successful RNAi biopesticides of the future will be able to increase RNAi repeatability in the field, by incorporating modifications of the dsRNA, such as 2′-F- pyrimidines, that will improve delivery after applied to fruit trees or crop plants, with increased activity after ingestion by insects. Costs of RNA modification have decreased significantly over the past few years such that biopesticides can now compete on pricing with commercial chemical products.
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Affiliation(s)
- Wayne Brian Hunter
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Subtropical Insects Res., Fort Pierce, FL 34945, USA
- Correspondence:
| | - William M. Wintermantel
- U.S. Department of Agriculture, Agriculture Research Service, Crop Improvement and Protection Research, Salinas, CA 93905, USA;
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