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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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2
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Mathur A, Singh A, Hussain Y, Mishra A, Meena A, Mishra N, Luqman S. Regulating pri/pre-microRNA up/down expressed in cancer proliferation, angiogenesis and metastasis using selected potent triterpenoids. Int J Biol Macromol 2024; 257:127945. [PMID: 37951434 DOI: 10.1016/j.ijbiomac.2023.127945] [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: 09/14/2023] [Revised: 10/17/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
MicroRNAs (miRNAs) play a crucial role in cancer progression by selectively inducing translational degradation of messenger RNA (mRNA) via sequence-specific interactions with the 3'-untranslated region (3'-UTR). The potential targeting of miRNA has been recognized as a significant avenue for investigating the biological progression of diverse cancer types. Consequently, targeting of pri-miRNA and pre-miRNA by phytochemicals emerges as a viable strategy in the realm of anticancer therapies. Among phytochemicals, triterpenoids have garnered significant recognition for their chemotherapeutic and chemopreventive capabilities in combating multiple cancers. To date, there is a dearth of literature about the molecular interactions between triterpenoids and miRNAs. The primary objective of this investigation is to discern the potential triterpenoids that can function as modulators for specific miRNAs, namely pri-miRNA-19b-2, pre-miR21, microRNA 20b, pri-miRNA-208a, pri-miRNA-378a, pri-miRNA-320b-2, and pri-miRNA-300, achieved through the use of in silico investigations. The study primarily focused on performing drug-likeness, computer-aided toxicity, and pharmacokinetic prediction studies for triterpenoids. Furthermore, molecular docking and simulation techniques were employed to investigate these compounds. The triterpenoids studied were shown to have drug-likeness characteristics, although asiatic acid, lupeol, and pristimerin were able to pass all toxicity tests. Among the triterpenoids that underwent docking, pristimerin had a significant binding energy of -10.9 kcal/mol during its interaction with pri-miR-378a. The stable interaction between the pristimerin and miRNA complex was demonstrated by molecular dynamics simulation. As a result, pristimerin has the potential to act as a modulator of carcinogenic miRNAs, making it a promising candidate for cancer prevention and treatment due to its tailored modulation of miRNA activity.
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Affiliation(s)
- Anurag Mathur
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Akanksha Singh
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Yusuf Hussain
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anamika Mishra
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj 211012, Uttar Pradesh, India
| | - Abha Meena
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Nidhi Mishra
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj 211012, Uttar Pradesh, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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3
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Singh H. Role of gene therapy in treatment of cancer with craniofacial regeneration-current molecular strategies, future perspectives, and challenges: a narrative review. JOURNAL OF YEUNGNAM MEDICAL SCIENCE 2024; 41:13-21. [PMID: 37218144 PMCID: PMC10834268 DOI: 10.12701/jyms.2023.00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/30/2023] [Indexed: 05/24/2023]
Abstract
Gene therapy involves the introduction of foreign genetic material into host tissue to alter the expression of genetic products. Gene therapy represents an opportunity to alter the course of various diseases. Hence, genetic products utilizing safe and reliable vectors with improved biotechnology will play a critical role in the treatment of various diseases in the future. This review summarizes various important vectors for gene therapy along with modern techniques for potential craniofacial regeneration using gene therapy. This review also explains current molecular approaches for the management and treatment of cancer using gene therapy. The existing literature was searched to find studies related to gene therapy and its role in craniofacial regeneration and cancer treatment. Various databases such as PubMed, Science Direct, Scopus, Web of Science, and Google Scholar were searched for English language articles using the keywords "gene therapy," "gene therapy in present scenario," "gene therapy in cancer," "gene therapy and vector," "gene therapy in diseases," and "gene therapy and molecular strategies."
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Affiliation(s)
- Himanshu Singh
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, Index Institute of Dental Sciences, Indore, India
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4
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Balachandran AA, Raguraman P, Rahimizadeh K, Veedu RN. Splice-Switching Antisense Oligonucleotides Targeting Extra- and Intracellular Domains of Epidermal Growth Factor Receptor in Cancer Cells. Biomedicines 2023; 11:3299. [PMID: 38137520 PMCID: PMC10741442 DOI: 10.3390/biomedicines11123299] [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: 10/27/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cancer is one of the leading causes of death globally. Epidermal growth factor receptor is one of the proteins involved in cancer cell proliferation, differentiation, and invasion. Antisense oligonucleotides are chemical nucleic acids that bind to target messenger ribonucleic acid and modulate its expression. Herein, we demonstrate the efficacy of splice-modulating antisense oligonucleotides to target specific exons in the extracellular (exon 3) and intracellular (exon 18, 21) domains of epidermal growth factor receptor. These antisense oligonucleotides were synthesized as 25mer 2'-O methyl phosphorothioate-modified ribonucleic acids that bind to complementary specific regions in respective exons. We found that PNAT524, PNAT525, PNAT576, and PNAT578 effectively skipped exon 3, exon 18, and exon 21 in glioblastoma, liver cancer, and breast cancer cell lines. PNAT578 treatment also skipped partial exon 19, complete exon 20, and partial exon 21 in addition to complete exon 21 skipping. We also found that a cocktail of PNAT576 and PNAT578 antisense oligonucleotides performed better than their individual counterparts. The migration potential of glioblastoma cancer cells was reduced to a greater extent after treatment with these antisense oligonucleotides. We firmly believe that using these splice-modulating antisense oligonucleotides in combination with existing EGFR-targeted therapies could improve therapeutic outcomes.
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Affiliation(s)
- Akilandeswari Ashwini Balachandran
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
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5
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Malfanti A, Sami H, Balasso A, Marostica G, Arpac B, Mastrotto F, Mantovani G, Cola E, Anton M, Caliceti P, Ogris M, Salmaso S. Control of cell penetration enhancer shielding and endosomal escape-kinetics crucial for efficient and biocompatible siRNA delivery. J Control Release 2023; 363:101-113. [PMID: 37722420 DOI: 10.1016/j.jconrel.2023.09.022] [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: 03/16/2023] [Revised: 07/21/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Although cationic liposomes are efficient carriers for nucleic acid delivery, their toxicity often hampers the clinical translation. Polyethylene glycol (PEG) coating has been largely used to improve their stability and reduce toxicity. Nevertheless, it has been found to decrease the transfection process. In order to exploit the advantages of cationic liposomes and PEG decoration for nucleic acid delivery, liposomes decorated with tetraArg-[G-1]-distearoyl glycerol (Arg4-DAG) dendronic oligo-cationic lipid enhancer (OCE) and PEG-lipid have been investigated. Non decorated or OCE-decorated lipoplexes (OCEfree-LPX and OCE-LPX, respectively) were obtained by lipid film hydration using oligonucleotide (ON) solutions. PEG and OCE/PEG decorated lipoplexes (PEG-OCEfree-LPX and PEG-OCE-LPX, respectively) were obtained by post-insertion of 2 or 5 kDa PEG-DSPE on preformed lipoplexes. The OCE decoration yielded lipoplexes with size of about 240 nm, 84% loading efficiency at 10 N/P ratio, ten times higher than OCEfree-LPX, and prevented the ON release when incubated with physiological heparin concentration or with plasma. The PEG decoration reduced the zeta potential, enhanced the lipoplex stability in serum and decreased both hemolysis and cytotoxicity, while it did not affect the lipoplex size and ON loading. With respect to OCEfree-LPX, the OCE-LPX remarkably associated with cells and were taken up by different cancer cell lines (HeLa and MDA-MB-231). Interestingly, 2 or 5 kDa PEG decoration did not reduce either the cell interaction or the cell up-take of the cationic lipoplexes. With siRNA as a payload, OCE enabled efficient internalization, but endosomal release was hampered. Post-transfection treatment with the lysosomotropic drug chloroquine allowed to identify the optimal time point for endosomal escape. Chloroquine treatment after 12 to 20 h of LPX pre-incubation enabled siRNA mediated target knockdown indicating that this is the time window of endo-lysosomal processing. This indicates that OCE can protect siRNA from lysosomal degradation for up to 20 h, as shown by these rescue experiments.
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Affiliation(s)
- Alessio Malfanti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy
| | - Haider Sami
- University of Vienna, Faculty of Life Sciences, Department of Pharmaceutical Sciences, Laboratory of Macromolecular Cancer Therapeutics (MMCT), Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Anna Balasso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy
| | - Giulia Marostica
- University of Vienna, Faculty of Life Sciences, Department of Pharmaceutical Sciences, Laboratory of Macromolecular Cancer Therapeutics (MMCT), Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Busra Arpac
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy
| | | | - Elisa Cola
- University of Vienna, Faculty of Life Sciences, Department of Pharmaceutical Sciences, Laboratory of Macromolecular Cancer Therapeutics (MMCT), Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Martina Anton
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Paolo Caliceti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy
| | - Manfred Ogris
- University of Vienna, Faculty of Life Sciences, Department of Pharmaceutical Sciences, Laboratory of Macromolecular Cancer Therapeutics (MMCT), Josef-Holaubek-Platz 2, Vienna 1090, Austria.
| | - Stefano Salmaso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, Padova 35131, Italy.
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6
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Hannauer F, Black R, Ray AD, Stulz E, Langley GJ, Holman SW. Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9596. [PMID: 37580500 PMCID: PMC10909466 DOI: 10.1002/rcm.9596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 08/16/2023]
Abstract
The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.
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Affiliation(s)
- Fabien Hannauer
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Rachelle Black
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Andrew D. Ray
- New Modalities & Parenteral Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
| | - Eugen Stulz
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - G. John Langley
- Chemistry, Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonUK
| | - Stephen W. Holman
- Chemical Development, Pharmaceutical Technology & Development, OperationsAstraZenecaMacclesfieldUK
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Ajeeb R, Clegg JR. Intrathecal delivery of Macromolecules: Clinical status and emerging technologies. Adv Drug Deliv Rev 2023; 199:114949. [PMID: 37286086 DOI: 10.1016/j.addr.2023.114949] [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: 01/30/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
The proximity and association of cerebrospinal fluid (CSF) and the intrathecal (IT) space with deep targets in the central nervous system (CNS) parenchyma makes IT injection an attractive route of administration for brain drug delivery. However, the extent to which intrathecally administered macromolecules are effective in treating neurological diseases is a question of both clinical debate and technological interest. We present the biological, chemical, and physical properties of the intrathecal space that are relevant to drug absorption, distribution, metabolism, and elimination from CSF. We then analyze the evolution of IT drug delivery in clinical trials over the last 20 years. Our analysis revealed that the percentage of clinical trials assessing IT delivery for the delivery of biologics (i.e., macromolecules, cells) for treatment of chronic conditions (e.g., neurodegeneration, cancer, and metabolic diseases) has steadily increased. Clinical trials exploring cell or macromolecular delivery within the IT space have not evaluated engineering technologies, such as depots, particles, or other delivery systems. Recent pre-clinical studies have evaluated IT macromolecule delivery in small animals, postulating that delivery efficacy can be assisted by external medical devices, micro- or nanoparticles, bulk biomaterials, and viral vectors. Further studies are necessary to evaluate the extent to which engineering technologies and IT administration improve CNS targeting and therapeutic outcome.
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Affiliation(s)
- Rana Ajeeb
- Stephenson School of Biomedical Engineering, The University of Oklahoma, Norman, OK, United States
| | - John R Clegg
- Stephenson School of Biomedical Engineering, The University of Oklahoma, Norman, OK, United States; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States; Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States; Institute for Biomedical Engineering, Science, and Technology, University of Oklahoma, Norman, OK, United States.
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8
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Uchida S, Lau CYJ, Oba M, Miyata K. Polyplex designs for improving the stability and safety of RNA therapeutics. Adv Drug Deliv Rev 2023; 199:114972. [PMID: 37364611 DOI: 10.1016/j.addr.2023.114972] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Nanoparticle-based delivery systems have contributed to the recent clinical success of RNA therapeutics, including siRNA and mRNA. RNA delivery using polymers has several distinct properties, such as enabling RNA delivery into extra-hepatic organs, modulation of immune responses to RNA, and regulation of intracellular RNA release. However, delivery systems should overcome safety and stability issues to achieve widespread therapeutic applications. Safety concerns include direct damage to cellular components, innate and adaptive immune responses, complement activation, and interaction with surrounding molecules and cells in the blood circulation. The stability of the delivery systems should balance extracellular RNA protection and controlled intracellular RNA release, which requires optimization for each RNA species. Further, polymer designs for improving safety and stability often conflict with each other. This review covers advances in polymer-based approaches to address these issues over several years, focusing on biological understanding and design concepts for delivery systems rather than material chemistry.
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Affiliation(s)
- Satoshi Uchida
- Department of Advanced Nanomedical Engineering, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan; Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
| | - Chun Yin Jerry Lau
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Oba
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Senthilvelan A, Shanmugasundaram M, Kore AR. Protocols for Efficient Chemical Synthesis of N 2 -Modified Guanosine Phosphate Derivatives: Versatile Probes for mRNA Labeling. Curr Protoc 2023; 3:e863. [PMID: 37639626 DOI: 10.1002/cpz1.863] [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: 08/31/2023]
Abstract
A facile, reliable, and efficient method for the synthesis of N2 -modified guanosine nucleotides such as N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-monophosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-diphosphate, N2 -[benzyl-N-(propyl)carbamate]-guanosine-5'-O-triphosphate, and N2 -[benzyl-N-(propyl)carbamate]-N7 -methyl-guanosine-5'-O-diphosphate, starting from the corresponding nucleotide is described. The general process entails condensation between the exocyclic amine of guanosine nucleotide and 3-[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2 -modified guanosine nucleotide in moderate yield with high purity (>99.5%). © 2023 Wiley Periodicals LLC. Basic Protocol: Synthesis of N2 -modified guanosine derivatives.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences and Laboratory Products Group, Thermo Fisher Scientific, Austin, Texas
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10
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Zhu A, Chiba S, Shimizu Y, Kunitake K, Okuno Y, Aoki Y, Yokota T. Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping. Pharmaceutics 2023; 15:1808. [PMID: 37513994 PMCID: PMC10384346 DOI: 10.3390/pharmaceutics15071808] [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: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine-learning-based computational methods, such as eSkip-Finder, have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce the computational burden and improve the prediction performance by using feature selection within machine-learning algorithms and ensemble-learning techniques. We evaluated our approach using a dataset of experimentally validated exon-skipping events, dividing it into training and testing sets. Our results demonstrate that using a three-way-voting approach with random forest, gradient boosting, and XGBoost can significantly reduce the computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2'-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.
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Affiliation(s)
- Alex Zhu
- Phillips Academy, Andover, MA 01810, USA
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shuntaro Chiba
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Yuki Shimizu
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Yasushi Okuno
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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11
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Annamalai S, Muthian S, Kore AR. Efficient chemical synthesis of N2-modified guanosine derivatives: a versatile probes for mRNA labeling. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:867-876. [PMID: 37211782 DOI: 10.1080/15257770.2023.2215828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/23/2023]
Abstract
An efficient method for the synthesis of N2-modified guanosine nucleotides such as N2-[benzyl-N-(propyl)carbamate]-guanosine-5'-O-monophosphate, N2-[benzyl-N-(propyl)carbamate]-guanosine-5'-O-diphosphate, N2-[benzyl-N-(propyl)carbamate]-guanosine-5'-O-triphosphate, and N2-[benzyl-N-(propyl)carbamate]-N7-methyl-guanosine-5'-O-diphosphate, starting from the corresponding nucleotide is described. The overall reaction involves the condensation between the exocyclic amine of guanosine nucleotide with 3-[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2-modified guanosine nucleotide in moderate yield with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences and Laboratory Product Group, Thermo Fisher Scientific, Austin, TX, USA
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12
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Sen P, Ghosh SS. The Intricate Notch Signaling Dynamics in Therapeutic Realms of Cancer. ACS Pharmacol Transl Sci 2023; 6:651-670. [PMID: 37200816 PMCID: PMC10186364 DOI: 10.1021/acsptsci.2c00239] [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: 11/29/2022] [Indexed: 05/20/2023]
Abstract
The Notch pathway is remarkably simple without the interventions of secondary messengers. It possesses a unique receptor-ligand interaction that imparts signaling upon cleavage of the receptor followed by the nuclear localization of its cleaved intracellular domain. It is found that the transcriptional regulator of the Notch pathway lies at the intersection of multiple signaling pathways that enhance the aggressiveness of cancer. The preclinical and clinical evidence supports the pro-oncogenic function of Notch signaling in various tumor subtypes. Owing to its oncogenic role, the Notch signaling pathway assists in enhanced tumorigenesis by facilitating angiogenesis, drug resistance, epithelial to mesenchymal transition, etc., which is also attributed to the poor outcome in patients. Therefore, it is extremely vital to discover a suitable inhibitor to downregulate the signal-transducing ability of Notch. The Notch inhibitory agents, such as receptor decoys, protease (ADAM and γ-secretase) inhibitors, and monoclonal/bispecific antibodies, are being investigated as candidate therapeutic agents. Studies conducted by our group exemplify the promising results in ablating tumorigenic aggressiveness by inhibiting the constituents of the Notch pathway. This review deals with the detailed mechanism of the Notch pathways and their implications in various malignancies. It also bestows us with the recent therapeutic advances concerning Notch signaling in the context of monotherapy and combination therapy.
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Affiliation(s)
- Plaboni Sen
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Siddhartha Sankar Ghosh
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, Assam, India
- Centre
for Nanotechnology, Indian Institute of
Technology Guwahati, Guwahati 781039, Assam, India
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13
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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: 9] [Impact Index Per Article: 9.0] [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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14
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bioTCIs: Middle-to-Macro Biomolecular Targeted Covalent Inhibitors Possessing Both Semi-Permanent Drug Action and Stringent Target Specificity as Potential Antibody Replacements. Int J Mol Sci 2023; 24:ijms24043525. [PMID: 36834935 PMCID: PMC9968108 DOI: 10.3390/ijms24043525] [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: 12/26/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Monoclonal antibody therapies targeting immuno-modulatory targets such as checkpoint proteins, chemokines, and cytokines have made significant impact in several areas, including cancer, inflammatory disease, and infection. However, antibodies are complex biologics with well-known limitations, including high cost for development and production, immunogenicity, a limited shelf-life because of aggregation, denaturation, and fragmentation of the large protein. Drug modalities such as peptides and nucleic acid aptamers showing high-affinity and highly selective interaction with the target protein have been proposed alternatives to therapeutic antibodies. The fundamental limitation of short in vivo half-life has prevented the wide acceptance of these alternatives. Covalent drugs, also known as targeted covalent inhibitors (TCIs), form permanent bonds to target proteins and, in theory, eternally exert the drug action, circumventing the pharmacokinetic limitation of other antibody alternatives. The TCI drug platform, too, has been slow in gaining acceptance because of its potential prolonged side-effect from off-target covalent binding. To avoid the potential risks of irreversible adverse drug effects from off-target conjugation, the TCI modality is broadening from the conventional small molecules to larger biomolecules possessing desirable properties (e.g., hydrolysis resistance, drug-action reversal, unique pharmacokinetics, stringent target specificity, and inhibition of protein-protein interactions). Here, we review the historical development of the TCI made of bio-oligomers/polymers (i.e., peptide-, protein-, or nucleic-acid-type) obtained by rational design and combinatorial screening. The structural optimization of the reactive warheads and incorporation into the targeted biomolecules enabling a highly selective covalent interaction between the TCI and the target protein is discussed. Through this review, we hope to highlight the middle to macro-molecular TCI platform as a realistic replacement for the antibody.
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15
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Shanmugasundaram M, Senthilvelan A, Kore AR. An efficient green synthesis of UNA-nucleoside-5′-triphosphates: a versatile synthon for RNA modification with broad therapeutic potential. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
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16
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2'-N-Alkylaminocarbonyl-2'-amino-LNA: Synthesis, duplex stability, nuclease resistance, and in vitro anti-microRNA activity. Bioorg Med Chem 2023; 78:117148. [PMID: 36580743 DOI: 10.1016/j.bmc.2022.117148] [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: 11/19/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
2'-Amino-LNA has the potential to acquire various functions through chemical modification at the 2'-nitrogen atom. This study focused on 2'-N-alkylaminocarbonyl 2'-amino-LNA, which is a derivative of 2'-amino-LNA. We evaluated its practical usefulness as a chemical modification of anti-miRNA oligonucleotide. The synthesis of phosphoramidites of 2'-N-alkylaminocarbonyl substituted 2'-amino-LNA bearing thymine and 5-methylcytosine proceeded in good yields. Incorporating the 2'-N-alkylaminocarbonyl-2'-amino-LNA monomers into oligonucleotides improved the duplex stability for complementary RNA strands and robust nuclease resistance. Moreover, 2'-N-alkylaminocarbonyl-2'-amino-LNA is a promising scaffold that significantly increases the potency of anti-miRNA oligonucleotides.
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17
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Hari Y, Fuchi Y, Yamamoto K, Ito Y. Benzo-Fused 7-Oxabicyclo[2.2.1]heptane-2,3-diol Derivatives as Universal Linkers for Solid-Phase Oligonucleotide Synthesis. SYNTHESIS-STUTTGART 2023. [DOI: 10.1055/s-0042-1751405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
AbstractIn solid-phase oligonucleotide (ON) synthesis, especially for 3′-modified ONs, a universal linker attached to a solid support is widely used. In this study, benzo-fused 7-oxabicyclo[2.2.1]heptane-2,3-diol derivatives are designed, synthesized, and evaluated as universal linkers. The designed linkers show reactivity comparable to that of a conventional universal linker for releasing the desired ONs. Additionally, these materials exhibit a more robust structure under basic conditions, as generally used in ON synthesis, and hydrophobic properties relative to the conventional universal linker. Notably, when diphenyl-substituted (terphenyl) and phenanthrene-type (PT) linkers are used, cyclic phosphodiesters derived from linker units as byproducts, which are produced by release of ONs from the linker units, are detected in the HPLC chromatograms. The PT linker is applicable to various ON syntheses using controlled pore glass (CPG) and polystyrene (PS) resins. These results demonstrate that the PT linker can serve as an alternative to conventional universal linkers.
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18
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Haseeb A, Rova M, Samuelsson J. Method development for the acquisition of adsorption isotherm of ion pair reagents Tributylamine and Triethylamine in ion pair chromatography. J Chromatogr A 2023; 1687:463687. [PMID: 36470076 DOI: 10.1016/j.chroma.2022.463687] [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: 08/17/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022]
Abstract
Tributylamine (TBuA) and triethylamine (TEtA) are the most commonly used ion pair reagents in ion pair chromatography especially for the analysis of oligonucleotides. In order to improve the understanding of the retention and separation mechanism of oligonucleotides in ion pair chromatography, it is important to understand the retention mechanism and the nature of interaction of these ion pair reagents with the stationary phase in the chromatographic column. Adsorption isotherm is helpful in evaluating such interactions, and subsequently predicting the retention mechanism. Alkylamines are very polar molecules which lack suitable chromophore and are commonly present in charged forms. Therefore, their determination and the subsequent acquisition of their adsorption isotherms using traditional liquid chromatography is very difficult. In this study, we first developed an analytical method for the determination of TBuA and TEtA in a typical chromatographic mobile phase (acetonitrile-water) and then used the same method to acquire the adsorption isotherms for tributylammonium acetate (TBuAA) and triethylammonium acetate (TEtAA). This method started with the conversion of the alkylammonium ions to free neutral forms by treating the sample with a strong base, followed by pentane-mediated extraction and finally the analysis of the extracts using gas chromatography-flame ionization detector (GC-FID). This three-step method was validated for parameters like range, linearity, intra-day and inter-day precision and accuracy, limit of detection and limit of quantitation. For the adsorption isotherms, the C18 column was first equilibrated with the solutions having different concentrations of alkylammonium ions and then stripped with eluent devoid of alkylammonium ions. Several stripping eluents were investigated and it was discovered that the eluent requirement could be decreased by the addition of sodium chloride. The effluents from the stripping phase were collected and analyzed using the developed analytical method to acquire the adsorption data. Under the investigated conditions, adsorption of TBuAA and TEtAA showed type III and type I isotherm behavior respectively.
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Affiliation(s)
- Abdul Haseeb
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad SE-651 88, Sweden
| | - Maria Rova
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad SE-651 88, Sweden
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences, Karlstad University, Karlstad SE-651 88, Sweden.
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19
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Kim Y, Takahashi S, Miyao M. Relationship between reduction in rice (Nipponbare) leaf blade size under elevated CO 2 and miR396- GRF module. PLANT SIGNALING & BEHAVIOR 2022; 17:2041280. [PMID: 35318879 PMCID: PMC8959511 DOI: 10.1080/15592324.2022.2041280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 05/27/2023]
Abstract
Elevated CO2 (eCO2; 1000 ppm) influences developing rice leaf formation, reducing leaf blade length and width as compared to rice grown under ambient CO2 (aCO2; 400 ppm). Since micro RNAs (miRNAs) are known to play multiple roles in plant development, we hypothesized that miRNAs might be involved in modulating leaf size under eCO2 conditions. To identify miRNAs responding to eCO2, we profiled miRNA levels in developing rice leaves (P4; plastochron number of the fourth-youngest leaf) under eCO2 using small RNA-seq. We detected 18 mature miRNA sequences for which expression levels varied more than two-fold between the eCO2 and aCO2 conditions. Among them, only miR396e and miR396f significantly differed between the two conditions. Additionally, the expression of growth-regulating factors (GRFs), potential target mRNA of miR396s, were repressed under the eCO2 condition. We used an antisense oligonucleotide approach to confirm that single-strand DNA corresponding to the miR396e sequence effectively downregulated GRF expression in developing leaves, reducing the leaf blade length, such as for rice grown under eCO2. These results suggest that the miR396-GRF module is crucially relevant to controlling rice leaf blade length in eCO2 environments.
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Affiliation(s)
- Yonghyun Kim
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sumire Takahashi
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mitsue Miyao
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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20
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Zhang L, Liang Y, Liang G, Tian Z, Zhang Y, Liu Z, Ji X. The therapeutic prospects of N-acetylgalactosamine-siRNA conjugates. Front Pharmacol 2022; 13:1090237. [PMID: 36588695 PMCID: PMC9794871 DOI: 10.3389/fphar.2022.1090237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
RNA interference has become increasingly used for genetic therapy following the rapid development of oligonucleotide drugs. Significant progress has been made in its delivery system and implementation in the treatment of target organs. After a brief introduction of RNA interference technology and siRNA, the efficiency and stability of GalNAc-siRNA conjugates are highlighted since several oligonucleotide drugs of GalNAc have been approved for clinical use in recent years. The structure and features of GalNAc-siRNA conjugates are studied and the clinical efficiency and limitations of oligonucleotide-based drugs are summarized and investigated. Furthermore, another delivery system, lipid nanoparticles, that confer many advantages, is concluded, includ-ing stability and mass production, compared with GalNAc-siRNA conjugates. Importantly, developing new approaches for the use of oligonucleotide drugs brings hope to genetic therapy.
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Affiliation(s)
- Lei Zhang
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yayu Liang
- School of Stomatology, Henan University, Kaifeng, China
| | - Guohui Liang
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Zhili Tian
- School of Clinical Medical Sciences, Henan University, Kaifeng, China
| | - Yue Zhang
- Department of Obstetrics and Gynecology, Zhengzhou, China
| | - Zhihui Liu
- Department of General Practice, Henan Provincial People’s Hospital, Zhengzhou University, Zhengzhou, China,*Correspondence: Zhihui Liu, ; Xinying Ji,
| | - Xinying Ji
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China,*Correspondence: Zhihui Liu, ; Xinying Ji,
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21
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Takegawa-Araki T, Yasukawa K, Iwazaki N, Maruyama H, Furukawa H, Sawamoto H, Obika S. Parallel synthesis of oligonucleotides containing N-acyl amino-LNA and their therapeutic effects as anti-microRNAs. Org Biomol Chem 2022; 20:9351-9361. [PMID: 36383101 DOI: 10.1039/d2ob01809h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
2'-Amino-locked nucleic acid (ALNA), maintains excellent duplex stability, and the nitrogen at the 2'-position is an attractive scaffold for functionalization. Herein, a facile and efficient method for the synthesis of various 2'-N-acyl amino-LNA derivatives by direct acylation of the 2'-amino moiety contained in the synthesized oligonucleotides and its fundamental properties are described. The introduction of the acylated amino-LNA enhances the potency of the molecules as therapeutic anti-microRNA oligonucleotides.
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Affiliation(s)
- Tomo Takegawa-Araki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kai Yasukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Norihiko Iwazaki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hideto Maruyama
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Furukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroaki Sawamoto
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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22
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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23
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Kwon S, Giessen TW. Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo. ACS Synth Biol 2022; 11:3504-3515. [PMID: 36170610 PMCID: PMC9944510 DOI: 10.1021/acssynbio.2c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.
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Affiliation(s)
- Seokmu Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tobias W. Giessen
- Department of Biological Chemistry and Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
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24
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Wang Y, Zheng X, Liu J, Chen L, Chen Q, Zhao Y. Virus-like siRNA construct dynamically responsive to sequential microenvironments for potent RNA interference. J Colloid Interface Sci 2022; 622:938-949. [PMID: 35561612 DOI: 10.1016/j.jcis.2022.05.006] [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: 01/27/2022] [Revised: 04/22/2022] [Accepted: 05/01/2022] [Indexed: 11/18/2022]
Abstract
Cytoplasmic transportation of therapeutic nucleic acids is deemed as an onerous task with aim of precise knockdown towards the targeted genes. Pertaining to the programed functionalities of natural virus in circumventing the biological barriers, we tailored multifaceted chemistries into manufacture of synthetic siRNA delivery vehicles in resembling the functionalities of viral vectors to dynamically tackle with a sequential of biological obstacles encountered in the journey of systemic anti-tumor RNAi therapy. Once harnessing ligands with RGD motif for specific internalization into subcellular endosomal compartments of the tumor cells, the architecture of the proposed delivery vehicles was subjected to facile transformation responsive to pH stimuli in acidic endosomal compartments. The external biocompatible PEGylation palisade was consequently detached, unveiling the cytomembrane-lytic cationic components to commit disruptive potencies to the anionic endosomal membranes for translocation of siRNA conjugates into cytosol. Eventually, liberation of active siRNA could be accomplished due to its responsiveness to the strikingly high level of glutathione in cytosol, thereby contributing to potent RNAi. Hence, our elaborated virus-mimicking platform has demonstrated significant anti-tumor efficacy through systemic administration of anti-angiogenic RNAi payloads, which inspired prosperous potentials in a variety of therapeutic applications.
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Affiliation(s)
- Yue Wang
- Department of Gastric Cancer, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning 110042, China; School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Xiujue Zheng
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jun Liu
- School of Materials Science and Engineering, Tsinghua University, Haidian District, Beijing 100084, China; Ningbo Hygeia Medical Technology Co., Ltd., No. 6 Jinyuan Road, High-Tech Zone, Ningbo 315201, China
| | - Li Chen
- School of Mechanical Engineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Qixian Chen
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China.
| | - Yan Zhao
- Department of Gastric Cancer, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, Liaoning 110042, China.
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25
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Bano N, Ehlinger C, Yang TY, Swanson M, Allen S. Considerations in the Immunogenicity Assessment Strategy for Oligonucleotide Therapeutics (ONTs). AAPS J 2022; 24:93. [DOI: 10.1208/s12248-022-00741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
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26
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Tomassi S, Ieranò C, Del Bene A, D’Aniello A, Napolitano M, Rea G, Auletta F, Portella L, Capiluongo A, Mazzarella V, Russo R, Chambery A, Scala S, Di Maro S, Messere A. Tailoring the Structure of Cell Penetrating DNA and RNA Binding Nucleopeptides. Int J Mol Sci 2022; 23:ijms23158504. [PMID: 35955638 PMCID: PMC9369335 DOI: 10.3390/ijms23158504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic nucleic acid interactors represent an exciting research field due to their biotechnological and potential therapeutic applications. The translation of these molecules into drugs is a long and difficult process that justifies the continuous research of new chemotypes endowed with favorable binding, pharmacokinetic and pharmacodynamic properties. In this scenario, we describe the synthesis of two sets of homo-thymine nucleopeptides, in which nucleobases are inserted in a peptide structure, to investigate the role of the underivatized amino acid residue and the distance of the nucleobase from the peptide backbone on the nucleic acid recognition process. It is worth noting that the CD spectroscopy investigation showed that two of the reported nucleopeptides, consisting of alternation of thymine functionalized L-Orn and L-Dab and L-Arg as underivatized amino acids, were able to efficiently bind DNA and RNA targets and cross both cell and nuclear membranes.
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Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico” II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Caterina Ieranò
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Antonia D’Aniello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Maria Napolitano
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Giuseppina Rea
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Federica Auletta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Anna Capiluongo
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
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Patino CA, Pathak N, Mukherjee P, Park SH, Bao G, Espinosa HD. Multiplexed high-throughput localized electroporation workflow with deep learning-based analysis for cell engineering. SCIENCE ADVANCES 2022; 8:eabn7637. [PMID: 35867793 PMCID: PMC9307252 DOI: 10.1126/sciadv.abn7637] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/07/2022] [Indexed: 05/06/2023]
Abstract
Manipulation of cells for applications such as biomanufacturing and cell-based therapeutics involves introducing biomolecular cargoes into cells. However, successful delivery is a function of multiple experimental factors requiring several rounds of optimization. Here, we present a high-throughput multiwell-format localized electroporation device (LEPD) assisted by deep learning image analysis that enables quick optimization of experimental factors for efficient delivery. We showcase the versatility of the LEPD platform by successfully delivering biomolecules into different types of adherent and suspension cells. We also demonstrate multicargo delivery with tight dosage distribution and precise ratiometric control. Furthermore, we used the platform to achieve functional gene knockdown in human induced pluripotent stem cells and used the deep learning framework to analyze protein expression along with changes in cell morphology. Overall, we present a workflow that enables combinatorial experiments and rapid analysis for the optimization of intracellular delivery protocols required for genetic manipulation.
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Affiliation(s)
- Cesar A. Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL 60208, USA
| | - Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL 60208, USA
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX 77030, USA
| | - Horacio D. Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL 60208, USA
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28
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Analysis of therapeutic nucleic acids by capillary electrophoresis. J Pharm Biomed Anal 2022; 219:114928. [PMID: 35853263 DOI: 10.1016/j.jpba.2022.114928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/04/2022] [Accepted: 07/02/2022] [Indexed: 12/19/2022]
Abstract
Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.
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29
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Dai H, Abdullah R, Wu X, Li F, Ma Y, Lu A, Zhang G. Pancreatic Cancer: Nucleic Acid Drug Discovery and Targeted Therapy. Front Cell Dev Biol 2022; 10:855474. [PMID: 35652096 PMCID: PMC9149368 DOI: 10.3389/fcell.2022.855474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/07/2022] [Indexed: 12/20/2022] Open
Abstract
Pancreatic cancer (PC) is one of the most lethal cancers with an almost 10% 5-year survival rate. Because PC is implicated in high heterogeneity, desmoplastic tumor-microenvironment, and inefficient drug-penetration, the chemotherapeutic strategy currently recommended for the treatment of PC has limited clinical benefit. Nucleic acid-based targeting therapies have become strong competitors in the realm of drug discovery and targeted therapy. A vast evidence has demonstrated that antibody-based or alternatively aptamer-based strategy largely contributed to the elevated drug accumulation in tumors with reduced systematic cytotoxicity. This review describes the advanced progress of antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNAs (miRNAs), messenger RNA (mRNAs), and aptamer-drug conjugates (ApDCs) in the treatment of PC, revealing the bright application and development direction in PC therapy.
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Affiliation(s)
- Hong Dai
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Razack Abdullah
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute for the Advancement of Chinese medicine (IACM) .Ltd, Shatin, Hong Kong SAR, China
| | - Xiaoqiu Wu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Fangfei Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, China
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30
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Gram-Scale Chemical Synthesis of Purine Locked Nucleic Acid Nucleoside-5'-O-Triphosphates. Curr Protoc 2022; 2:e436. [PMID: 35723503 DOI: 10.1002/cpz1.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article presents a simple, reliable, straight-forward, general, and efficient chemical method for the gram-scale synthesis of purine locked nucleic acid (LNA) nucleotides, such as LNA guanosine-5'-O-triphosphate (LNA-GTP) and LNA adenosine-5'-O-triphosphate (LNA-ATP), starting from the corresponding nucleoside. The reaction pathway employs an improved protection-free "one-pot, three-step" Ludwig synthetic strategy. The first step involves monophosphorylation of nucleoside with phosphorus oxychloride followed by reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate to furnish the corresponding LNA nucleotide in good yields. It is noteworthy that the reaction affords high-purity (>99.5%) LNA nucleotide after diethylaminoethyl Sepharose column purification. © 2022 Wiley Periodicals LLC. Basic Protocol: Synthesis of LNA nucleoside-5'-O-triphosphates.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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31
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The Usefulness of Autoradiography for DNA Repair Proteins Activity Detection in the Cytoplasm towards Radiolabeled Oligonucleotides Containing 5′,8-Cyclo-2′-deoxyAdenosine. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10060204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Autoradiography of 32P-radiolabeled oligonucleotides is one of the most precise detection methods of DNA repair processes. In this study, autoradiography allowed assessing the activity of proteins in the cytoplasm involved in DNA repair. The cytoplasm is the site of protein biosynthesis but is also a target cellular compartment of synthetic therapeutic oligonucleotide (STO) delivery. The DNA-based drugs may be impaired by radiation-induced lesions, such as clustered DNA lesions (CDL) and/or 5′,8-cyclo-2′-deoxypurines (cdPu). CDL and cdPu may appear in the sequence of STO after irradiation and subsequently impair DNA repair, as shown in previous studies. Hence, the interesting questions are (1) is it safe to combine STO treatment with radiotherapy; (2) are repair proteins active in the cytoplasm; and (3) is their activity different in the cytoplasm than in the nucleus? This unique study examined whether the proteins involved in the DNA repair are affected by the CDL while they are still present in the cytoplasm of xrs5, BJ, and XPC cells. Double-stranded oligonucleotides with bi-stranded CDL were used (containing AP site in one strand and a (5′S) or (5′R) 5′,8-cyclo-2′-deoxyadenosine (cdA) in the other strand located 1 or 4 bp in both directions). The results have shown that the proteins involved in the repair were active in the cytoplasm, but less than in the nucleus. The general trends aligned for cytoplasm and nucleus—lesions located in the 5′-end direction inhibited the course of DNA repair. The combination of STO with radiotherapy should be applied carefully, as unrepaired lesions within STO may impair their therapeutic efficiency.
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Honcharenko D, Rocha CSJ, Lundin KE, Maity J, Milton S, Tedebark U, Murtola M, Honcharenko M, Slaitas A, Smith CIE, Zain R, Strömberg R. 2'- O-( N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity. Nucleic Acid Ther 2022; 32:221-233. [PMID: 35238623 PMCID: PMC9221157 DOI: 10.1089/nat.2021.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
2′-O-(N-(Aminoethyl)carbamoyl)methyl (2′-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2′-O-methyl oligonucleotides (2′-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2′-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2′-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2′-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cristina S J Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Jyotirmoy Maity
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Milton
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ulf Tedebark
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | | | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Singh S, Srivastava PN, Meena A, Luqman S. Dietary flavonoid narirutin as a prospective antagonist of oncogenic pri/pre-microRNAs. Phytother Res 2022; 36:963-983. [PMID: 35040205 DOI: 10.1002/ptr.7367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are involved in cancer progression via translational degradation in a sequence-specific manner of the 3'-untranslated region (3'UTR) of messenger RNA (mRNA). The involvement of miRNA in the biological progression of various cancer types is considered to be a potential target. Primary miRNA (pri-miRNA) and precursor-miRNA (pre-miRNA) synthesize the miRNA by dicer-catalyzed processes thus targeting pri/pre-miRNA by phytochemicals is amongst the appropriate approaches for anticancer therapies. Flavonoids category of phytochemicals is well-known for its chemotherapeutic and chemopreventive potential against multiple cancer types. However, the molecular interactions of flavonoids with miRNAs are not reported so far. Thus, this study aims to identify the promising flavonoids as the antagonist of miRNAs (pre-miR21, pri-miR-208a, pri-miR-378a, pri-miR320b, pri-miR-300, pri-miR-19b, and pre-miR-20b) using molecular docking simulations studies. Among the tested flavonoids, narirutin showed highest binding energy (-11.7 kcal/mol) against pri-miR19b followed by pri-miR-378a (-11.4 kcal/mol) > pri-miR320b (-11.2 kcal/mol) = pri-miR-300 (-11.2 kcal/mol) > pri-miR-208a (-9.0 kcal/mol) > pre-miR-20b (- 8.3 kcal/mol). The molecular dynamic simulation experiment confirmed that narirutin destabilizes the tertiary structure of pri-miRNA in comparison to apo-RNA. The finding indicates that narirutin binding with pre-miRNA causes disruption of pri-RNA structure that creates a loss of DICER-pre-miRNA interactions by hindering the pre-miRNA synthesis, thereby affecting miRNA processing. Further pharmacokinetics and toxicity prediction revealed that it is non-carcinogenic, non-mutagenic, and does not inhibit the CYPs activity. Thus, narirutin could be a possible antagonist of oncogenic miRNAs, therefore could be useful for miRNA-targeted cancer prevention and treatment.
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Affiliation(s)
- Shilpi Singh
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pratik Narain Srivastava
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Abha Meena
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Lee MJ, Lee I, Wang K. Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders. Biomedicines 2022; 10:biomedicines10010158. [PMID: 35052837 PMCID: PMC8773368 DOI: 10.3390/biomedicines10010158] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/07/2023] Open
Abstract
The development of new sequencing technologies in the post-genomic era has accelerated the identification of causative mutations of several single gene disorders. Advances in cell and animal models provide insights into the underlining pathogenesis, which facilitates the development and maturation of new treatment strategies. The progress in biochemistry and molecular biology has established a new class of therapeutics—the short RNAs and expressible long RNAs. The sequences of therapeutic RNAs can be optimized to enhance their stability and translatability with reduced immunogenicity. The chemically-modified RNAs can also increase their stability during intracellular trafficking. In addition, the development of safe and high efficiency carriers that preserves the integrity of therapeutic RNA molecules also accelerates the transition of RNA therapeutics into the clinic. For example, for diseases that are caused by genetic defects in a specific protein, an effective approach termed “protein replacement therapy” can provide treatment through the delivery of modified translatable mRNAs. Short interference RNAs can also be used to treat diseases caused by gain of function mutations or restore the splicing aberration defects. Here we review the applications of newly developed RNA-based therapeutics and its delivery and discuss the clinical evidence supporting the potential of RNA-based therapy in single-gene neurological disorders.
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Affiliation(s)
- Ming-Jen Lee
- Department of Neurology, National Taiwan University Hospital, Taipei 10012, Taiwan;
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10012, Taiwan
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA;
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA;
- Correspondence: ; Tel.: +1-206-732-1336
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35
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Arthur GK, Cruse G. Regulation of Trafficking and Signaling of the High Affinity IgE Receptor by FcεRIβ and the Potential Impact of FcεRIβ Splicing in Allergic Inflammation. Int J Mol Sci 2022; 23:ijms23020788. [PMID: 35054974 PMCID: PMC8776166 DOI: 10.3390/ijms23020788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 12/23/2022] Open
Abstract
Mast cells are tissue-resident immune cells that function in both innate and adaptive immunity through the release of both preformed granule-stored mediators, and newly generated proinflammatory mediators that contribute to the generation of both the early and late phases of the allergic inflammatory response. Although mast cells can be activated by a vast array of mediators to contribute to homeostasis and pathophysiology in diverse settings and contexts, in this review, we will focus on the canonical setting of IgE-mediated activation and allergic inflammation. IgE-dependent activation of mast cells occurs through the high affinity IgE receptor, FcεRI, which is a multimeric receptor complex that, once crosslinked by antigen, triggers a cascade of signaling to generate a robust response in mast cells. Here, we discuss FcεRI structure and function, and describe established and emerging roles of the β subunit of FcεRI (FcεRIβ) in regulating mast cell function and FcεRI trafficking and signaling. We discuss current approaches to target IgE and FcεRI signaling and emerging approaches that could target FcεRIβ specifically. We examine how alternative splicing of FcεRIβ alters protein function and how manipulation of splicing could be employed as a therapeutic approach. Targeting FcεRI directly and/or IgE binding to FcεRI are promising approaches to therapeutics for allergic inflammation. The characteristic role of FcεRIβ in both trafficking and signaling of the FcεRI receptor complex, the specificity to IgE-mediated activation pathways, and the preferential expression in mast cells and basophils, makes FcεRIβ an excellent, but challenging, candidate for therapeutic strategies in allergy and asthma, if targeting can be realized.
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Affiliation(s)
- Greer K. Arthur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA;
| | - Glenn Cruse
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, NC State University, Raleigh, NC 27607, USA
- Correspondence: ; Tel.: +1-919-515-8865
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Snider DB, Arthur GK, Falduto GH, Olivera A, Ehrhardt-Humbert LC, Smith E, Smith C, Metcalfe DD, Cruse G. Targeting KIT by frameshifting mRNA transcripts as a therapeutic strategy for aggressive mast cell neoplasms. Mol Ther 2022; 30:295-310. [PMID: 34371183 PMCID: PMC8753370 DOI: 10.1016/j.ymthe.2021.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/21/2021] [Accepted: 07/31/2021] [Indexed: 01/07/2023] Open
Abstract
Activating mutations in c-KIT are associated with the mast cell (MC) clonal disorders cutaneous mastocytosis and systemic mastocytosis and its variants, including aggressive systemic mastocytosis, MC leukemia, and MC sarcoma. Currently, therapies inhibiting KIT signaling are a leading strategy to treat MC proliferative disorders. However, these approaches may have off-target effects, and in some patients, complete remission or improved survival time cannot be achieved. These limitations led us to develop an approach using chemically stable exon skipping oligonucleotides (ESOs) that induce exon skipping of precursor (pre-)mRNA to alter gene splicing and introduce a frameshift into mature KIT mRNA transcripts. The result of this alternate approach results in marked downregulation of KIT expression, diminished KIT signaling, inhibition of MC proliferation, and rapid induction of apoptosis in neoplastic HMC-1.2 MCs. We demonstrate that in vivo administration of KIT targeting ESOs significantly inhibits tumor growth and systemic organ infiltration using both an allograft mastocytosis model and a humanized xenograft MC tumor model. We propose that our innovative approach, which employs well-tolerated, chemically stable oligonucleotides to target KIT expression through unconventional pathways, has potential as a KIT-targeted therapeutic alone, or in combination with agents that target KIT signaling, in the treatment of KIT-associated malignancies.
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Affiliation(s)
- Douglas B. Snider
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA
| | - Greer K. Arthur
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA
| | - Guido H. Falduto
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Olivera
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren C. Ehrhardt-Humbert
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Emmaline Smith
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Cierra Smith
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA
| | - Dean D. Metcalfe
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Glenn Cruse
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27607, USA,Corresponding author: Glenn Cruse, PhD, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Biomedical Partnership Center, 1060 William Moore Drive, Raleigh, NC 27607, USA.
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Jablonka S, Hennlein L, Sendtner M. Therapy development for spinal muscular atrophy: perspectives for muscular dystrophies and neurodegenerative disorders. Neurol Res Pract 2022; 4:2. [PMID: 34983696 PMCID: PMC8725368 DOI: 10.1186/s42466-021-00162-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Major efforts have been made in the last decade to develop and improve therapies for proximal spinal muscular atrophy (SMA). The introduction of Nusinersen/Spinraza™ as an antisense oligonucleotide therapy, Onasemnogene abeparvovec/Zolgensma™ as an AAV9-based gene therapy and Risdiplam/Evrysdi™ as a small molecule modifier of pre-mRNA splicing have set new standards for interference with neurodegeneration. MAIN BODY Therapies for SMA are designed to interfere with the cellular basis of the disease by modifying pre-mRNA splicing and enhancing expression of the Survival Motor Neuron (SMN) protein, which is only expressed at low levels in this disorder. The corresponding strategies also can be applied to other disease mechanisms caused by loss of function or toxic gain of function mutations. The development of therapies for SMA was based on the use of cell culture systems and mouse models, as well as innovative clinical trials that included readouts that had originally been introduced and optimized in preclinical studies. This is summarized in the first part of this review. The second part discusses current developments and perspectives for amyotrophic lateral sclerosis, muscular dystrophies, Parkinson's and Alzheimer's disease, as well as the obstacles that need to be overcome to introduce RNA-based therapies and gene therapies for these disorders. CONCLUSION RNA-based therapies offer chances for therapy development of complex neurodegenerative disorders such as amyotrophic lateral sclerosis, muscular dystrophies, Parkinson's and Alzheimer's disease. The experiences made with these new drugs for SMA, and also the experiences in AAV gene therapies could help to broaden the spectrum of current approaches to interfere with pathophysiological mechanisms in neurodegeneration.
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Affiliation(s)
- Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Versbacher Str. 5, 97078, Wuerzburg, Germany.
| | - Luisa Hennlein
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Versbacher Str. 5, 97078, Wuerzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital of Wuerzburg, Versbacher Str. 5, 97078, Wuerzburg, Germany.
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38
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Nagata T, Dwyer CA, Yoshida-Tanaka K, Ihara K, Ohyagi M, Kaburagi H, Miyata H, Ebihara S, Yoshioka K, Ishii T, Miyata K, Miyata K, Powers B, Igari T, Yamamoto S, Arimura N, Hirabayashi H, Uchihara T, Hara RI, Wada T, Bennett CF, Seth PP, Rigo F, Yokota T. Cholesterol-functionalized DNA/RNA heteroduplexes cross the blood-brain barrier and knock down genes in the rodent CNS. Nat Biotechnol 2021; 39:1529-1536. [PMID: 34385691 DOI: 10.1038/s41587-021-00972-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023]
Abstract
Achieving regulation of endogenous gene expression in the central nervous system (CNS) with antisense oligonucleotides (ASOs) administered systemically would facilitate the development of ASO-based therapies for neurological diseases. We demonstrate that DNA/RNA heteroduplex oligonucleotides (HDOs) conjugated to cholesterol or α-tocopherol at the 5' end of the RNA strand reach the CNS after subcutaneous or intravenous administration in mice and rats. The HDOs distribute throughout the brain, spinal cord and peripheral tissues and suppress the expression of four target genes by up to 90% in the CNS, whereas single-stranded ASOs conjugated to cholesterol have limited activity. Gene knockdown was observed in major CNS cell types and was greatest in neurons and microglial cells. Side effects, such as thrombocytopenia and focal brain necrosis, were limited by using subcutaneous delivery or by dividing intravenous injections. By crossing the blood-brain barrier more effectively, cholesterol-conjugated HDOs may overcome the limited efficacy of ASOs targeting the CNS without requiring intrathecal administration.
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Affiliation(s)
- Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kensuke Ihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Ohyagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidetoshi Kaburagi
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoe Ebihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Ishii
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenichi Miyata
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Tomoko Igari
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Naoto Arimura
- Research, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | | | - Toshiki Uchihara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. .,Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan.
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39
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Hari Y, Yamamoto K, Fuchi Y, Okabe M, Osawa T, Ito Y. New Cleavable Spacers for Tandem Synthesis of Multiple Oligonucleotides. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1538-9883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractIn solid-phase oligonucleotide synthesis, a single oligonucleotide is generally acquired from a column loaded with a specific solid support. Herein, we have developed new cleavable spacer (CS) derivatives for tandem synthesis of multiple oligonucleotides on a single column. Four CS analogues were designed, synthesized, and inserted between two oligonucleotide sequences using an automated oligonucleotide synthesizer. The CS derivatives bearing a cyclic cis-1,2-diol exhibited efficient release of the two oligonucleotides under commonly employed basic conditions of aqueous ammonia. Among the CS analogues, it was found that CS with a robust structure can potentially be applied as a spacer molecule in the tandem synthesis of multiple oligonucleotides in a single sequence.
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40
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Shanmugasundaram M, Senthilvelan A, Kore AR. An improved protection-free one-pot chemical synthesis of purine locked nucleic acid nucleoside-5'-triphosphates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:36-44. [PMID: 34696692 DOI: 10.1080/15257770.2021.1994992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A simple, reliable, straightforward, and efficient method for the gram-scale chemical synthesis of purine locked nucleic acid (LNA) nucleotides such as LNA-guanosine-5'-triphosphate (LNA-GTP) and LNA-adenosine-5'-triphosphate (LNA-ATP) starting from the corresponding nucleoside is described. The overall reaction utilizes an improved "one-pot, three-step" Ludwig synthetic strategy that involves the monophosphorylation of LNA nucleoside, followed by the reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate using water to furnish the corresponding purine LNA nucleotide in good yield with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas, USA
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41
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Della Sala F, Fabozzi A, di Gennaro M, Nuzzo S, Makvandi P, Solimando N, Pagliuca M, Borzacchiello A. Advances in Hyaluronic-Acid-Based (Nano)Devices for Cancer Therapy. Macromol Biosci 2021; 22:e2100304. [PMID: 34657388 DOI: 10.1002/mabi.202100304] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/08/2021] [Indexed: 12/12/2022]
Abstract
Cancer is the main cause of fatality all over the world with a considerable growth rate. Many biologically active nanoplatforms are exploited for tumor treatment. Of nanodevices, hyaluronic acid (HA)-based systems have shown to be promising candidates for cancer therapy due to their high biocompatibility and cell internalization. Herein, surface functionalization of different nanoparticles (NPs), e.g., organic- and inorganic-based NPs, is highlighted. Subsequently, HA-based nanostructures and their applications in cancer therapy are presented.
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Affiliation(s)
- Francesca Della Sala
- Institute of Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Viale J.F. Kennedy 54, Naples, 80125, Italy
| | - Antonio Fabozzi
- Altergon Italia s.r.l, Zona Industriale ASI, Morra De Sanctis (AV), 83040, Italy
| | - Mario di Gennaro
- Institute of Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Viale J.F. Kennedy 54, Naples, 80125, Italy
| | - Stefano Nuzzo
- Altergon Italia s.r.l, Zona Industriale ASI, Morra De Sanctis (AV), 83040, Italy
| | - Pooyan Makvandi
- Institute of Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Viale J.F. Kennedy 54, Naples, 80125, Italy
| | - Nicola Solimando
- Altergon Italia s.r.l, Zona Industriale ASI, Morra De Sanctis (AV), 83040, Italy
| | - Maurizio Pagliuca
- Altergon Italia s.r.l, Zona Industriale ASI, Morra De Sanctis (AV), 83040, Italy
| | - Assunta Borzacchiello
- Institute of Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Viale J.F. Kennedy 54, Naples, 80125, Italy
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42
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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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43
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Yamamoto K, Fuchi Y, Ito Y, Hari Y. Bicyclo[2.2.2]octane-2,3-diol as an universal linker for the solid-phase synthesis of oligonucleotides. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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44
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Attia N, Mashal M, Puras G, Pedraz JL. Mesenchymal Stem Cells as a Gene Delivery Tool: Promise, Problems, and Prospects. Pharmaceutics 2021; 13:843. [PMID: 34200425 PMCID: PMC8229096 DOI: 10.3390/pharmaceutics13060843] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
The cell-based approach in gene therapy arises as a promising strategy to provide safe, targeted, and efficient gene delivery. Owing to their unique features, as homing and tumor-tropism, mesenchymal stem cells (MSCs) have recently been introduced as an encouraging vehicle in gene therapy. Nevertheless, non-viral transfer of nucleic acids into MSCs remains limited due to various factors related to the main stakeholders of the process (e.g., nucleic acids, carriers, or cells). In this review, we have summarized the main types of nucleic acids used to transfect MSCs, the pros and cons, and applications of each. Then, we have emphasized on the most efficient lipid-based carriers for nucleic acids to MSCs, their main features, and some of their applications. While a myriad of studies have demonstrated the therapeutic potential for engineered MSCs therapy in various illnesses, optimization for clinical use is an ongoing challenge. On the way of improvement, genetically modified MSCs have been combined with various novel techniques and tools (e.g., exosomes, spheroids, 3D-Bioprinting, etc.,) aiming for more efficient and safe applications in biomedicine.
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Affiliation(s)
- Noha Attia
- Laboratory of Pharmaceutics, NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (N.A.); (M.M.)
- Department of Basic Sciences, The American University of Antigua-College of Medicine, Coolidge 1451, Antigua and Barbuda
- The Center of Research and Evaluation, The American University of Antigua-College of Medicine, Coolidge 1451, Antigua and Barbuda
- Histology and Cell Biology Department, Faculty of Medicine, University of Alexandria, Alexandria 21561, Egypt
| | - Mohamed Mashal
- Laboratory of Pharmaceutics, NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (N.A.); (M.M.)
- The Center of Research and Evaluation, The American University of Antigua-College of Medicine, Coolidge 1451, Antigua and Barbuda
| | - Gustavo Puras
- Laboratory of Pharmaceutics, NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (N.A.); (M.M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 28029 Madrid, Spain
- Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain
- Laboratory of Pharmacy and Pharmaceutical Technology, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Jose Luis Pedraz
- Laboratory of Pharmaceutics, NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (N.A.); (M.M.)
- Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Institute of Health Carlos III, 28029 Madrid, Spain
- Bioaraba, NanoBioCel Research Group, 01006 Vitoria-Gasteiz, Spain
- Laboratory of Pharmacy and Pharmaceutical Technology, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
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45
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Ren H, Song L, Zhang W, Xu L. Synthesis, Stability, and Anti-Tumour Activity of a New Category of "Stapled" Antisense Oligonucleotides with Stimuli-Responsive Feature. J Pharm Sci 2021; 110:3166-3170. [PMID: 34102202 DOI: 10.1016/j.xphs.2021.05.024] [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: 01/08/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The development of nucleic acid drugs with unique structures and mechanisms has stimulated great research interest. Herein, we report a general strategy to construct "stapled" structures of single-stranded antisense oligonucleotides (ASONs) with a stimuli-responsive feature. "Stapled" cyclic structures can be synthesized with reactive bifunctional handles that react with thiol groups of phosphorothioate (PS)-modified ASONs, and can be alternatively adjusted depending on the desired PS sites in the ASON strand. The disulphide group in the stapled handle can be cleaved in the reducing microenvironment of tumour cells. Thus, "stapled" ASONs may be transformed back to a linear conformation to facilitate binding to target mRNAs. Stapling conferred protection against degradation, and enhanced anti-tumour activity compared to linear counterparts. This study provides a new, effective, and convenient strategy for designing ASONs with "stapled" structures, and also adds a further contribution to facilitate the stability and biological efficacy of novel nucleic acid-based therapeutics.
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Affiliation(s)
- Hongqian Ren
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liya Song
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Wei Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Liang Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
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46
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Uppuladinne MVN, Dowerah D, Sonavane UB, Ray SK, Deka RC, Joshi RR. Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level. J Mol Graph Model 2021; 107:107945. [PMID: 34102527 DOI: 10.1016/j.jmgm.2021.107945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/04/2021] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/6-31G(d,p) using a Gaussian03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.
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Affiliation(s)
- Mallikarjunachari V N Uppuladinne
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
| | - Dikshita Dowerah
- Department of Chemical Sciences, Tezpur University, Assam, India.
| | - Uddhavesh B Sonavane
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, India.
| | - Ramesh C Deka
- Department of Chemical Sciences, Tezpur University, Assam, India.
| | - Rajendra R Joshi
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India.
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47
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Forbes TA, Brown BD, Lai C. Therapeutic RNA interference: A novel approach to the treatment of primary hyperoxaluria. Br J Clin Pharmacol 2021; 88:2525-2538. [PMID: 34022071 PMCID: PMC9291495 DOI: 10.1111/bcp.14925] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/19/2021] [Accepted: 05/08/2021] [Indexed: 12/13/2022] Open
Abstract
RNA interference (RNAi) is a natural biological pathway that inhibits gene expression by targeted degradation or translational inhibition of cytoplasmic mRNA by the RNA induced silencing complex. RNAi has long been exploited in laboratory research to study the biological consequences of the reduced expression of a gene of interest. More recently RNAi has been demonstrated as a therapeutic avenue for rare metabolic diseases. This review presents an overview of the cellular RNAi machinery as well as therapeutic RNAi design and delivery. As a clinical example we present primary hyperoxaluria, an ultrarare inherited disease of increased hepatic oxalate production which leads to recurrent calcium oxalate kidney stones. In the most common form of the disease (Type 1), end‐stage kidney disease occurs in childhood or young adulthood, often necessitating combined kidney and liver transplantation. In this context we discuss nedosiran (Dicerna Pharmaceuticals, Inc.) and lumasiran (Alnylam Pharmaceuticals), which are both novel RNAi therapies for primary hyperoxaluria that selectively reduce hepatic expression of lactate dehydrogenase and glycolate oxidase respectively, reducing hepatic oxalate production and urinary oxalate levels. Finally, we consider future optimizations advances in RNAi therapies.
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Affiliation(s)
- Thomas A Forbes
- Royal Children's Hospital, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,University of Melbourne, Parkville, Victoria, Australia
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48
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Chen Z, Zhang F, Zhang H, Cheng L, Chen K, Shen J, Qi J, Deng L, He C, Santos HA, Cui W. DNA-Grafted Hyaluronic Acid System with Enhanced Injectability and Biostability for Photo-Controlled Osteoarthritis Gene Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004793. [PMID: 33977074 PMCID: PMC8097319 DOI: 10.1002/advs.202004793] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/25/2021] [Indexed: 05/10/2023]
Abstract
Gene therapy is identified as a powerful strategy to overcome the limitations of traditional therapeutics to achieve satisfactory effects. However, various challenges related to the dosage form, delivery method, and, especially, application value, hampered the clinical transition of gene therapy. Here, aiming to regulate the cartilage inflammation and degeneration related abnormal IL-1β mRNA expression in osteoarthritis (OA), the interference oligonucleotides is integrated with the Au nanorods to fabricate the spherical nucleic acids (SNAs), to promote the stability and cell internalization efficiency. Furthermore, the complementary oligonucleotides are grafted onto hyaluronic acid (HA) to obtained DNA-grafted HA (DNAHA) for SNAs delivery by base pairing, resulting in significantly improved injectability and bio-stability of the system. After loading SNAs, the constructed DNAHA-SNAs system (HA-SNAs) performs a reversible NIR-triggered on-demand release of SNAs by photo-thermal induced DNA dehybridization and followed by post-NIR in situ hybridization. The in vitro and in vivo experiments showed that this system down-regulated catabolic proteases and up-regulated anabolic components in cartilage over extended periods of time, to safeguard the chondrocytes against degenerative changes and impede the continual advancement of OA.
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Affiliation(s)
- Zhijie Chen
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Feng Zhang
- Drug Research ProgramDivision of Pharmaceutical Chemistry and TechnologyFaculty of PharmacyUniversity of HelsinkiHelsinkiFI‐00014Finland
| | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory and Turku Bioscience CentreÅbo Akademi UniversityTurkuFI‐20520Finland
| | - Liang Cheng
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Kaizhe Chen
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Jieliang Shen
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Jin Qi
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Lianfu Deng
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Chuan He
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
| | - Hélder A. Santos
- Drug Research ProgramDivision of Pharmaceutical Chemistry and TechnologyFaculty of PharmacyUniversity of HelsinkiHelsinkiFI‐00014Finland
- Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFI‐00014Finland
| | - Wenguo Cui
- Department of OrthopaedicsShanghai Key Laboratory for Prevention and Treatment of Bone and Joint DiseasesShanghai Institute of Traumatology and OrthopaedicsRuijin HospitalShanghai Jiao Tong University School of Medicine197 Ruijin 2nd RoadShanghai200025P. R. China
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49
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Metelev VG, Oretskaya TS. Modified Oligonucleotides: New Structures, New Properties, and New Spheres of Application. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:339-343. [PMID: 33935479 PMCID: PMC8074280 DOI: 10.1134/s1068162021020175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022]
Abstract
Nucleic acids have made a long and arduous journey "from the bench to the bedside." At present, it can be assumed that drugs based on modified oligonucleotides will find a worthy application in personalized medicine of the future.
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Affiliation(s)
- V. G. Metelev
- Lomonosov Moscow State University, Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia
| | - T. S. Oretskaya
- Lomonosov Moscow State University, Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia
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Gagliardi M, Ashizawa AT. The Challenges and Strategies of Antisense Oligonucleotide Drug Delivery. Biomedicines 2021; 9:biomedicines9040433. [PMID: 33923688 PMCID: PMC8072990 DOI: 10.3390/biomedicines9040433] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/01/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are used to selectively inhibit the translation of disease-associated genes via Ribonuclease H (RNaseH)-mediated cleavage or steric hindrance. They are being developed as a novel and promising class of drugs targeting a wide range of diseases. Despite the great potential and numerous ASO drugs in preclinical research and clinical trials, there are many limitations to this technology. In this review we will focus on the challenges of ASO delivery and the strategies adopted to improve their stability in the bloodstream, delivery to target sites, and cellular uptake. Focusing on liposomal delivery, we will specifically describe liposome-incorporated growth factor receptor-bound protein-2 (Grb2) antisense oligodeoxynucleotide BP1001. BP1001 is unique because it is uncharged and is essentially non-toxic, as demonstrated in preclinical and clinical studies. Additionally, its enhanced biodistribution makes it an attractive therapeutic modality for hematologic malignancies as well as solid tumors. A detailed understanding of the obstacles that ASOs face prior to reaching their targets and continued advances in methods to overcome them will allow us to harness ASOs’ full potential in precision medicine.
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