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Goodnow RA. Reality check: lipid-oligonucleotide conjugates for therapeutic applications. Expert Opin Drug Discov 2023; 18:129-134. [PMID: 36546308 DOI: 10.1080/17460441.2022.2157399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Despite much progress in the field of oligonucleotide therapeutics, delivery in general remains an important aspect for innovation. Various lipids and lipophilic small molecules have long been conjugated to many oligonucleotides in hopes of creating better, drug-like substances. A few conjugates are beginning to enter clinical development as the understanding grows of how such conjugations change the pharmacology of the conjugate relative to the unmodified oligonucleotide. The delivery of different forms of oligonucleotides, such as antisense oligonucleotides and siRNA, is often a challenging, limiting aspect to this form of therapeutics. AREAS COVERED Herein, the origins of covalent attachment of lipophilic moieties to oligonucleotides are described as well as listing a few of those lipids commonly used for lipidation. The author also describes the mechanism by which lipidation may enhance delivery and/or exposure of oligonucleotides in vitro and in vivo. EXPERT OPINION The covalent attachment of lipophilic moieties is one means to enhance the delivery and exposure of oligonucleotides. Such methods may also be applicable to other oligonucleotide-based modalities as long as the lipidation does not interfere with some key interaction. Lipidation may also be useful to modulate the cell type-specific delivery within tissues. As the understanding of the effects of such covalent modification grows, more lipidated oligos are soon likely to enter clinical development.
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Affiliation(s)
- Robert A Goodnow
- Takeda Pharmaceutical Company Inc., Cambridge, Massachusetts USA
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Stoodley J, Vallejo-Bedia F, Seone-Miraz D, Debasa-Mouce M, Wood MJA, Varela MA. Application of Antisense Conjugates for the Treatment of Myotonic Dystrophy Type 1. Int J Mol Sci 2023; 24:ijms24032697. [PMID: 36769018 PMCID: PMC9916419 DOI: 10.3390/ijms24032697] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is one of the most common muscular dystrophies and can be potentially treated with antisense therapy decreasing mutant DMPK, targeting miRNAs or their binding sites or via a blocking mechanism for MBNL1 displacement from the repeats. Unconjugated antisense molecules are able to correct the disease phenotype in mouse models, but they show poor muscle penetration upon systemic delivery in DM1 patients. In order to overcome this challenge, research has focused on the improvement of the therapeutic window and biodistribution of antisense therapy using bioconjugation to lipids, cell penetrating peptides or antibodies. Antisense conjugates are able to induce the long-lasting correction of DM1 pathology at both molecular and functional levels and also efficiently penetrate hard-to-reach tissues such as cardiac muscle. Delivery to the CNS at clinically relevant levels remains challenging and the use of alternative administration routes may be necessary to ameliorate some of the symptoms experienced by DM1 patients. With several antisense therapies currently in clinical trials, the outlook for achieving a clinically approved treatment for patients has never looked more promising.
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Affiliation(s)
- Jessica Stoodley
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
| | - Francisco Vallejo-Bedia
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
| | - David Seone-Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
| | - Manuel Debasa-Mouce
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
| | - Matthew J A Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
| | - Miguel A Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, Oxford OX3 7TY, UK
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Gawlig C, Rühl M. Investigation of the Influence of Charge State and Collision Energy on Oligonucleotide Fragmentation by Tandem Mass Spectrometry. Molecules 2023; 28:1169. [PMID: 36770836 DOI: 10.3390/molecules28031169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Due to the increasing pharmaceutical interest of oligonucleotides, for example in antisense therapy and vaccines, their analytical characterization is of fundamental importance due to their complex structure. For this purpose, mass spectrometry is a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid can reliably be gained via tandem mass spectrometry (MSMS) fragmentation. In this work, we present the characteristic fragmentation behavior of short-chain oligonucleotides (15-35 nucleotides) with respect to the collision-induced dissociation (CID) voltage used. The relationship and influence of the length of the oligonucleotide and its charge state is also discussed. The results presented here can be helpful for estimating the required fragmentation energies of short-chain oligonucleotides and their sequencing.
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Van Giesen KJ, Thompson MJ, Meng Q, Lovelock SL. Biocatalytic Synthesis of Antiviral Nucleosides, Cyclic Dinucleotides, and Oligonucleotide Therapies. JACS Au 2023; 3:13-24. [PMID: 36711092 PMCID: PMC9875237 DOI: 10.1021/jacsau.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 05/27/2023]
Abstract
Nucleosides, nucleotides, and oligonucleotides modulate diverse cellular processes ranging from protein production to cell signaling. It is therefore unsurprising that synthetic analogues of nucleosides and their derivatives have emerged as a versatile class of drug molecules for the treatment of a wide range of disease areas. Despite their great therapeutic potential, the dense arrangements of functional groups and stereogenic centers present in nucleic acid analogues pose a considerable synthetic challenge, especially in the context of large-scale manufacturing. Commonly employed synthetic methods rely on extensive protecting group manipulations, which compromise step-economy and result in high process mass intensities. Biocatalytic approaches have the potential to address these limitations, enabling the development of more streamlined, selective, and sustainable synthetic routes. Here we review recent achievements in the biocatalytic manufacturing of nucleosides and cyclic dinucleotides along with progress in developing enzymatic strategies to produce oligonucleotide therapies. We also highlight opportunities for innovations that are needed to facilitate widespread adoption of these biocatalytic methods across the pharmaceutical industry.
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Affiliation(s)
| | | | | | - Sarah L. Lovelock
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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de la Torre BG, Albericio F. The Pharmaceutical Industry in 2022: An Analysis of FDA Drug Approvals from the Perspective of Molecules. Molecules 2023; 28:molecules28031038. [PMID: 36770706 PMCID: PMC9921400 DOI: 10.3390/molecules28031038] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
While 2021 ended with the world engulfed in the COVID-19 Omicron wave, 2022 has ended in almost all countries, except China, with COVID-19 being likened to the flu. In this context, the U.S. Food and Drug Administration (FDA) has authorized only 37 new drugs this year compared to an average of 52 in the last four years. Thus 2022 is the second lowest harvest after 2016 in the last six years. This ranking may be transient and will be confirmed in the coming years. In this regard, the reduction in the number of drugs accepted by the FDA this year applies only to the so-called small molecules as there has been no variation in the respective numbers of biologics or TIDES (peptides and oligonucleotides). Monoclonal antibodies (mAbs) continue to be the class with the most drugs authorized (9), while proteins/enzymes (5) and an antibody-drug conjugate complete the biologics harvest. In 2022, five TIDES and seven drugs inspired by natural products have received the green light, thus showing the same tendency as in previous years. Finally, pharmaceutical agents with nitrogen aromatic heterocycles and/or fluorine atoms continue to be predominant among small molecules this year. Furthermore, three drugs have been approved for imaging, reinforcing the trend in recent years for this class of treatments. A keyword in 2022 is bispecificity since four drugs have this property (two mAbs, one protein, and one peptide). Herein, the 37 new drugs approved by the FDA in 2022 are analyzed. On the basis of chemical structure alone, these drugs are classified as the following: biologics (antibodies, antibody-drug conjugates, proteins/enzymes), TIDES (peptide and oligonucleotides), combined drugs, natural products; nitrogen aromatic heterocycles, fluorine-containing molecules, and other small molecules.
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Affiliation(s)
- Beatriz G. de la Torre
- Kwazulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: + 27-614047528 (B.G.d.l.T.); +27-614009144 (F.A.)
| | - Fernando Albericio
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: + 27-614047528 (B.G.d.l.T.); +27-614009144 (F.A.)
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Nicholson TA, Sagmeister M, Wijesinghe SN, Farah H, Hardy RS, Jones SW. Oligonucleotide Therapeutics for Age-Related Musculoskeletal Disorders: Successes and Challenges. Pharmaceutics 2023; 15:237. [PMID: 36678864 PMCID: PMC9866666 DOI: 10.3390/pharmaceutics15010237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/04/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Age-related disorders of the musculoskeletal system including sarcopenia, osteoporosis and arthritis represent some of the most common chronic conditions worldwide, for which there remains a great clinical need to develop safer and more efficacious pharmacological treatments. Collectively, these conditions involve multiple tissues, including skeletal muscle, bone, articular cartilage and the synovium within the joint lining. In this review, we discuss the potential for oligonucleotide therapies to combat the unmet clinical need in musculoskeletal disorders by evaluating the successes of oligonucleotides to modify candidate pathological gene targets and cellular processes in relevant tissues and cells of the musculoskeletal system. Further, we discuss the challenges that remain for the clinical development of oligonucleotides therapies for musculoskeletal disorders and evaluate some of the current approaches to overcome these.
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Affiliation(s)
- Thomas A. Nicholson
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Michael Sagmeister
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Susanne N. Wijesinghe
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Hussein Farah
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Rowan S. Hardy
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Simon W. Jones
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
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Zhang Z, Huang Y, Li J, Su F, Kuo JCT, Hu Y, Zhao X, Lee RJ. Antitumor Activity of Anti-miR-21 Delivered through Lipid Nanoparticles. Adv Healthc Mater 2023; 12:e2202412. [PMID: 36412002 DOI: 10.1002/adhm.202202412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/17/2022] [Indexed: 11/23/2022]
Abstract
The ability of lipid nanoparticles (LNPs) to deliver nucleic acids have shown a great therapeutic potential to treat a variety of diseases. Here, an optimized formulation of QTsome lipid nanoparticles (QTPlus) is utilized to deliver an anti-miR-21 (AM21) against cancer. The miR-21 downstream gene regulation and antitumor activity is evaluated using mouse and human cancer cells and macrophages. The antitumor activity of QTPlus encapsulating AM21 (QTPlus-AM21) is further evaluated in combination with erlotinib and atezolizumab (ATZ). QTPlus-AM21 demonstrates a superior miR-21-dependent gene regulation and eventually inhibits A549 non-small cell lung cancer growth in vitro. QTPlus-AM21 further induces chemo-sensitization of A549 cells to erlotinib with a combination index of 0.6 in inhibiting A549 cell growth. When systemically administers to MC38 tumor-bearing mouse model, QTPlus-AM21 exhibits an antitumor immune response with over 80% tumor growth inhibition (TGI%) and over twofold and fourfold PD-1 and PD-L1 upregulation in tumors and spleens. The combination therapy of QTPlus-AM21 and ATZ further shows a higher antitumor response (TGI% over 90%) and successfully increases M1 macrophages and CD8 T cells into TME. This study provides new insights into the antitumor mechanism of AM21 and shows great promise of QTPlus-AM21 in combination with chemotherapies and immunotherapies.
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Affiliation(s)
- Zhongkun Zhang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 W 12th Avenue, Columbus, OH, 43210, USA
| | - Yirui Huang
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 W 12th Avenue, Columbus, OH, 43210, USA
| | - Jing Li
- Zhejiang Haichang Biotechnology Co., Ltd., Hangzhou, Zhejiang, 310000, P. R. China
| | - Fei Su
- Zhejiang Haichang Biotechnology Co., Ltd., Hangzhou, Zhejiang, 310000, P. R. China
| | - Jimmy Chun-Tien Kuo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 W 12th Avenue, Columbus, OH, 43210, USA
| | - Yingwen Hu
- The Whiteoak Group, Inc., Rockville, MD, 20855, USA
| | - Xiaobin Zhao
- The Whiteoak Group, Inc., Rockville, MD, 20855, USA
| | - Robert J Lee
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, 500 W 12th Avenue, Columbus, OH, 43210, USA
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58
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Han G, Lin C, Yin H. Use of Glycine to Augment Exon Skipping and Cell Therapies for Duchenne Muscular Dystrophy. Methods Mol Biol 2023; 2587:165-182. [PMID: 36401030 DOI: 10.1007/978-1-0716-2772-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antisense oligonucleotide (AO)-based exon-skipping and cell therapies are the main therapeutic approaches for Duchenne muscular dystrophy (DMD). Insufficient systemic delivery leading to low therapeutic efficacy limits the former; low transplantation efficiency hampers the latter. Here we describe how glycine can address these issues by augmenting satellite proliferation and muscle regeneration, resulting in enhanced AO uptake in regenerating myofibers and cell transplantation efficiency in dystrophic mice. The dual functionality of glycine demonstrated in AO-based exon-skipping and cell therapies presents a simple and efficient method to augment AO potency and cell transplantation efficacy in DMD and other muscle diseases.
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Affiliation(s)
- Gang Han
- School of Medical Laboratory & Department of Cell Biology, Tianjin Medical University, Tianjin, China.
| | - Caorui Lin
- School of Medical Laboratory & Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - HaiFang Yin
- School of Medical Laboratory & Department of Cell Biology, Tianjin Medical University, Tianjin, China.
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Il’in VA, Pyzhik EV, Balakhonov AB, Kiryushin MA, Shcherbatova EV, Kuznetsov AA, Kostin PA, Golovin AV, Korshun VA, Brylev VA, Sapozhnikova KA, Kopylov AM, Pavlova GV, Pronin IN. Radiochemical Synthesis of 4-[ 18F]FluorobenzylAzide and Its Conjugation with EGFR-Specific Aptamers. Molecules 2022; 28:molecules28010294. [PMID: 36615487 PMCID: PMC9821934 DOI: 10.3390/molecules28010294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Central nervous system tumors related to gliomas are of neuroectodermal origin and cover about 30% of all primary brain tumors. Glioma is not susceptible to any therapy and surgical attack remains one of the main approaches to its treatment. Preoperative tumor imaging methods, such as positron emission tomography (PET), are currently used to distinguish malignant tissue to increase the accuracy of glioma removal. However, PET is lacking a specific visualization of cells possessing certain molecular markers. Here, we report an application of aptamers to enhancing specificity in imaging tumor cells bearing the epidermal growth factor receptor (EGFR). Glioblastoma is characterized by increased EGFR expression, as well as mutations of this receptor associated with active division, migration, and adhesion of tumor cells. Since 2021, EGFR has been included into the WHO classification of gliomas as a molecular genetic marker. To obtain conjugates of aptamers GR20 and GOL1-specific to EGFR, a 4-[18F]fluorobenzylazide radiotracer was used as a synthon. For the production of the synthon, a method of automatic synthesis on an Eckert & Ziegler research module was adapted and modified using spirocyclic iodonium ylide as a precursor. Conjugation of 4-[18F]fluorobenzylazide and alkyne-modified aptamers was carried out using Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) with/without the TBTA ligand. As a result, it was possible to obtain 18F-labelled conjugates with 97% radiochemical purity for [18F]FB-GR20 and 98% for [18F]FB-GOL1. The obtained conjugates can be used for further studies in PET analysis on model animals with grafted glioblastoma.
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Affiliation(s)
- Viktor A. Il’in
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
- Correspondence: ; Tel.: +7-929-938-50-30
| | - Elena V. Pyzhik
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Anton B. Balakhonov
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Maksim A. Kiryushin
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Evgeniya V. Shcherbatova
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Andrey A. Kuznetsov
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Pavel A. Kostin
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
| | - Andrey V. Golovin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir A. Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Kseniya A. Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexey M. Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Galina V. Pavlova
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
- Medical Genetics Department, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences, 117485 Moscow, Russia
| | - Igor N. Pronin
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia
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Zhang A, Kondhare D, Leonard P, Seela F. DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction. Chemistry 2022; 28:e202202412. [PMID: 36178316 PMCID: PMC10100337 DOI: 10.1002/chem.202202412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 12/30/2022]
Abstract
Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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Shepard CP, Emehiser RG, Karmakar S, Hrdlicka PJ. Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA. Molecules 2022; 28. [PMID: 36615321 DOI: 10.3390/molecules28010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
The development of chemically modified oligonucleotides enabling robust, sequence-unrestricted recognition of complementary chromosomal DNA regions has been an aspirational goal for scientists for many decades. While several groove-binding or strand-invading probes have been developed towards this end, most enable recognition of DNA only under limited conditions (e.g., homopurine or short mixed-sequence targets, low ionic strength, fully modified probe strands). Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of intercalator-functionalized nucleotides, are predisposed to recognize DNA targets due to their labile nature and high affinity towards complementary DNA. Here, we set out to gain further insight into the design parameters that impact the thermal denaturation properties and binding affinities of Invader probes. Towards this end, ten Invader probes were designed, and their biophysical properties and binding to model DNA hairpins and chromosomal DNA targets were studied. A Spearman's rank-order correlation analysis of various parameters was then performed. Densely modified Invader probes were found to result in efficient recognition of chromosomal DNA targets with excellent binding specificity in the context of denaturing or non-denaturing fluorescence in situ hybridization (FISH) experiments. The insight gained from the initial phase of this study informed subsequent probe optimization, which yielded constructs displaying improved recognition of chromosomal DNA targets. The findings from this study will facilitate the design of efficient Invader probes for applications in the life sciences.
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Kalinova R, Mladenova K, Petrova S, Doumanov J, Dimitrov I. Nanoarchitectonics of Spherical Nucleic Acids with Biodegradable Polymer Cores: Synthesis and Evaluation. Materials (Basel) 2022; 15:8917. [PMID: 36556721 PMCID: PMC9786340 DOI: 10.3390/ma15248917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Spherical nucleic acids (SNAs) have gained significant attention due to their unique properties allowing them to overcome the challenges that face current nanocarriers used for gene therapies. The aim of this study is to synthesize and characterize polymer-oligonucleotide conjugates of different architecture and to evaluate the possibility of forming SNAs with biodegradable cores. Initially, two types of azide (multi)functional polyester-based (co)polymers were successfully synthesized and characterized. In the next step, short oligonucleotide strands were attached to the polymer chains applying the highly efficient and metal-free "click" reaction, thus forming conjugates with block or graft architecture. Both conjugates spontaneously self-assembled in aqueous media forming nanosized SNAs with a biodegradable polyester core and a surface of oligonucleotide chains as evidenced from dynamic and electrophoretic light scattering measurements. The nano-assemblies were in vitro evaluated for potential cytotoxicity. Furthermore, the interactions of the newly synthesized SNAs with membrane lipids were studied. The preliminary results indicate that both types of polymer-based SNAs are good candidates for potential application in gene therapy and that it is worth to be further evaluated.
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Affiliation(s)
- Radostina Kalinova
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St., bl. 103-A, 1113 Sofia, Bulgaria
| | - Kirilka Mladenova
- Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Svetla Petrova
- Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Jordan Doumanov
- Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Ivaylo Dimitrov
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St., bl. 103-A, 1113 Sofia, Bulgaria
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Kotammagari TK, Tähtinen P, Lönnberg T. Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences. Chemistry 2022; 28:e202202530. [PMID: 36108095 PMCID: PMC10092508 DOI: 10.1002/chem.202202530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 12/14/2022]
Abstract
Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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64
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Burel SA, Machemer T, Baker BF, Kwoh TJ, Paz S, Younis H, Henry SP. Early-Stage Identification and Avoidance of Antisense Oligonucleotides Causing Species-Specific Inflammatory Responses in Human Volunteer Peripheral Blood Mononuclear Cells. Nucleic Acid Ther 2022; 32:457-472. [PMID: 35976085 DOI: 10.1089/nat.2022.0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A human peripheral blood mononuclear cell (PBMC)-based assay was developed to identify antisense oligonucleotide (ASO) with the potential to activate a cellular innate immune response outside of an acceptable level. The development of this assay was initiated when ISIS 353512 targeting the messenger ribonucleic acid for human C-reactive protein (CRP) was tested in a phase I clinical trial, in which healthy human volunteers unexpectedly experienced increases in interleukin-6 (IL-6) and CRP. This level of immune stimulation was not anticipated following rodent and nonhuman primate safety studies in which no evidence of exaggerated proinflammatory effects were observed. The IL-6 increase induced by ISIS 353512 was caused by activation of B cells. The IL-6 induction was inhibited by chloroquine pretreatment of PBMCs and the nature of ASOs suggested that the response is mediated by a Toll-like receptor (TLR), in all likelihood TLR9. While assessing the inter PBMC donor variability, two classes of human PBMC responders to ISIS 353512 were identified (discriminator and nondiscriminators). The discriminator donor PBMCs were shown to produce low level of IL-6 after 24 h in culture, in the absence of ASO treatment. The PBMC assay using discriminator donors was shown to be reproducible, allowing to assess reliably the immune potential of ASOs by comparison to known benchmark ASO controls that were previously shown to be either safe or inflammatory in clinical trials. Clinical Trial registration numbers: NCT00048321 NCT00330330 NCT00519727.
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Affiliation(s)
| | - Todd Machemer
- IONIS Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | - T Jesse Kwoh
- IONIS Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Suzanne Paz
- IONIS Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Husam Younis
- IONIS Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Scott P Henry
- IONIS Pharmaceuticals, Inc., Carlsbad, California, USA
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65
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Minkner R, Boonyakida J, Park EY, Wätzig H. Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks? Electrophoresis 2022; 43:2402-2427. [PMID: 36285667 DOI: 10.1002/elps.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.
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Affiliation(s)
- Robert Minkner
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jirayu Boonyakida
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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66
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Terada C, Kawamoto S, Yamayoshi A, Yamamoto T. Chemistry of Therapeutic Oligonucleotides That Drives Interactions with Biomolecules. Pharmaceutics 2022; 14:pharmaceutics14122647. [PMID: 36559141 PMCID: PMC9781680 DOI: 10.3390/pharmaceutics14122647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Oligonucleotide therapeutics that can modulate gene expression have been gradually developed for clinical applications over several decades. However, rapid advances have been made in recent years. Artificial nucleic acid technology has overcome many challenges, such as (1) poor target affinity and selectivity, (2) low in vivo stability, and (3) classical side effects, such as immune responses; thus, its application in a wide range of disorders has been extensively examined. However, even highly optimized oligonucleotides exhibit side effects, which limits the general use of this class of agents. In this review, we discuss the physicochemical characteristics that aid interactions between drugs and molecules that belong to living organisms. By systematically organizing the related data, we hope to explore avenues for symbiotic engineering of oligonucleotide therapeutics that will result in more effective and safer drugs.
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Abstract
Drug discovery and development has experienced an incredible paradigm shift in the past two decades. What once was considered a predominant R&D landscape of small molecules within a prescribed properties and mechanism space now includes an innovative wave of new chemical modalities. Scientists in the pharmaceutical industry can now strategize across a variety of modalities to find the best option to modulate a given target and provide treatment for a specific disease. We have witnessed a remarkable change not only in molecular design but also in creative approaches to drug delivery that have enabled advancement of novel modalities to clinical studies. In this Microperspective, we evaluate the critical differences between traditional small molecules and beyond rule of 5 compounds, peptides, oligonucleotides, and biologics for advancing into development, particularly their pharmacokinetic profiles and drug delivery strategies.
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Affiliation(s)
- Maria-Jesus Blanco
- Chemical
Sciences, Atavistik Bio, 75 Sidney Street, Cambridge Massachusetts 02139, United States
| | - Kevin M. Gardinier
- Discovery
Research, Karuna Therapeutics, 99 High Street Boston, Massachusetts 02110, United States
| | - Mark N. Namchuk
- Department
of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 25 Shattuck Street Boston, Massachusetts 02115, United States
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68
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da Silva AG, Goulart LR, Löffler P, Code C, Neves AF. Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples. Int J Mol Sci 2022; 23:ijms232213866. [PMID: 36430340 PMCID: PMC9693377 DOI: 10.3390/ijms232213866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Limitations in the detection of cocirculating flaviviruses such as Dengue and Zika lead us to propose the use of aptameric capture of the viral RNA in combination with RT-PCR (APTA-RT-PCR). Aptamers were obtained via SELEX and next-generation sequencing, followed by colorimetric and fluorescent characterizations. An APTA-RT-PCR assay was developed, optimized, and tested against the viral RNAs in 108 serum samples. After selection, sequence APTAZC10 was designed as a bifunctional molecular beacon (APTAZC10-MB), exhibiting affinity for the viral targets. APTA-RT-PCR was able to detect Dengue and Zika RNA in 43% and 8% of samples, respectively. Our results indicate that APTAZC10-MB and APTA-RT-PCR will be useful to improve the detection of Dengue and Zika viruses in a fast molecular assay for the improvement of infectious disease surveillance.
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Affiliation(s)
- Amanda Gabrielle da Silva
- Institute of Physics, Postgraduate Program in Exact and Technological Sciences, Universidade Federal de Catalão, Catalão 75704-020, Brazil
| | - Luiz Ricardo Goulart
- Nanobiotechnology Laboratory, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia 38402-022, Brazil
| | - Philipp Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Christian Code
- Dianox ApS, Fruebjergvej 3, 2100 København, Denmark
- PhyLife Physical Life Sciences, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Catalão, Catalão 75704-020, Brazil
- Correspondence:
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69
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Kumar RK, Sanghvi YS, Reddy PY, Banerjee S. An Improved Scalable Synthesis of the Potent Antiviral (S)-HPMPA. Curr Protoc 2022; 2:e602. [PMID: 36440983 DOI: 10.1002/cpz1.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We present an improved synthesis of (S)-HPMPA (1) from an easily accessible and commercially available compound, (S)-3-(benzyloxy)propane-1,2-diol (10). Tritylation of primary alcohol 10 was highly selective, and pure product was isolated in good yield. Alkylation of (R)-1-(benzyloxy)-3-(trityloxy)propan-2-ol (11) with diethyl p-toluenesulfonyloxymethyl phosphonate (6) using sodium hydride in tetrahydrofuran followed by detritylation afforded the desired chiral synthon 12. Tosylation of the primary alcohol and subsequent reaction with sodium adeninate afforded protected S-HPMPA (14). Global deprotection using concentrated hydrochloric acid in a sealed tube afforded S-HPMA (1), and the deprotected 1 was crystallized from water and acetone to obtain a 99% pure product. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of (R)-1-(benzyloxy)-3-(trityloxy)propan-2-ol (11) Basic Protocol 2: Preparation of diethyl (S)-(((1-(benzyloxy)-3-hydroxypropan-2-yl)oxy)methyl)phosphonate (12) Basic Protocol 3: Preparation of (R)-3-(benzyloxy)-2-((diethoxyphosphoryl)methoxy)propyl-4-methylbenzenesulfonate (13) Basic Protocol 4: Preparation of diethyl (S)-(((1-(6-amino-9H-purin-9-yl)-3-(benzyloxy)propan-2-yl)oxy)methyl)phosphonate (14) Support Protocol 1: Preparation of sodium adeninate Basic Protocol 5: Preparation of (S)-(((1-(6-amino-9H-purin-9-yl)-3-hydroxypropan-2-yl)oxy)methyl)phosphonic acid (1).
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Affiliation(s)
| | - Yogesh S Sanghvi
- Sapala Organics Pvt. Ltd, Hyderabad, Telangana, India
- Rasayan Inc., Encinitas, California, USA
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70
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Stincarelli MA, Rocca A, Antonelli A, Rossolini GM, Giannecchini S. Antiviral Activity of Oligonucleotides Targeting the SARS-CoV-2 Genomic RNA Stem-Loop Sequences within the 3'-End of the ORF1b. Pathogens 2022; 11:1286. [PMID: 36365037 PMCID: PMC9696570 DOI: 10.3390/pathogens11111286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/30/2023] Open
Abstract
Increased evidence shows vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited no long-term efficacy and limited worldwide availability, while existing antivirals and treatment options have only limited efficacy. In this study, the main objective was the development of antiviral strategies using nucleic acid-based molecules. To this purpose, partially overlapped 6-19-mer phosphorothioate deoxyoligonucleotides (S-ONs) designed on the SARS-CoV-2 genomic RNA stem-loop packaging sequences within the 3' end of the ORF1b were synthetized using the direct and complementary sequence. Among the S-ONs tested, several oligonucleotides exhibited a fifty percent inhibitory concentration antiviral activity ranging from 0.27 to 34 μM, in the absence of cytotoxicity. The S-ON with a scrambled sequence used in the same conditions was not active. Moreover, selected 10-mer S-ONs were tested using different infectious doses and against different SARS-CoV-2 variants, showing comparable antiviral activity that was abrogated when the central sequence was mutated. Experiments to evaluate the intracellular functional target localization of the S-ON inhibitory activity were also performed. Collectively the data indicate that the SARS-CoV-2 packaging region in the 3' end of the ORF1b may be a promising target candidate for further investigation to develop innovative nucleic-acid-based antiviral therapy.
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Affiliation(s)
| | - Arianna Rocca
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, I-50134 Florence, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
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71
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Kennelly SA, Moorthy R, Otero RS, Harki DA. Expanding Catch and Release DNA Decoy (CRDD) Technology with Pyrimidine Mimics. Chemistry 2022; 28:e202201355. [PMID: 35849314 PMCID: PMC9588621 DOI: 10.1002/chem.202201355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Catch and release DNA decoys (CRDDs) utilize photochemically responsive nucleoside analogues that generate abasic sites upon exposure to light. Herein, we describe the synthesis and evaluation of four candidate CRDD monomers containing nucleobases that mimic endogenous pyrimidines: 2-nitroimidazole (2-NI), 2-nitrobenzene (2-NB), 2-nitropyrrole (2-NP) and 3-nitropyrrole (3-NP). Our studies reveal that 2-NI and 2-NP can function as CRDDs, whereas 3-NP and 2-NB undergo decomposition and transformation to a higher-ordered structure upon photolysis, respectively. When incorporated into DNA, 2-NP undergoes rapid photochemical cleavage of the anomeric bond (1.8 min half-life) to yield an abasic site. Finally, we find that all four pyrimidine mimics show significantly greater stability when base-paired against the previously reported 7-nitroindole CRDD monomer. Our work marks the expansion of CRDD technology to both purine and pyrimidine scaffolds.
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Affiliation(s)
- Samantha A. Kennelly
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ramkumar Moorthy
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ruben Silva Otero
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Daniel A. Harki
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
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72
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Dimitrov E, Toncheva-Moncheva N, Bakardzhiev P, Forys A, Doumanov J, Mladenova K, Petrova S, Trzebicka B, Rangelov S. Original Synthesis of a Nucleolipid for Preparation of Vesicular Spherical Nucleic Acids. Nanomaterials (Basel) 2022; 12:3645. [PMID: 36296836 PMCID: PMC9609631 DOI: 10.3390/nano12203645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Spherical nucleic acids (SNAs)-nanostructures, consisting of a nanoparticle core densely functionalized with a shell of short oligonucleotide strands-are a rapidly emerging class of nanoparticle-based therapeutics with unique properties and specific applications as drug and nucleic acid delivery and gene regulation materials. In this contribution, we report on the preparation of hollow SNA nanoconstructs by co-assembly of an originally synthesized nucleolipid-a hybrid biomacromolecule, composed of a lipidic residue, covalently linked to a DNA oligonucleotide strand-with other lipids. The nucleolipid was synthesized via a click chemistry approach employing initiator-free, UV light-induced thiol-ene coupling of appropriately functionalized intermediates, performed in mild conditions using a custom-made UV light-emitting device. The SNA nanoconstructs were of a vesicular structure consisting of a self-closed bilayer membrane in which the nucleolipid was intercalated via its lipid-mimetic residue. They were in the lower nanometer size range, moderately negatively charged, and were found to carry thousands of oligonucleotide strands per particle, corresponding to a grafting density comparable to that of other SNA structures. The surface density of the strands on the bilayer implied that they adopted an unextended conformation. We demonstrated that preformed vesicular structures could be successfully loaded with either hydrophilic or hydrophobic dyes.
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Affiliation(s)
- Erik Dimitrov
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
| | - Natalia Toncheva-Moncheva
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
| | - Pavel Bakardzhiev
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
| | - Aleksander Forys
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, M. Curie-Sklodowskiej 34, 41-819 Zabrze, Poland
| | - Jordan Doumanov
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski, Dragan Tsankov Blvd. 8, 1164 Sofia, Bulgaria
| | - Kirilka Mladenova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski, Dragan Tsankov Blvd. 8, 1164 Sofia, Bulgaria
| | - Svetla Petrova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski, Dragan Tsankov Blvd. 8, 1164 Sofia, Bulgaria
| | - Barbara Trzebicka
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, M. Curie-Sklodowskiej 34, 41-819 Zabrze, Poland
| | - Stanislav Rangelov
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St. 103A, 1113 Sofia, Bulgaria
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73
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Sherazi SAM, Abbasi A, Jamil A, Uzair M, Ikram A, Qamar S, Olamide AA, Arshad M, Fried PJ, Ljubisavljevic M, Wang R, Bashir S. Molecular hallmarks of long non-coding RNAs in aging and its significant effect on aging-associated diseases. Neural Regen Res 2022; 18:959-968. [PMID: 36254975 PMCID: PMC9827784 DOI: 10.4103/1673-5374.355751] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aging is linked to the deterioration of many physical and cognitive abilities and is the leading risk factor for Alzheimer's disease. The growing aging population is a significant healthcare problem globally that researchers must investigate to better understand the underlying aging processes. Advances in microarrays and sequencing techniques have resulted in deeper analyses of diverse essential genomes (e.g., mouse, human, and rat) and their corresponding cell types, their organ-specific transcriptomes, and the tissue involved in aging. Traditional gene controllers such as DNA- and RNA-binding proteins significantly influence such programs, causing the need to sort out long non-coding RNAs, a new class of powerful gene regulatory elements. However, their functional significance in the aging process and senescence has yet to be investigated and identified. Several recent researchers have associated the initiation and development of senescence and aging in mammals with several well-reported and novel long non-coding RNAs. In this review article, we identified and analyzed the evolving functions of long non-coding RNAs in cellular processes, including cellular senescence, aging, and age-related pathogenesis, which are the major hallmarks of long non-coding RNAs in aging.
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Affiliation(s)
- Syed Aoun Mehmood Sherazi
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Asim Abbasi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Abdullah Jamil
- Department of Pharmacology, Government College University, Faisalabad, Pakistan
| | - Mohammad Uzair
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Ayesha Ikram
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Shanzay Qamar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | - Muhammad Arshad
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Islamabad, Pakistan
| | - Peter J. Fried
- Department of Neurology, Berenson-Allen Center for Noninvasive Brain Stimulation and Division of Cognitive Neurology, Beth Israel Deaconess Medical Center (KS 158), Harvard Medical School, Boston, MA, USA
| | - Milos Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ran Wang
- Department of Psychiatry, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China,Mental Health Institute of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Shahid Bashir
- Neuroscience Center, King Fahad Specialist Hospital, Dammam, Saudi Arabia,Correspondence to: Shahid Bashir, .
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74
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Henry SP, Arfvidsson C, Arrington J, Canadi J, Crowe D, Gupta S, Lohmann S, Massonnet B, Mytych D, Rogers T, Rogers H, Stebbins C, Stovold C, Verthelyi D, Vigil A, Xuan C, Xu Y, Yu R, Klem T. Assessment of the Immunogenicity Potential for Oligonucleotide-Based Drugs. Nucleic Acid Ther 2022; 32:369-377. [PMID: 36178478 DOI: 10.1089/nat.2021.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Therapeutic oligonucleotides (ONs) have characteristics of both small molecules and biologics. Although safety assessment of ONs largely follows guidelines established for small molecules, the unique characteristics of ONs often require incorporation of concepts from the safety assessment of biologics. The assessment of immunogenicity for ON therapeutics is one area where the approach is distinct from either established small molecule or biologic platforms. Information regarding immunogenicity of ONs is limited, but indicates that administration of ONs can result in antidrug antibody formation. In this study, we summarize the collective experience of the Oligonucleotide Safety Working Group in designing the immunogenicity assessment appropriate for this class of therapeutic, including advice on assay development, clinical monitoring, and evaluation of the impact of immunogenicity on exposure, efficacy, and safety of therapeutic ONs.
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Affiliation(s)
- Scott P Henry
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | | | | | | | - Dave Crowe
- Disc Medicine, Cambridge, Massachusetts, USA
| | | | - Sabine Lohmann
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | | | | | | | | | | | | | | | - Adam Vigil
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Chi Xuan
- Alnylam, Cambridge, Massachusetts, USA
| | - Yuanxin Xu
- Intellia Therapeutics, Cambridge, Massachusetts, USA
| | - Rosie Yu
- Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Thomas Klem
- Homology Medicines, Bedford, Massachusetts, USA (formerly with Sarepta Therapeutics Headquarters, Cambridge, Massachusetts, USA)
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75
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Gerbatin RR, Augusto J, Morris G, Campbell A, Worm J, Langa E, Reschke CR, Henshall DC. Investigation of MicroRNA-134 as a Target against Seizures and SUDEP in a Mouse Model of Dravet Syndrome. eNeuro 2022; 9:ENEURO. [PMID: 36240080 DOI: 10.1523/ENEURO.0112-22.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/31/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022] Open
Abstract
Dravet syndrome (DS) is a catastrophic form of pediatric epilepsy mainly caused by noninherited mutations in the SCN1A gene. DS patients suffer severe and life-threatening focal and generalized seizures which are often refractory to available anti-seizure medication. Antisense oligonucleotides (ASOs) based approaches may offer treatment opportunities in DS. MicroRNAs are short noncoding RNAs that play a key role in brain structure and function by post-transcriptionally regulating gene expression, including ion channels. Inhibiting miRNA-134 (miR-134) using an antimiR ASO (Ant-134) has been shown to reduce evoked seizures in juvenile and adult mice and reduce epilepsy development in models of focal epilepsy. The present study investigated the levels of miR-134 and whether Ant-134 could protect against hyperthermia-induced seizures, spontaneous seizures and mortality (SUDEP) in F1.Scn1a(+/-)tm1kea mice. At P17, animals were intracerebroventricular injected with 0.1-1 nmol of Ant-134 and subject to a hyperthermia challenge at postnatal day (P)18. A second cohort of P21 F1.Scn1a(+/-)tm1kea mice received Ant-134 and were followed by video and EEG monitoring until P28 to track the incidence of spontaneous seizures and SUDEP. Hippocampal and cortical levels of miR-134 were similar between wild-type (WT) and F1.Scn1a(+/-)tm1kea mice. Moreover, Ant-134 had no effect on hyperthermia-induced seizures, spontaneous seizures and SUDEP incidence were unchanged in Ant-134-treated DS mice. These findings suggest that targeting miR-134 does not have therapeutic applications in DS.
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76
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Davis SM, Hariharan VN, Lo A, Turanov AA, Echeverria D, Sousa J, McHugh N, Biscans A, Alterman JF, Karumanchi SA, Moore MJ, Khvorova A. Chemical optimization of siRNA for safe and efficient silencing of placental sFLT1. Mol Ther Nucleic Acids 2022; 29:135-49. [PMID: 35847173 DOI: 10.1016/j.omtn.2022.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
Preeclampsia (PE) is a rising, potentially lethal complication of pregnancy. PE is driven primarily by the overexpression of placental soluble fms-like tyrosine kinase 1 (sFLT1), a validated diagnostic and prognostic marker of the disease when normalized to placental growth factor (PlGF) levels. Injecting cholesterol-conjugated, fully modified, small interfering RNAs (siRNAs) targeting sFLT1 mRNA into pregnant mice or baboons reduces placental sFLT1 and ameliorates clinical signs of PE, providing a strong foundation for the development of a PE therapeutic. siRNA delivery, potency, and safety are dictated by conjugate chemistry, siRNA duplex structure, and chemical modification pattern. Here, we systematically evaluate these parameters and demonstrate that increasing 2'-O-methyl modifications and 5' chemical stabilization and using sequence-specific duplex asymmetry and a phosphocholine-docosanoic acid conjugate enhance placental accumulation, silencing efficiency and safety of sFLT1-targeting siRNAs. The optimization strategy here provides a framework for the chemical optimization of siRNAs for PE as well as other targets and clinical indications.
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77
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Studzińska S, Mazurkiewicz-Bełdzińska M, Buszewski B. Development of the Method for Nusinersen and Its Metabolites Identification in the Serum Samples of Children Treated with Spinraza for Spinal Muscular Atrophy. Int J Mol Sci 2022; 23:ijms231710166. [PMID: 36077568 PMCID: PMC9456300 DOI: 10.3390/ijms231710166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
The application of oligonucleotides as drugs for different genetic diseases is increasing rapidly. Since 2016 they are used during spinal muscular atrophy treatment with the use of nusinersen oligonucleotide. The purpose of this study was to improve methods for the analysis of serum samples of patients treated with nusinersen. The results showed that liquid-liquid extraction (with phenol/chloroform) is insufficient and an additional purification step using solid-phase extraction is necessary. The best results were obtained for microextraction by packed sorbents. Important parameters in the optimization of the method were mainly the type of amine in the mobile phase and the stationary phase. Both influenced the selectivity of metabolite separation and thus their correct identification; while amine type impacted also the intensity of signals. Finally, the highest resolution of separation and the highest peak areas were obtained for N,N-dimethylbutylamine or N,N-diisopropylthylamine with an octadecyl column with a terminal aryl group. Over a dozen of metabolites were successfully identified with the use of methods developed during the study. The 3′ exonucleases and 5′ exonucleases were mainly responsible for nusinersen metabolism, consequently, 3′end shortmers, and 5′end shortmers were observed, as well as metabolites with simultaneous loss of bases at both ends of the sequence. However, some depurination and depyrimidination products were also identified. To the best of our knowledge, this is the first report on nusinersen and its metabolite identification in serum samples by liquid chromatography and mass spectrometry.
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Affiliation(s)
- Sylwia Studzińska
- Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland
- Correspondence: ; Tel.: +48-56-6114753
| | | | - Bogusław Buszewski
- Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland
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78
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Zhang A, Kondhare D, Leonard P, Seela F. Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration. Chemistry 2022; 28:e202201294. [PMID: 35652726 PMCID: PMC9543212 DOI: 10.1002/chem.202201294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/15/2022]
Abstract
DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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79
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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80
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures. Chemistry 2022; 11:e202200090. [PMID: 35608081 PMCID: PMC9127747 DOI: 10.1002/open.202200090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 04/22/2022] [Indexed: 12/27/2022]
Abstract
DNA G‐quadruplexes (G4s) are key structures for the development of targeted anticancer therapies. In this context, ligands selectively interacting with G4s can represent valuable anticancer drugs. Aiming at speeding up the identification of G4‐targeting synthetic or natural compounds, we developed an affinity chromatography‐based assay, named G‐quadruplex on Oligo Affinity Support (G4‐OAS), by synthesizing G4‐forming sequences on commercially available polystyrene OAS. Then, due to unspecific binding of several hydrophobic ligands on nude OAS, we moved to Controlled Pore Glass (CPG). We thus conceived an ad hoc functionalized, universal support on which both the on‐support elongation and deprotection of the G4‐forming oligonucleotides can be performed, along with the successive affinity chromatography‐based assay, renamed as G‐quadruplex on Controlled Pore Glass (G4‐CPG) assay. Here we describe these assays and their applications to the screening of several libraries of chemically different putative G4 ligands. Finally, ongoing studies and outlook of our G4‐CPG assay are reported.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy.,Institute of Biostructures and Bioimages, CNR, Via Tommaso De Amicis, 95, 80145, Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
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81
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Fernández-Delgado M, Sendra L, Herrero MJ, Olivera-Pasquini GG, Batista-Duharte A, Aliño SF. Study of Oligonucleotides Access and Distribution in Human Peripheral Blood Mononuclear Cells. Int J Mol Sci 2022; 23:5839. [PMID: 35628649 PMCID: PMC9143973 DOI: 10.3390/ijms23105839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Therapeutic oligonucleotides have achieved great clinical interest since their approval as drug agents by regulatory agencies but their access and distribution in blood cells are not completely known. We evaluated by flow cytometry the ability of short fluorescent scramble oligonucleotides (ON*) to access human peripheral blood mononuclear cells (PBMC) after incubating with ON* during 1 h and 7 days of culture follow-up 'in vitro'. Blood samples were treated with chemically modified oligonucleotides (phosphorothioate backbone and 2' O-Me ends) to resist nuclease digestion under culture conditions. The ON* internalization was determined after discarding the membrane-associated fluorescence by trypan blue quenching. Whereas the oligonucleotide accessed neutrophils and monocytes rapidly, achieving their maximum in 1 h and 24 h, respectively, lymphocytes required 7 days to achieve the maximum (80% of cells) transfection. The ON*ability to access lymphocyte types (T, B, and NK) and T cell subtypes (CD4+, CD8+, and CD4-CD8-) were similar, with T cells being more accessible. Regulatory CD4+ and CD8+ T cells were classified in low and high Foxp3 expressers, whose expression proved not to alter the ON* internalization during the first hour, achieving 53% of CD4+Foxp3+ and 40% of CD8+Foxp3+ cells. Our results contribute to understanding and improving the management of therapeutic ONs.
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Affiliation(s)
- Manuel Fernández-Delgado
- Service of Hematology and Hemotherapy, Hospital General Universitario de Castellón, 12004 Castelló de la Plana, Spain;
| | - Luis Sendra
- Farmacogenetics and Gene Therapy Group, Instituto de Investigación Sanitaria La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (M.J.H.); (G.G.O.-P.); (S.F.A.)
- Gene Therapy and Pharmacogenomics Group, Department of Pharmacology, Faculty of Medicine, University of Valencia, Av. Blasco Ibáñez 15, 46010 Valencia, Spain
| | - María José Herrero
- Farmacogenetics and Gene Therapy Group, Instituto de Investigación Sanitaria La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (M.J.H.); (G.G.O.-P.); (S.F.A.)
- Gene Therapy and Pharmacogenomics Group, Department of Pharmacology, Faculty of Medicine, University of Valencia, Av. Blasco Ibáñez 15, 46010 Valencia, Spain
| | - Gladys G. Olivera-Pasquini
- Farmacogenetics and Gene Therapy Group, Instituto de Investigación Sanitaria La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (M.J.H.); (G.G.O.-P.); (S.F.A.)
| | - Alexander Batista-Duharte
- GC01 Immunology and Allergy Group, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Av. Menéndez Pidal, s/n, 14004 Córdoba, Spain;
- Laboratório de Imunología Clínica, Dpto Analises Clinicas, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Rod. Araraquara-Jaú—Km 1, Campus Ville, 14800 Araraquara, Sao Paulo, Brazil
| | - Salvador F. Aliño
- Farmacogenetics and Gene Therapy Group, Instituto de Investigación Sanitaria La Fe, Av. Fernando Abril Martorell, 106, 46026 Valencia, Spain; (M.J.H.); (G.G.O.-P.); (S.F.A.)
- Gene Therapy and Pharmacogenomics Group, Department of Pharmacology, Faculty of Medicine, University of Valencia, Av. Blasco Ibáñez 15, 46010 Valencia, Spain
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82
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Abstract
Nucleic Acid (NA) aptamers are oligonucleotides. They are unique due to their secondary and tertiary structure; namely, the secondary structure defines the tertiary one by means of affinity and specificity. Our review is devoted only to DNA and RNA aptamers, since the majority of achievements in this direction were obtained with their application. NA aptamers can be used as macromolecular devices and consist of short single-stranded molecules, which adopt unique three-dimensional structures due to the interaction of complementary parts of the chain and stacking interactions. The review is devoted to the recent nanotechnological advances in NA aptamers application.
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Affiliation(s)
- Valentina V. Sinitsyna
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences 36, Nahimovskiy Prospect, Moscow 117997, Russia
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia
- Complementary and Integrative Health Clinic of Dr. Shishonin 5, Yasnogorskaya St., Moscow 117588, Russia
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83
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Johnston C, Migaud ME. Solvent-Assisted Mechanochemical Synthesis of a Nucleotide Dimer. Curr Protoc 2022; 2:e418. [PMID: 35447016 DOI: 10.1002/cpz1.418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This article contains a synthetic protocol for solvent-assisted mechanochemical synthesis of a nucleotide dimer. First, a dinucleoside phosphite is prepared by solvent-assisted mechanochemistry via the phosphoramidite method. Second, the dinucleoside phosphite is oxidized to form the dinucleotide under mechanochemical conditions. Finally, the dinucleotide is purified by column chromatography. Support protocols are also provided for preparing the acidic salts that can be utilized for phosphoramidite couplings and for demonstrating that the reaction occurs under mechanochemical conditions rather than as a result of solvent added for analysis. Mechanochemistry as applied to synthesis of dinucleotides is a recent development and it is anticipated that the principles in this protocol will be widely applicable to a range of nucleoside and ribonucleoside monomers. The advantages of mechanochemistry over traditional solution-phase chemistry are the simplicity of the procedure, improved hydrolytic stability, and elimination of the need to solubilize poorly soluble compounds. © 2022 Wiley Periodicals LLC. Basic Protocol: Solvent-assisted mechanochemical synthesis of a nucleotide dimer Supplementary Protocol 1: Synthesis of N-methylimidazolium triflate Supplementary Protocol 2: Synthesis of pyridinium trifluoroacetate Supplementary Protocol 3: Confirmation of the efficacy of mechanochemical conditions.
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Affiliation(s)
| | - Marie E Migaud
- Mitchell Cancer Institute, Department of Pharmacology, College of Medicine, University of South Alabama, 1660 Springhill Avenue, Mobile, Alabama
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84
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Abstract
Cell-penetrating peptides (CPPs) can cross the cell membrane to enter the cytosol and deliver otherwise nonpenetrant macromolecules such as proteins and oligonucleotides. For example, recent clinical trials have shown that a CPP attached to phosphorodiamidate morpholino oligomers (PMOs) resulted in higher muscle concentration, increased exon skipping, and dystrophin production relative to another study of the PMO alone in patients of Duchenne muscular dystrophy. Therefore, effective design and the study of CPPs could help enhance therapies for difficult-to-treat diseases. So far, the study of CPPs for PMO delivery has been restricted to predominantly canonical l-peptides. We hypothesized that mirror-image d-peptides could have similar PMO delivery activity as well as enhanced proteolytic stability, facilitating their characterization and quantification from biological milieu. We found that several enantiomeric peptide sequences could deliver a PMO-biotin cargo with similar activities while remaining stable against serum proteolysis. The biotin label allowed for affinity capture of fully intact PMO-peptide conjugates from whole-cell and cytosolic lysates. By profiling a mixture of these constructs in cells, we determined their relative intracellular concentrations. When combined with PMO activity, these concentrations provide a new metric for delivery efficiency, which may be useful for determining which peptide sequence to pursue in further preclinical studies.
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Affiliation(s)
- Carly
K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charlotte E. Farquhar
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Annika B. Malmberg
- Sarepta
Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Andrei Loas
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute
of Technology, 500 Main
Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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85
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Asandei A, Mereuta L, Bucataru IC, Park Y, Luchian T. A single-molecule insight into the ionic strength dependent, cationic peptide nucleic acids - oligonucleotides interactions. Chem Asian J 2022; 17:e202200261. [PMID: 35419929 DOI: 10.1002/asia.202200261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/12/2022] [Indexed: 11/08/2022]
Abstract
To alleviate solubility-related shortcomings associated with the use of neutral peptide nucleic acids (PNA), a powerful strategy is incorporate various charged sidechains onto the PNA structure. Here we employ a single-molecule technique and prove that the ionic current blockade signature of free poly(Arg)-PNAs and their corresponding duplexes with target ssDNAs interacting with a single a-hemolysin (a-HL) nanopore is highly ionic strength dependent, with high salt-containing electrolytes facilitating both capture and isolation of such complexes. Our data illustrate the effect of low ionic strength in reducing the effective volume of free poly(Arg)-PNAs and augmentation of their electrophoretic mobility while traversing the nanopore. We found that unlike in high salt electrolytes, the specific hybridization of cationic moiety-containing PNAs with complementary negatively charged ssDNAs in a salt concentration as low as 0.5 M is dramatically impeded. We suggest a scenario in which reduced charge screening by counterions in low salt electrolytes enables non-specific, electrostatic interactions with the anionic backbone of polynucleotides, thus reducing the ability of PNA-DNA complementary association via hydrogen bonding patterns. We applied an experimental strategy with spatially-separated poly(Arg)-PNAs and ssDNAs, and present evidence at the single-molecule level suggestive of the real-time, long-range interactions-driven formation of poly(Arg)-PNA-DNA complexes, as individual strands entering the nanopore from opposite directions collide inside a nanocavity.
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Affiliation(s)
- Alina Asandei
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, ICI, ROMANIA
| | - Loredana Mereuta
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, Physics, ROMANIA
| | - Ioana C Bucataru
- Alexandru Ioan Cuza University: Universitatea Alexandru Ioan Cuza, Physics, ROMANIA
| | - Yoonkyung Park
- Chosun University, Department of Biomedical Science, ROMANIA
| | - Tudor Luchian
- Alexandru I. Cuza University, Physics, Blvd. Carol I, no. 11, 700506, Iasi, ROMANIA
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86
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Kihal N, Nazemi A, Bourgault S. Supramolecular Nanostructures Based on Perylene Diimide Bioconjugates: From Self-Assembly to Applications. Nanomaterials (Basel) 2022; 12:nano12071223. [PMID: 35407341 PMCID: PMC9000806 DOI: 10.3390/nano12071223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 12/18/2022]
Abstract
Self-assembling π-conjugated systems constitute efficient building blocks for the construction of supramolecular structures with tailored functional properties. In this context, perylene diimide (PDI) has attracted attention owing to its chemical robustness, thermal and photo-stability, and outstanding optical and electronic properties. Recently, the conjugation of PDI derivatives to biological molecules, including oligonucleotides and peptides, has opened new avenues for the design of nanoassemblies with unique structures and functionalities. In the present review, we offer a comprehensive summary of supramolecular bio-assemblies based on PDI. After briefly presenting the physicochemical, structural, and optical properties of PDI derivatives, we discuss the synthesis, self-assembly, and applications of PDI bioconjugates.
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Affiliation(s)
- Nadjib Kihal
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
| | - Ali Nazemi
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
- Correspondence: (A.N.); (S.B.)
| | - Steve Bourgault
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
- Correspondence: (A.N.); (S.B.)
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87
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Adeoye RI, Okaiyeto K, Igunnu A, Oguntibeju OO. Systematic mapping of DNAzymes research from 1995 to 2019. Nucleosides Nucleotides Nucleic Acids 2022; 41:384-406. [PMID: 35343361 DOI: 10.1080/15257770.2022.2052318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.
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Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- Biochemistry Unit, Department of Chemistry and Biochemistry, College of Pure and Applied Sciences, Caleb University, Imota, Lagos, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Adedoyin Igunnu
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
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88
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Apartsin E, Venyaminova A, Majoral JP, Caminade AM. Dendriplex-Impregnated Hydrogels With Programmed Release Rate. Front Chem 2022; 9:780608. [PMID: 35071182 PMCID: PMC8766751 DOI: 10.3389/fchem.2021.780608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
Hydrogels are biocompatible matrices for local delivery of nucleic acids; however, functional dopants are required to provide efficient delivery into cells. In particular, dendrimers, known as robust nucleic acid carriers, can be used as dopants. Herein, we report the first example of impregnating neutral hydrogels with siRNA-dendrimer complexes. The surface chemistry of dendrimers allows adjusting the release rate of siRNA-containing complexes. This methodology can bring new materials for biomedical applications.
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Affiliation(s)
- Evgeny Apartsin
- Laboratoire de Chimie de Coordination, CNRS, Toulouse, France.,LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France.,Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination, CNRS, Toulouse, France.,LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Anne-Marie Caminade
- Laboratoire de Chimie de Coordination, CNRS, Toulouse, France.,LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France
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89
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Mavila S, Culver HR, Anderson AJ, Prieto TR, Bowman CN. Athermal, Chemically Triggered Release of RNA from Thioester Nucleic Acids. Angew Chem Int Ed Engl 2022; 61:e202110741. [PMID: 34697873 DOI: 10.1002/anie.202110741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Indexed: 12/21/2022]
Abstract
An athermal approach to mRNA enrichment from total RNA using a self-immolative thioester linked nucleic acids (TENA) is described. Oligo(thymine) (oT) TENA has a six-atom spacing between bases which allowed TENA to selectively base-pair with polyadenine RNA. As a result of the neutral backbone of TENA and the hydrophobicity of the octanethiol end group, oT TENA is water insoluble and efficiently pulled down 93±2 % of EGFP mRNA at a concentration of 10 ng μL-1 . Self-immolative degradation of TENA upon ambient temperature exposure to nucleophilic buffer components (Tris, DTT) allowed recovery of 55±27 ng of mRNA from 3.1 μg of total RNA, which was not statistically different from the amount recovered using Dynabeads® mRNA DIRECT Kit (89±24 ng). Gene expression as measured by RT-qPCR was comparable for both enrichment methods, suggesting that the mild conditions required for enrichment of mRNA using oT TENA are compatible with RT-qPCR and other downstream molecular biology applications.
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Affiliation(s)
- Sudheendran Mavila
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Heidi R Culver
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Alex J Anderson
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Tania R Prieto
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80309, USA
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90
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Bakowski K, Vogel S. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biol 2022; 19:1256-1275. [PMID: 36411594 PMCID: PMC9683052 DOI: 10.1080/15476286.2022.2147278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From the early days of research on RNA biology and biochemistry, there was an interest to utilize this knowledge and RNA itself for therapeutic applications. Today, we have a series of oligonucleotide therapeutics on the market and many more in clinical trials. These drugs - exploit different chemistries of oligonucleotides, such as modified DNAs and RNAs, peptide nucleic acids (PNAs) or phosphorodiamidate morpholino oligomers (PMOs), and different mechanisms of action, such as RNA interference (RNAi), targeted RNA degradation, splicing modulation, gene expression and modification. Despite major successes e.g. mRNA vaccines developed against SARS-CoV-2 to control COVID-19 pandemic, development of therapies for other diseases is still limited by inefficient delivery of oligonucleotides to specific tissues and organs and often prohibitive costs for the final drug. This is even more critical when targeting multifactorial disorders and patient-specific biological variations. In this review, we will present the evolution of complexity of oligonucleotide delivery methods with focus on increasing complexity of formulations from gymnotic delivery to bioconjugates and to lipid nanoparticles in respect to developments that will enable application of therapeutic oligonucleotides as drugs in personalized therapies.
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Affiliation(s)
- Kamil Bakowski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark,CONTACT Stefan Vogel Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230Odense, Denmark
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91
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Abstract
The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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92
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Sýkorová V, Tichý M, Hocek M. Polymerase Synthesis of DNA Containing Iodinated Pyrimidine or 7-Deazapurine Nucleobases and Their Post-synthetic Modifications through the Suzuki-Miyaura Cross-Coupling Reactions. Chembiochem 2021; 23:e202100608. [PMID: 34821441 DOI: 10.1002/cbic.202100608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/24/2021] [Indexed: 11/08/2022]
Abstract
All four iodinated 2'-deoxyribonucleoside triphosphates (dNTPs) derived from 5-iodouracil, 5-iodocytosine, 7-iodo-7-deazaadenine and 7-iodo-7-deazaguanine were prepared and studied as substrates for KOD XL DNA polymerase. All of the nucleotides were readily incorporated by primer extension and by PCR amplification to form DNA containing iodinated nucleobases. Systematic study of the Suzuki-Miyaura cross-coupling reactions with two bulkier arylboronic acids revealed that the 5-iodopyrimidines were more reactive and gave cross-coupling products both in the terminal or internal position in single-stranded oligonucleotides (ssONs) and in the terminal position of double-stranded DNA (dsDNA), whereas the 7-iodo-7-deazapurines were less reactive and gave cross-coupling products only in the terminal position. None of the four iodinated bases reacted in an internal position of dsDNA. These findings are useful for the use of the iodinated nucleobases for post-synthetic modification of DNA with functional groups for various applications.
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Affiliation(s)
- Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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93
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López-Vidal EM, Schissel CK, Mohapatra S, Bellovoda K, Wu CL, Wood JA, Malmberg AB, Loas A, Gómez-Bombarelli R, Pentelute BL. Deep Learning Enables Discovery of a Short Nuclear Targeting Peptide for Efficient Delivery of Antisense Oligomers. JACS Au 2021; 1:2009-2020. [PMID: 34841414 PMCID: PMC8611673 DOI: 10.1021/jacsau.1c00327] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 06/01/2023]
Abstract
Therapeutic macromolecules such as proteins and oligonucleotides can be highly efficacious but are often limited to extracellular targets due to the cell's impermeable membrane. Cell-penetrating peptides (CPPs) are able to deliver such macromolecules into cells, but limited structure-activity relationships and inconsistent literature reports make it difficult to design effective CPPs for a given cargo. For example, polyarginine motifs are common in CPPs, promoting cell uptake at the expense of systemic toxicity. Machine learning may be able to address this challenge by bridging gaps between experimental data in order to discern sequence-activity relationships that evade our intuition. Our earlier data set and deep learning model led to the design of miniproteins (>40 amino acids) for antisense delivery. Here, we leveraged and expanded our model with data augmentation in the short CPP sequence space of the data set to extrapolate and discover short, low-arginine-content CPPs that would be easier to synthesize and amenable to rapid conjugation to desired cargo, and with minimal in vivo toxicity. The lead predicted peptide, termed P6, is as active as a polyarginine CPP for the delivery of an antisense oligomer, while having only one arginine side chain and 18 total residues. We determined the pentalysine motif and the C-terminal cysteine of P6 to be the main drivers of activity. The antisense conjugate was able to enhance corrective splicing in an animal model to produce functional eGFP in heart tissue in vivo while remaining nontoxic up to a dose of 60 mg/kg. In addition, P6 was able to deliver an enzyme to the cytosol of cells. Our findings suggest that, given a data set of long CPPs, we can discover by extrapolation short, active sequences that deliver antisense oligomers.
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Affiliation(s)
- Eva M. López-Vidal
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carly K. Schissel
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Somesh Mohapatra
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kamela Bellovoda
- Sarepta
Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Chia-Ling Wu
- Sarepta
Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Jenna A. Wood
- Sarepta
Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Annika B. Malmberg
- Sarepta
Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Andrei Loas
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rafael Gómez-Bombarelli
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute
of MIT and Harvard, 415
Main Street, Cambridge, Massachusetts 02142, United States
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94
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Karalė K, Bollmark M, Stulz R, Honcharenko D, Tedebark U, Strömberg R. A Study on Synthesis and Upscaling of 2'- O-AECM-5-methyl Pyrimidine Phosphoramidites for Oligonucleotide Synthesis. Molecules 2021; 26:6927. [PMID: 34834019 PMCID: PMC8619030 DOI: 10.3390/molecules26226927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022] Open
Abstract
2'-O-(N-(Aminoethyl)carbamoyl)methyl-modified 5-methyluridine (AECM-MeU) and 5-methylcytidine (AECM-MeC) phosphoramidites are reported for the first time and prepared in multigram quantities. The syntheses of AECM-MeU and AECM-MeC nucleosides are designed for larger scales (approx. 20 g up until phosphoramidite preparation steps) using low-cost reagents and minimizing chromatographic purifications. Several steps were screened for best conditions, focusing on the most crucial steps such as N3 and/or 2'-OH alkylations, which were improved for larger scale synthesis using phase transfer catalysis (PTC). Moreover, the need of chromatographic purifications was substantially reduced by employing one-pot synthesis and improved work-up strategies.
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Affiliation(s)
- Kristina Karalė
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 57 Huddinge, Sweden; (K.K.); (R.S.); (D.H.)
- RISE, Department Chemical Process and Pharmaceutical Development, Forskargatan 18, 151 36 Södertälje, Sweden; (M.B.); (U.T.)
| | - Martin Bollmark
- RISE, Department Chemical Process and Pharmaceutical Development, Forskargatan 18, 151 36 Södertälje, Sweden; (M.B.); (U.T.)
| | - Rouven Stulz
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 57 Huddinge, Sweden; (K.K.); (R.S.); (D.H.)
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Dmytro Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 57 Huddinge, Sweden; (K.K.); (R.S.); (D.H.)
| | - Ulf Tedebark
- RISE, Department Chemical Process and Pharmaceutical Development, Forskargatan 18, 151 36 Södertälje, Sweden; (M.B.); (U.T.)
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 57 Huddinge, Sweden; (K.K.); (R.S.); (D.H.)
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95
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Epple S, El-Sagheer AH, Brown T. Artificial nucleic acid backbones and their applications in therapeutics, synthetic biology and biotechnology. Emerg Top Life Sci 2021; 5:691-697. [PMID: 34297063 PMCID: PMC8726046 DOI: 10.1042/etls20210169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The modification of DNA or RNA backbones is an emerging technology for therapeutic oligonucleotides, synthetic biology and biotechnology. Despite a plethora of reported artificial backbones, their vast potential is not fully utilised. Limited synthetic accessibility remains a major bottleneck for the wider application of backbone-modified oligonucleotides. Thus, a variety of readily accessible artificial backbones and robust methods for their introduction into oligonucleotides are urgently needed to utilise their full potential in therapeutics, synthetic biology and biotechnology.
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Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Afaf H. El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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96
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Golyshev VM, Pyshnyi DV, Lomzov AA. [Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation]. Mol Biol (Mosk) 2021; 55:1030-1044. [PMID: 34837707 DOI: 10.31857/s0026898421060069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
The development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches to calculate the enthalpy (ΔH°) component, and the quasi-harmonic approximation (Q-Harm) or the normal mode analysis (NMA) methods to calculate the entropy (ΔS°) contribution to the Gibbs energy (ΔG°37) of the NA complex formation. We have found that the MMGBSA method in the analysis of the MD trajectory of only the NA duplex and the empirical linear approximation allow calculation of the enthalpy of formation of the DNA, RNA, and hybrid duplexes of various lengths and GC content with an accuracy of 8.6%. Within each type of complex, the combination of rather efficient MMGBSA and Q-Harm approaches being applied to the trajectory of only the bimolecular complex makes it possible to calculate the ΔG°37 of the duplex formation with an error value of 10%. The high accuracy of predictive calculation for different types of natural complexes (DNA/RNA, DNA/RNA, and RNA/RNA) indicates the possibility of extending the considered approach to analogs and derivatives of nucleic acids, which gives a fundamental opportunity in the future to perform rational design of new types of NA-targeted sequence-specific compounds.
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Affiliation(s)
- V M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - D V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk State University, Novosibirsk, 630090 Russia
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97
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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98
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Garcia DA, Powers AF, Bell TA, Guo S, Aghajan M. Antisense Oligonucleotide-Mediated Silencing of Mitochondrial Fusion and Fission Factors Modulates Mitochondrial Dynamics and Rescues Mitochondrial Dysfunction. Nucleic Acid Ther 2021; 32:51-65. [PMID: 34698563 PMCID: PMC8817704 DOI: 10.1089/nat.2021.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mitochondria are highly dynamic organelles that produce ATP and maintain metabolic, catabolic, and redox homeostasis. Mitochondria owe this dynamic nature to their constant fission and fusion—processes that are regulated, in part, by fusion factors (MFN1 and MFN2) and fission factors (DRP1, FIS1, MFF, MIEF1, MIEF2) located on the outer mitochondrial membrane. While mitochondrial fusion and fission are known to influence mitochondrial morphology and function, a key question is whether rebalancing mitochondrial morphology can ameliorate mitochondrial dysfunction in the context of mitochondrial pathology. In this study, we used antisense oligonucleotides (ASOs) to systematically evaluate the effects of fusion and fission factors in vitro. Free uptake by cells of fusion or fission factor ASOs caused robust decreases in target gene expression and altered a variety of mitochondrial parameters, including mitochondrial size and respiration, which were dose dependent. In Mfn1 knockout mouse embryonic fibroblasts (MEFs) and MFN2-R94Q (Charcot-Marie-Tooth Type 2 Disease-associated mutation) MEFs, two cellular models of mitochondrial dysfunction, we found that ASO-mediated silencing of only Drp1 restored mitochondrial morphology and enhanced mitochondrial respiration. Together, these data demonstrate in vitro proof-of-concept for rebalancing mitochondrial morphology to rescue function using ASOs and suggest that ASO-mediated modulation of mitochondrial dynamics may be a viable therapeutic approach to restore mitochondrial homeostasis in diseases driven by mitochondrial dysfunction.
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Affiliation(s)
| | | | - Thomas A Bell
- Ionis Pharmaceuticals, Inc., Carlsbad, California,, USA
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, California,, USA
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99
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Repkova M, Levina A, Ismagilov Z, Mazurkova N, Mazurkov O, Zarytova V. Effective Inhibition of Newly Emerged A/H7N9 Virus with Oligonucleotides Targeted to Conserved Regions of the Virus Genome. Nucleic Acid Ther 2021; 31:436-442. [PMID: 34665651 DOI: 10.1089/nat.2021.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Newly emerged highly pathogenic A/H7N9 viruses with pandemic potential are effectively transmitted from birds to humans and require the development of novel antiviral drugs. For the first time, we studied the in vitro and in vivo antiviral activity against A/H7N9 of oligodeoxyribonucleotides (ODNs), which were delivered into the cells in the proposed TiO2-based nanocomposites (TiO2∼ODN). The highest inhibition of A/H7N9 in vitro (∼400-fold) and efficient, sequence-specific, and dose-dependent protection (up to 100%) of A/H7N9-infected mice was revealed when ODN was targeted to the conserved terminal 3'-noncoding region of viral (-)RNA. After the treatment with ODN, the virus titer values in the lungs of mice decreased by several orders of magnitude. The TiO2∼ODN nanocomposite did not show toxicity in mice under the treatment conditions. The proposed approach for effective inhibition of the A/H7N9 can be tested against other viruses, for example, new emerging influenza viruses and coronaviruses with pandemic potential.
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Affiliation(s)
- Marina Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Asya Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Zinfer Ismagilov
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Mazurkova
- FBRI State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russia
| | - Oleg Mazurkov
- FBRI State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russia
| | - Valentina Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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100
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Søgaard PP, Lind M, Christiansen CR, Petersson K, Clauss A, Caffarel-Salvador E. Future Perspectives of Oral Delivery of Next Generation Therapies for Treatment of Skin Diseases. Pharmaceutics 2021; 13:1722. [PMID: 34684016 PMCID: PMC8537019 DOI: 10.3390/pharmaceutics13101722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Gene therapies have conspicuously bloomed in recent years as evidenced by the increasing number of cell-, gene-, and oligo-based approved therapies. These therapies hold great promise for dermatological disorders with high unmet need, for example, epidermolysis bullosa or pachyonychia congenita. Furthermore, the recent clinical success of clustered regularly interspaced short palindromic repeats (CRISPR) for genome editing in humans will undoubtedly contribute to defining a new wave of therapies. Like biologics, naked nucleic acids are denatured inside the gastrointestinal tract and need to be administered via injections. For a treatment to be effective, a sufficient amount of a given regimen needs to reach systemic circulation. Multiple companies are racing to develop novel oral drug delivery approaches to circumvent the proteolytic and acidic milieu of the gastrointestinal tract. In this review, we provide an overview of the evolution of the gene therapy landscape, with a deep focus on gene and oligonucleotide therapies in clinical trials aimed at treating skin diseases. We then examine the progress made in drug delivery, with particular attention on the peptide field and drug-device combinations that deliver macromolecules into the gastrointestinal tract. Such novel devices could potentially be applied to administer other therapeutics including genes and CRISPR-based systems.
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Affiliation(s)
- Pia Pernille Søgaard
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
| | - Marianne Lind
- Explorative Formulation and Technologies, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (M.L.); (K.P.)
| | | | - Karsten Petersson
- Explorative Formulation and Technologies, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (M.L.); (K.P.)
| | - Adam Clauss
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
| | - Ester Caffarel-Salvador
- Regenerative Medicine Department, LEO Pharma A/S, Industriparken 55, 2750 Ballerup, Denmark; (P.P.S.); (C.R.C.); (A.C.)
- LEO Science & Tech Hub, One Broadway, Cambridge, MA 02142, USA
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