1
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Dowerah D, V N Uppuladinne M, Paul S, Das D, Gour NK, Biswakarma N, Sarma PJ, Sonavane UB, Joshi RR, Ray SK, Deka RC. A Study Modeling Bridged Nucleic Acid-Based ASOs and Their Impact on the Structure and Stability of ASO/RNA Duplexes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39370641 DOI: 10.1021/acs.langmuir.4c02171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Antisense medications treat diseases that cannot be treated using traditional pharmacological technologies. Nucleotide monomers of bare and phosphorothioate (PS)-modified LNA, N-MeO-amino-BNA, 2',4'-BNANC[NH], 2',4'-BNANC[NMe], and N-Me-aminooxy-BNA antisense modifications were considered for a detailed DFT-based quantum chemical study to estimate their molecular-level structural and electronic properties. Oligomer hybrid duplex stability is described by performing an elaborate MD simulation study by incorporating the PS-LNA and PS-BNA antisense modifications onto 14-mer ASO/RNA hybrid gapmer type duplexes targeting protein PTEN mRNA nucleic acid sequence (5'-CTTAGCACTGGCCT-3'/3'-GAAUCGUGACCGGA-5'). Replica sets of MD simulations were performed accounting to two data sets, each set simulated for 1 μs simulation time. Bulk properties of oligomers are regulated by the chemical properties of their monomers. As such, the primary goal of this work focused on establishing an organized connection between the monomeric BNA nucleotide's electronic effects observed in DFT studies and the macroscopic behavior of the BNA antisense oligomers, as observed in MD simulations. The results from this study predicted that spatial orientation of MO-isosurfaces of the BNA nucleotides are concentrated in the nucleobase region. These BNA nucleotides may become less accessible for various electronic interactions when coupled as ASOs forming duplexes with target RNAs and when the ASO/RNA duplexes further bind with the RNase H. Understanding such electronic interactions is crucial to design superior antisense modifications with specific electronic properties. Also, for the particular nucleic acid sequence solvation of the duplexes although were higher compared to the natural oligonucleotides, their binding energies being relatively lower may lead to decreased antisense activity compared to existing analogs such as the LNAs and MOEs. Fine tuning these BNAs to obtain superior binding affinity is thus a necessity.
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Affiliation(s)
- Dikshita Dowerah
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Mallikarjunachari V N Uppuladinne
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Subrata Paul
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Department of Chemistry, Assam University, Silchar, Assam 788011, India
| | - Dharitri Das
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Nand K Gour
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Nishant Biswakarma
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Plaban J Sarma
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Department of Chemistry, Gargaon College, Simaluguri, Sivasagar, Assam 785686, India
| | - Uddhavesh B Sonavane
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Rajendra R Joshi
- HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Suvendra K Ray
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Ramesh Ch Deka
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
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2
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Xu C, Zhao J, Zheng Y, Cai W, Wang C. Synthesis of P-Stereogenic Phosphinamides via Nickel-Catalyzed Kinetic Resolution of H-Phosphinamides by Alkenylation and Arylation. Org Lett 2024. [PMID: 39365154 DOI: 10.1021/acs.orglett.4c02648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
A nickel-catalyzed enantioselective cross-coupling for the synthesis of P-stereogenic phosphinamides has been developed. The asymmetric alkenylation and arylation of racemic H-phosphinamides using alkenyl and aryl bromides resulted in the formation of P-stereogenic N-phosphinyl compounds with good yields and high enantioselectivities. This method tolerates a variety of functional groups, and its applications are explored through scale-up reactions and product transformations.
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Affiliation(s)
- Cheng Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Jing Zhao
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Yu Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, P. R. China
| | - Wei Cai
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225002, China
| | - Chuanyong Wang
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
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3
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Lu G, Shivalila C, Monian P, Yu H, Harding I, Briem S, Byrne M, Faraone A, Friend S, Huth O, Iwamoto N, Kawamoto T, Kumarasamy J, Lamattina A, Longo K, McCarthy L, McGlynn A, Molski A, Pan Q, Pu T, Purcell-Estabrook E, Rossi J, Standley S, Thomas C, Walen A, Yang H, Kandasamy P, Vargeese C. Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing. Nucleic Acids Res 2024; 52:10068-10084. [PMID: 39149897 PMCID: PMC11417349 DOI: 10.1093/nar/gkae681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
AIMers are short, chemically modified oligonucleotides that induce A-to-I RNA editing through interaction with endogenous adenosine deaminases acting on RNA (ADAR) enzymes. Here, we describe the development of new AIMer designs with base, sugar and backbone modifications that improve RNA editing efficiency over our previous design. AIMers incorporating a novel pattern of backbone and 2' sugar modifications support enhanced editing efficiency across multiple sequences. Further efficiency gains were achieved through incorporation of an N-3-uridine (N3U), in place of cytidine (C), in the 'orphan base' position opposite the edit site. Molecular modeling suggests that N3U might enhance ADAR catalytic activity by stabilizing the AIMer-ADAR interaction and potentially reducing the energy required to flip the target base into the active site. Supporting this hypothesis, AIMers containing N3U consistently enhanced RNA editing over those containing C across multiple target sequences and multiple nearest neighbor sequence combinations. AIMers combining N3U and the novel pattern of 2' sugar chemistry and backbone modifications improved RNA editing both in vitro and in vivo. We provide detailed N3U synthesis methods and, for the first time, explore the impact of N3U and its analogs on ADAR-mediated RNA editing efficiency and targetable sequence space.
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Affiliation(s)
| | | | | | - Hui Yu
- Wave Life Sciences, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tom Pu
- Wave Life Sciences, Cambridge, MA, USA
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4
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McDowall S, Aung-Htut M, Wilton S, Li D. Antisense oligonucleotides and their applications in rare neurological diseases. Front Neurosci 2024; 18:1414658. [PMID: 39376536 PMCID: PMC11456401 DOI: 10.3389/fnins.2024.1414658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/20/2024] [Indexed: 10/09/2024] Open
Abstract
Rare diseases affect almost 500 million people globally, predominantly impacting children and often leading to significantly impaired quality of life and high treatment costs. While significant contributions have been made to develop effective treatments for those with rare diseases, more rapid drug discovery strategies are needed. Therapeutic antisense oligonucleotides can modulate target gene expression with high specificity through various mechanisms determined by base sequences and chemical modifications; and have shown efficacy in clinical trials for a few rare neurological conditions. Therefore, this review will focus on the applications of antisense oligonucleotides, in particular splice-switching antisense oligomers as promising therapeutics for rare neurological diseases, with key examples of Duchenne muscular dystrophy and spinal muscular atrophy. Challenges and future perspectives in developing antisense therapeutics for rare conditions including target discovery, antisense chemical modifications, animal models for therapeutic validations, and clinical trial designs will also be briefly discussed.
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Affiliation(s)
- Simon McDowall
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
| | - May Aung-Htut
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Steve Wilton
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dunhui Li
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA, Australia
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5
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Iwamoto N, Liu Y, Frank-Kamenetsky M, Maguire A, Tseng WC, Taborn K, Kothari N, Akhtar A, Bowman K, Shelke JD, Lamattina A, Hu XS, Jang HG, Kandasamy P, Liu F, Longo K, Looby R, Meena, Metterville J, Pan Q, Purcell-Estabrook E, Shimizu M, Prakasha PS, Standley S, Upadhyay H, Yang H, Yin Y, Zhao A, Francis C, Byrne M, Dale E, Verdine GL, Vargeese C. Preclinical evaluation of stereopure antisense oligonucleotides for allele-selective lowering of mutant HTT. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102246. [PMID: 39027419 PMCID: PMC11255113 DOI: 10.1016/j.omtn.2024.102246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Huntington's disease (HD) is an autosomal dominant disease caused by the expansion of cytosine-adenine-guanine (CAG) repeats in one copy of the HTT gene (mutant HTT, mHTT). The unaffected HTT gene encodes wild-type HTT (wtHTT) protein, which supports processes important for the health and function of the central nervous system. Selective lowering of mHTT for the treatment of HD may provide a benefit over nonselective HTT-lowering approaches, as it aims to preserve the beneficial activities of wtHTT. Targeting a heterozygous single-nucleotide polymorphism (SNP) where the targeted variant is on the mHTT gene is one strategy for achieving allele-selective activity. Herein, we investigated whether stereopure phosphorothioate (PS)- and phosphoryl guanidine (PN)-containing oligonucleotides can direct allele-selective mHTT lowering by targeting rs362273 (SNP3). We demonstrate that our SNP3-targeting molecules are potent, durable, and selective for mHTT in vitro and in vivo in mouse models. Through comparisons with a surrogate for the nonselective investigational compound tominersen, we also demonstrate that allele-selective molecules display equivalent potency toward mHTT with improved durability while sparing wtHTT. Our preclinical findings support the advancement of WVE-003, an investigational allele-selective compound currently in clinical testing (NCT05032196) for the treatment of patients with HD.
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Affiliation(s)
| | | | | | | | | | | | | | - Ali Akhtar
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | - Fangjun Liu
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Ken Longo
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Meena
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Qianli Pan
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Hailin Yang
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Yuan Yin
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | - Mike Byrne
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Elena Dale
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Gregory L. Verdine
- Department of Stem Cell and Regenerative Biology, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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6
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Gulumkar VN, Dowdy SF. Stereopure ASOs: An unanticipated increase in selectivity for targeting mutant HTT. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102312. [PMID: 39281704 PMCID: PMC11399643 DOI: 10.1016/j.omtn.2024.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Affiliation(s)
- Vijay N Gulumkar
- Department of Cellular & Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Steven F Dowdy
- Department of Cellular & Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
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7
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Sharon EM, O'Keefe SM, Grassmyer KT, Raab SA, Maloney TD, Clemmer DE. Diastereomer Characterization of PS-Modified Synthetic Oligonucleotides Using Cyclic IMS-MS. Anal Chem 2024. [PMID: 39250816 DOI: 10.1021/acs.analchem.4c02836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Synthetic oligonucleotides have emerged as effective therapeutics that regulate gene expression to treat and prevent diseases. Oligonucleotide therapeutics are often modified with a substitution of a phosphorothioate (PS) linkage along the phosphodiester backbone to improve the drug performance and stability. The PS modification creates a mixture of diastereomer structures, increasing by a factor of 2n where n is the number of PS linkages. Despite recent draft guidances highlighting the importance of their characterization, analytical methods to measure the resulting diastereomers are currently lacking. Here, we present a method combining tandem mass spectrometry (MS) and tandem ion mobility spectrometry (IMS) using a cyclic IMS-MS instrument to study diastereomers in PS-modified oligonucleotides. This approach requires no enzymatic digestion as the intact oligonucleotides are directly injected into the MS instrument. Analogous to top-down proteomics, MS fragmentation of the intact oligonucleotide results in 3' and 5' fragment ends that have fewer diastereomers than their intact counterpart. Tandem IMS allows for mobility resolution of the diastereomers at the terminal ends. We tested four model oligonucleotides that differ in either the number of PS bonds or sequence to demonstrate the capability of this method to elucidate diastereomer structures on modified oligonucleotides.
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Affiliation(s)
- Edie M Sharon
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Sarah M O'Keefe
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Kathleen T Grassmyer
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Shannon A Raab
- Bioproduct Research and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Todd D Maloney
- Synthetic Molecule Design and Development, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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8
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Ge F, Wang Y, Liu J, Yu H, Liu G, Deng Z, He X. Harnessing sulfur-binding domains to separate Sp and Rp isomers of phosphorothioate oligonucleotides. Appl Microbiol Biotechnol 2024; 108:448. [PMID: 39190037 DOI: 10.1007/s00253-024-13283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Chemical synthesis of phosphoromonothioate oligonucleotides (PS-ONs) is not stereo-specific and produces a mixture of Rp and Sp diastereomers, whose disparate reactivity can complicate applications. Although the current methods to separate these diastereomers which rely on chromatography are constantly improving, many Rp and Sp diastereomers are still co-eluted. Here, based on sulfur-binding domains that specifically recognize phosphorothioated DNA and RNA in Rp configuration, we developed a universal separation system for phosphorothioate oligonucleotide isomers using immobilized SBD (SPOIS). With the scalable SPOIS, His-tagged SBD is immobilized onto Ni-nitrilotriacetic acid-coated magnetic beads to form a beads/SBD complex, Rp isomers of the mixture can be completely bound by SBD and separated from Sp isomers unbound in liquid phase, then recovered through suitable elution approach. Using the phosphoromonothioate single-stranded DNA as a model, SPOIS separated PS-ON diastereomers of 4 nt to 50 nt in length at yields of 60-90% of the starting Rp isomers, with PS linkage not locating at 5' or 3' end. Within this length range, PS-ON diastereomers that co-eluted in HPLC could be separated by SPOIS at yields of 84% and 89% for Rp and Sp stereoisomers, respectively. Furthermore, as each Rp phosphorothioate linkage can be bound by SBD, SPOIS allowed the separation of stereoisomers with multiple uniform Sp configurations for multiple phosphorothioate modifications. A second generation of SPOIS was developed using the thermolabile and non-sequence-specific SBDPed, enabling fast and high-yield recovery of PS substrate stereoisomers for the DNAzyme Cd16 and further demonstrating the efficiency of this method. KEY POINTS: • SPOIS allows isomer separations of the Rp and Sp isomers co-eluted on HPLC. • SPOIS can obtain Sp isomers with 5 min and Rp in 20 min from PS-ON diastereomers. • SPOIS was successfully applied to separate isomers of PS substrates of DNAzyme.
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Affiliation(s)
- Fulin Ge
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Yuli Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Jinling Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
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9
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Li F, Knappe C, Carstensen N, Favorat E, Gao M, Holkenjans W, Hetzel T, Pell R, Lämmerhofer M. Two-dimensional sequential selective comprehensive chiral×reversed-phase liquid chromatography of synthetic phosphorothioate oligonucleotide diastereomers. J Chromatogr A 2024; 1730:465076. [PMID: 38879975 DOI: 10.1016/j.chroma.2024.465076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
In recent years, many nucleic acid-based pharmaceuticals have been approved and entered the market, and even a larger number are in late stage clinical trials. Conventional oligonucleotides are facing issues in vivo like fast renal clearance and nuclease degradation. Therefore, to increase their stability, phosphorothioation is a frequent modification of therapeutic oligonucleotides (ONs) which also leads to improved binding affinity facilitating cell internalization and intracellular distribution. At the same time, by replacing a phosphodiester linkage with a phosphorothioate group, a phosphorous stereogenic center is generated which causes the formation of Rp- and Sp-diastereomers. It increases the structural diversity. For example, with 15 of those phosphorothioate (PS) linkages, 32,768 different diastereomers are expected. Since the phosphorothioate is introduced non-stereoselectively, the molecular complexity of the resultant phosphorothioate ON products is tremendously increased impeding the chromatographic separation in the course of quality control. Since distinct phosphorothioate diastereomers have different bioactivities and pharmacological properties, there is increasing interest in implications of stereoisomerism of phosphorothiate oligonucleotides. From a quality and regulatory viewpoint, batch-to-batch reproducibility of the diastereomer profile may be of significant concern. In order to address this issue, this study investigates the stereoselectivity of LC methods for two phosphorothioate oligonucleotide (PSO) compounds differing in their molecular size and numbers of PS linkages. Diastereoselectivity of ion-pairing reversed-phase liquid chromatography (IP-RPLC), RPLC without ion-pairing agents and LC with chiral polysaccharide-based column were evaluated for model PSOs and an active pharmaceutical ingredient (API) of PSO with trivalent N-acetylgalactosamine (GalNAc) conjugate. Due to the structural complexity of PSOs, the separation power for the diastereomer mixture was increased by using sequential selective comprehensive two-dimensional chromatography with an amylose tris(α-methylbenzylcarbamate)-immobilized chiral stationary phase (CSP) in the first dimension and ion-pair RPLC with ethylammonium acetate in the second dimension. Improved diastereomer selectivity was obtained and a larger number of peaks could be separated.
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Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Cornelius Knappe
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Niklas Carstensen
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Enrico Favorat
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mimi Gao
- Bayer AG, Pharmaceutical Division, Friedrich-Ebert-Strasse 217-333 42117 Wuppertal, Germany
| | - Wiebke Holkenjans
- Bayer AG, Pharmaceutical Division, Friedrich-Ebert-Strasse 217-333 42117 Wuppertal, Germany
| | - Terence Hetzel
- Bayer AG, Pharmaceutical Division, Friedrich-Ebert-Strasse 217-333 42117 Wuppertal, Germany
| | - Reinhard Pell
- Bayer AG, Pharmaceutical Division, Friedrich-Ebert-Strasse 217-333 42117 Wuppertal, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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10
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He L, Xiang Y. Interrogating the Presence of RNA Phosphorothioate in Nature by a Highly Selective and Sensitive Fluorescence Method. Anal Chem 2024. [PMID: 39138966 DOI: 10.1021/acs.analchem.4c01597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In nature, DNA phosphorothioate (PT) is found in the genomic materials of some prokaryotes. In contrast, whether there is natural RNA PT is still a question under debate. A groundbreaking study reported the discovery of RNA PT in cellular RNA samples from both prokaryotes and eukaryotes at contents of >100 PT per million nucleotides (PPM-nt) according to liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis. However, this finding was challenged by a later work showing that other RNA modifications, such as 2'-O-methylation, could give almost the same LC-MS/MS signal patterns as RNA PT. As the LC-MS/MS technique led to contradicting conclusions, another independent method is thus needed to interrogate the presence of RNA PT in nature. In this work, we have developed a highly selective and sensitive fluorescence method for RNA PT quantification based on a new RNA PT-specific conversion reaction. It can detect as low as 2.8 PPM-nt in RNA without interference from RNA thiobases or protein cysteines. We measured the total RNA samples from some bacteria and human cells using this method. None of these samples gave any RNA PT signal above the detection limit (2.8 PPM-nt), suggesting that the widespread presence of natural RNA PT at the 100 PPM-nt level or above is highly unlikely. Nevertheless, due to the limited number of cell species tested in this work, the possible existence of natural RNA PT cannot be excluded. The fluorescence method reported here is simple and low-cost; therefore, it should be an ideal assay for broadly screening various types of cells to search for the clue of RNA PT in nature.
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Affiliation(s)
- Luo He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Tsinghua University, Beijing 100084, China
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11
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Sahoo A, Gupta S, Das G, Ghosh A, Bagale SS, Sinha S, Gore KR. 2'- O-Alkyl- N 3-Methyluridine Functionalized Passenger Strand Improves RNAi Activity by Modulating the Thermal Stability. ACS Med Chem Lett 2024; 15:1250-1259. [PMID: 39140063 PMCID: PMC11318005 DOI: 10.1021/acsmedchemlett.4c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
Herein, we have demonstrated that the siRNA activity could be enhanced by incorporating the guide strand in the RISC complex through thermodynamic asymmetry caused by m3U-based destabilizing modifications. A nuclease stability study revealed that 2'-OMe-m3U and 2'-OEt-m3U modifications slightly improved the half-lives of siRNA strands in human serum. In the in vitro gene silencing assay, 2'-OMe-m3U modification at the 3'-overhang and cleavage site of the passenger strand in anti-renilla and anti-Bcl-2 siRNA duplexes were well-tolerated and exhibited improved gene silencing activity. However, gene silencing activity was attenuated when these modifications were incorporated at position 3 in the seed region of the antisense strand. The molecular modeling studies using these modifications at the seed region with the MID domain of hAGO2 explained that the 2'-alkoxy group makes steric interactions with the amino acid residues of the hAGO2 protein.
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Affiliation(s)
- Avijit Sahoo
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Shalini Gupta
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Gourav Das
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Surajit Sinha
- School
of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R. Gore
- Department
of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
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12
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Li Q, Dong M, Chen P. Advances in structural-guided modifications of siRNA. Bioorg Med Chem 2024; 110:117825. [PMID: 38954918 DOI: 10.1016/j.bmc.2024.117825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
To date, the US Food and Drug Administration (FDA) has approved six small interfering RNA (siRNA) drugs: patisiran, givosiran, lumasiran, inclisiran, vutrisiran, and nedosiran, serving as compelling evidence of the promising potential of RNA interference (RNAi) therapeutics. The successful implementation of siRNA therapeutics is improved through a combination of various chemical modifications and diverse delivery approaches. The utilization of chemically modified siRNA at specific sites on either the sense strand (SS) or antisense strand (AS) has the potential to enhance resistance to ribozyme degradation, improve stability and specificity, and prolong the efficacy of drugs. Herein, we provide comprehensive analyses concerning the correlation between chemical modifications and structure-guided siRNA design. Various modifications, such as 2'-modifications, 2',4'-dual modifications, non-canonical sugar modifications, and phosphonate mimics, are crucial for the activity of siRNA. We also emphasize the essential strategies for enhancing overhang stability, improving RISC loading efficacy and strand selection, reducing off-target effects, and discussing the future of targeted delivery.
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Affiliation(s)
- Qiang Li
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China; Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China.
| | - Mingxin Dong
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao 266021, China.
| | - Pu Chen
- Research and Development Department, NanoPeptide (Qingdao) Biotechnology Ltd., Qingdao, China; Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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13
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Le BT, Chen S, Veedu RN. Rational Design of Chimeric Antisense Oligonucleotides on a Mixed PO-PS Backbone for Splice-Switching Applications. Biomolecules 2024; 14:883. [PMID: 39062597 PMCID: PMC11274656 DOI: 10.3390/biom14070883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/15/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Synthetic antisense oligonucleotides (ASOs) are emerging as an attractive platform to treat various diseases. By specifically binding to a target mRNA transcript through Watson-Crick base pairing, ASOs can alter gene expression in a desirable fashion to either rescue loss of function or downregulate pathogenic protein expression. To be clinically relevant, ASOs are generally synthesized using modified analogs to enhance resistance to enzymatic degradation and pharmacokinetic and dynamic properties. Phosphorothioate (PS) belongs to the first generation of modified analogs and has played a vital role in the majority of approved ASO drugs, mainly based on the RNase H mechanism. In contrast to RNase H-dependent ASOs that bind and cleave target mature mRNA, splice-switching oligonucleotides (SSOs) mainly bind and alter precursor mRNA splicing in the cell nucleus. To date, only one approved SSO (Nusinersen) possesses a PS backbone. Typically, the synthesis of PS oligonucleotides generates two types of stereoisomers that could potentially impact the ASO's pharmaco-properties. This can be limited by introducing the naturally occurring phosphodiester (PO) linkage to the ASO sequence. In this study, towards fine-tuning the current strategy in designing SSOs, we reported the design, synthesis, and evaluation of several stereo-random SSOs on a mixed PO-PS backbone for their binding affinity, biological potency, and nuclease stability. Based on the results, we propose that a combination of PO and PS linkages could represent a promising approach toward limiting undesirable stereoisomers while not largely compromising the efficacy of SSOs.
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Affiliation(s)
- Bao T. Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- ProGenis Pharmaceuticals Pty Ltd., Bentley, WA 6102, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (B.T.L.); (S.C.)
- ProGenis Pharmaceuticals Pty Ltd., Bentley, WA 6102, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
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14
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Novikova D, Sagaidak A, Vorona S, Tribulovich V. A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone. Molecules 2024; 29:3025. [PMID: 38998973 PMCID: PMC11243533 DOI: 10.3390/molecules29133025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Aleksandra Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
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15
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Yamashita T, Nakamoto K, Hitaoka S, Mizoguchi J, Watanabe T, Hasebe T. Influence of oligonucleotides structures for separation of diastereomers by capillary electrophoresis method using polyvinylpyrrolidone 1,300,000. J Chromatogr A 2024; 1725:464945. [PMID: 38688053 DOI: 10.1016/j.chroma.2024.464945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
In the field of oligonucleotides drug discovery, phosphorothioate (PS) modification has been recognized as an effective tool to overcome the nuclease digestion, and generates 2n of possible diastereomers, where n equals the number of PS linkages. However, it is also well known that differences in drug efficacy and toxicity are caused by differences in stereochemistry of oligonucleotides. Therefore, the development of a high-resolution analytical method that enables stereo discrimination of oligonucleotides is desired. Under this circumstance, capillary electrophoresis (CE) using polyvinylpyrrolidone (PVP) is considered as one of the useful tools for the separation analysis of diastereomers. In this study, we evaluated the several oligonucleotides with the structural diversities in order to understand the separation mechanism of the diastereomers by CE. Especially, five kinds of 2'-moieties were deeply examined by CE with PVP 1,300,000 polymer solution. We found that different trend of the peak shapes and the peak resolution were observed among these oligonucleotides. For example, the better peak resolution was observed in 6 mer PS3-DNA compared to the rigid structure of 6 mer PS3-LNA. As for this reason, the computational simulation revealed that difference of accessible surface area caused by the steric structure of thiophosphate in each oligonucleotide is one of the key attributes to explain the separation of the diastereomers. In addition, we achieved the separation of sixteen peak tops of the diastereomers in 6 mer PS4-DNA, and the complete separation of fifteen diastereomers in 6 mer PS4-RNA. These knowledge for the separation of the diastereomers by CE will be expected to the quality control of the oligonucleotide drugs.
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Affiliation(s)
- Taro Yamashita
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan.
| | - Kosuke Nakamoto
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Seiji Hitaoka
- Emerging Modality Generation Department, Discovery Evidence Generation Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Junichi Mizoguchi
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Tomohiro Watanabe
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Takashi Hasebe
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
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16
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Li S, Xiong F, Zhang S, Liu J, Gao G, Xie J, Wang Y. Oligonucleotide therapies for nonalcoholic steatohepatitis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102184. [PMID: 38665220 PMCID: PMC11044058 DOI: 10.1016/j.omtn.2024.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Nonalcoholic steatohepatitis (NASH) represents a severe disease subtype of nonalcoholic fatty liver disease (NAFLD) that is thought to be highly associated with systemic metabolic abnormalities. It is characterized by a series of substantial liver damage, including hepatocellular steatosis, inflammation, and fibrosis. The end stage of NASH, in some cases, may result in cirrhosis and hepatocellular carcinoma (HCC). Nowadays a large number of investigations are actively under way to test various therapeutic strategies, including emerging oligonucleotide drugs (e.g., antisense oligonucleotide, small interfering RNA, microRNA, mimic/inhibitor RNA, and small activating RNA) that have shown high potential in treating this fatal liver disease. This article systematically reviews the pathogenesis of NASH/NAFLD, the promising druggable targets proven by current studies in chemical compounds or biological drug development, and the feasibility and limitations of oligonucleotide-based therapeutic approaches under clinical or pre-clinical studies.
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Affiliation(s)
- Sixu Li
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
| | - Feng Xiong
- Department of Cardiology, The Third People’s Hospital of Chengdu, Chengdu 610031, China
| | - Songbo Zhang
- Department of Breast Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Jinghua Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610066, China
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17
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Carlesso A, Hörberg J, Deganutti G, Reymer A, Matsson P. Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications. NAR Genom Bioinform 2024; 6:lqae058. [PMID: 38800826 PMCID: PMC11127634 DOI: 10.1093/nargab/lqae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/24/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Antisense oligonucleotides (ASOs) offer ground-breaking possibilities for selective pharmacological intervention for any gene product-related disease. Therapeutic ASOs contain extensive chemical modifications that improve stability to enzymatic cleavage and modulate binding affinity relative to natural RNA/DNA. Molecular dynamics (MD) simulation can provide valuable insights into how such modifications affect ASO conformational sampling and target binding. However, force field parameters for chemically modified nucleic acids (NAs) are still underdeveloped. To bridge this gap, we developed parameters to allow simulations of ASOs with the widely applied phosphorothioate (PS) backbone modification, and validated these in extensive all-atom MD simulations of relevant PS-modified NA systems representing B-DNA, RNA, and DNA/RNA hybrid duplex structures. Compared to the corresponding natural NAs, single PS substitutions had marginal effects on the ordered DNA/RNA duplex, whereas substantial effects of phosphorothioation were observed in single-stranded RNA and B-DNA, corroborated by the experimentally derived structure data. We find that PS-modified NAs shift between high and low twist states, which could affect target recognition and protein interactions for phosphorothioated oligonucleotides. Furthermore, conformational sampling was markedly altered in the PS-modified ssRNA system compared to that of the natural oligonucleotide, indicating sequence-dependent effects on conformational preference that may in turn influence duplex formation.
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Affiliation(s)
- Antonio Carlesso
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Box 431, SE-405 30 Gothenburg, Sweden
| | - Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | | | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Gothenburg, Sweden
| | - Pär Matsson
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Box 431, SE-405 30 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, Sweden
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18
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Zengin Kurt B, Dhara D, El-Sagheer AH, Brown T. Synthesis and Properties of Oligonucleotides Containing LNA-Sulfamate and Sulfamide Backbone Linkages. Org Lett 2024; 26:4137-4141. [PMID: 38717429 PMCID: PMC11110047 DOI: 10.1021/acs.orglett.4c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Oligonucleotides hold great promise as therapeutic agents but poor bioavailability limits their utility. Hence, new analogues with improved cell uptake are urgently needed. Here, we report the synthesis and physical study of reduced-charge oligonucleotides containing artificial LNA-sulfamate and sulfamide linkages combined with 2'-O-methyl sugars and phosphorothioate backbones. These oligonucleotides have high affinity for RNA and excellent nuclease resistance.
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Affiliation(s)
- Belma Zengin Kurt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Debashis Dhara
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
| | - Afaf H. El-Sagheer
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K.
| | - Tom Brown
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
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19
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Togawa H, Okubo T, Horiuchi K, Yamaguchi T, Tomita-Sudo E, Akita T, Kawakami J, Obika S. Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions. J Chromatogr A 2024; 1721:464847. [PMID: 38552370 DOI: 10.1016/j.chroma.2024.464847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.
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Affiliation(s)
- Hiroyuki Togawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takashi Okubo
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Kazuki Horiuchi
- CERI Hita, Chemicals Evaluation and Research Institute, Japan, 3-822 Ishii-machi, Hita, Oita 877-0061, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Elisa Tomita-Sudo
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoka Akita
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Junji Kawakami
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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20
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Obexer R, Nassir M, Moody ER, Baran PS, Lovelock SL. Modern approaches to therapeutic oligonucleotide manufacturing. Science 2024; 384:eadl4015. [PMID: 38603508 DOI: 10.1126/science.adl4015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.
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Affiliation(s)
- R Obexer
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - M Nassir
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - E R Moody
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - P S Baran
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - S L Lovelock
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
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21
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Liu T, Huang J, Luo D, Ren L, Ning L, Huang J, Lin H, Zhang Y. Cm-siRPred: Predicting chemically modified siRNA efficiency based on multi-view learning strategy. Int J Biol Macromol 2024; 264:130638. [PMID: 38460652 DOI: 10.1016/j.ijbiomac.2024.130638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/27/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
The rational modification of siRNA molecules is crucial for ensuring their drug-like properties. Machine learning-based prediction of chemically modified siRNA (cm-siRNA) efficiency can significantly optimize the design process of siRNA chemical modifications, saving time and cost in siRNA drug development. However, existing in-silico methods suffer from limitations such as small datasets, inadequate data representation capabilities, and lack of interpretability. Therefore, in this study, we developed the Cm-siRPred algorithm based on a multi-view learning strategy. The algorithm employs a multi-view strategy to represent the double-strand sequences, chemical modifications, and physicochemical properties of cm-siRNA. It incorporates a cross-attention model to globally correlate different representation vectors and a two-layer CNN module to learn local correlation features. The algorithm demonstrates exceptional performance in cross-validation experiments, independent dataset, and case studies on approved siRNA drugs, and showcasing its robustness and generalization ability. In addition, we developed a user-friendly webserver that enables efficient prediction of cm-siRNA efficiency and assists in the design of siRNA drug chemical modifications. In summary, Cm-siRPred is a practical tool that offers valuable technical support for siRNA chemical modification and drug efficiency research, while effectively assisting in the development of novel small nucleic acid drugs. Cm-siRPred is freely available at https://cellknowledge.com.cn/sirnapredictor/.
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Affiliation(s)
- Tianyuan Liu
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Junyang Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Delun Luo
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chengdu Jingrunze Gene Technology Company Limited, Chengdu 611138, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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22
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Yin L, Li J, Wu C, Zhang H, Zhao W, Fan Z, Liu M, Zhang S, Guo M, Dou X, Guo D. Asymmetric synthesis of P-stereogenic phosphindane oxides via kinetic resolution and their biological activity. Nat Commun 2024; 15:2548. [PMID: 38514631 PMCID: PMC10957969 DOI: 10.1038/s41467-024-46892-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
The importance of P-stereogenic heterocycles has been widely recognized with their extensive use as privileged chiral ligands and bioactive compounds. The catalytic asymmetric synthesis of P-stereogenic phosphindane derivatives, however, remains a challenging task. Herein, we report a catalytic kinetic resolution of phosphindole oxides via rhodium-catalyzed diastereo- and enantioselective conjugate addition to access enantiopure P-stereogenic phosphindane and phosphindole derivatives. This kinetic resolution method features high efficiency (s factor up to >1057), excellent stereoselectivities (all >20:1 dr, up to >99% ee), and a broad substrate scope. The obtained chiral phosphindane oxides exhibit promising therapeutic efficacy in autosomal dominant polycystic kidney disease (ADPKD), and compound 3az is found to significantly inhibit renal cyst growth both in vitro and in vivo, thus ushering in a promising scaffold for ADPKD drug discovery. This study will not only advance efforts towards the asymmetric synthesis of challenging P-stereogenic heterocycles, but also surely inspire further development of P-stereogenic entities for bioactive small-molecule discovery.
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Affiliation(s)
- Long Yin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Jiajia Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Changhui Wu
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing, China
| | - Haoran Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Wenchao Zhao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Zhiyuan Fan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Mengxuan Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Siqi Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China.
| | - Xiaowei Dou
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing, China.
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China.
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23
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Bednarska-Szczepaniak K, Ebenryter-Olbińska K, Gajek G, Śmiałkowski K, Suwara J, Fiedorowicz L, Leśnikowski Z. Synthesis of DNA-Boron Cluster Composites and Assembly into Functional Nanoparticles with Dual, Anti-EGFR, and Anti-c-MYC Oncogene Silencing Activity. Chemistry 2024; 30:e202303531. [PMID: 38214885 DOI: 10.1002/chem.202303531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
A versatile method for the automated synthesis of composites containing DNA-oligonucleotides and boron cluster scaffolds and their assembly into functional nanoparticles is described. The obtained, torus-like nanoparticles carry antisense oligonucleotides that target two different oncogenes simultaneously. The nanoparticles exhibited notable silencing efficiency in vitro in a pancreatic carcinoma cell line PANC-1 toward EGFR and c-Myc genes at the mRNA level, and a significant efficiency at the protein level. The proposed approach may be an attractive alternative to methods currently used, including one therapeutic nucleic acid, one genetic target, or the use of cocktails of therapeutic nucleic acids.
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Affiliation(s)
- Katarzyna Bednarska-Szczepaniak
- Laboratory of Medicinal Chemistry, Institute of Medical Biology, Polish Academy of Sciences, Lodowa Łódź, 106, 92-232, Lodz, Poland
| | - Katarzyna Ebenryter-Olbińska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza, Łódź, 112, 90-363 Lodz, Poland
| | - Gabriela Gajek
- Laboratory of Immunobiology of Infections, Institute of Medical Biology, Polish Academy of Sciences, Lodowa Łódź, 106, 92-232, Lodz, Poland
| | - Krzysztof Śmiałkowski
- Laboratory of Medicinal Chemistry, Institute of Medical Biology, Polish Academy of Sciences, Lodowa Łódź, 106, 92-232, Lodz, Poland
- Lodz Institutes of the Polish Academy of Science, The Bio-Med-Chem Doctoral School, University of Lodz, Poland
| | - Justyna Suwara
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza, Łódź, 112, 90-363 Lodz, Poland
| | - Lidia Fiedorowicz
- Laboratory of Mycobacterium Genetics and Physiology, Institute of Medical Biology Polish Academy of Sciences, Lodowa Łódź, 106, 92-232, Lodz, Poland
- Lodz Institutes of the Polish Academy of Science, The Bio-Med-Chem Doctoral School, University of Lodz, Poland
| | - Zbigniew Leśnikowski
- Laboratory of Medicinal Chemistry, Institute of Medical Biology, Polish Academy of Sciences, Lodowa Łódź, 106, 92-232, Lodz, Poland
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24
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Sahoo A, Das G, Ghosh A, Shivappa Bagale S, Kumar Choudhary N, Harikrishna S, Sinha S, Gore KR. N 3-Methyluridine and 2'-O-Alkyl/2'-Fluoro-N 3-methyluridine functionalized nucleic acids improve nuclease resistance while maintaining duplex geometry. Bioorg Med Chem 2024; 100:117616. [PMID: 38295488 DOI: 10.1016/j.bmc.2024.117616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N3-methyluridine (2'-O-alkyl/2'-F-m3U) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-m3U modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT20 with 2'-O-alkyl-m3U modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to m3U, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the m3U and 2'-O-methyl-m3U modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-m3U modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-m3U nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics.
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Affiliation(s)
- Avijit Sahoo
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Nishant Kumar Choudhary
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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25
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Tong AJ, Leylek R, Herzner AM, Rigas D, Wichner S, Blanchette C, Tahtinen S, Kemball CC, Mellman I, Haley B, Freund EC, Delamarre L. Nucleotide modifications enable rational design of TLR7-selective ligands by blocking RNase cleavage. J Exp Med 2024; 221:e20230341. [PMID: 38095631 PMCID: PMC10720541 DOI: 10.1084/jem.20230341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Toll-like receptors 7 (TLR7) and 8 (TLR8) each sense single-stranded RNA (ssRNA), but their activation results in different immune activation profiles. Attempts to selectively target either TLR7 or TLR8 have been hindered by their high degree of homology. However, recent studies revealed that TLR7 and TLR8 bind different ligands resulting from the processing of ssRNA by endolysosomal RNases. We demonstrate that by introducing precise 2' sugar-modified bases into oligoribonucleotides (ORNs) containing known TLR7 and TLR8 binding motifs, we could prevent RNase-mediated degradation into the monomeric uridine required for TLR8 activation while preserving TLR7 activation. Furthermore, a novel, optimized protocol for CRISPR-Cas9 knockout in primary human plasmacytoid dendritic cells showed that TLR7 activation is dependent on RNase processing of ORNs and revealed a previously undescribed role for RNase 6 in degrading ORNs into TLR ligands. Finally, 2' sugar-modified ORNs demonstrated robust innate immune activation in mice. Altogether, we identified a strategy for creating tunable TLR7-selective agonists.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ira Mellman
- Genentech, Inc., South San Francisco, CA, USA
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26
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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27
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Nishina K, Yoshioka K, Yokota T, Hara RI. Comparison of interaction between antimiR and microRNA versus HDO-antimiR and microRNA by molecular dynamics simulation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-16. [PMID: 38205778 DOI: 10.1080/15257770.2024.2302526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Recently, we found DNA/RNA heteroduplex oligonucleotide-based antimiR (HDO-antimiR) can more efficiently inhibit the target miRNA than conventional antimiR after its cellular uptake. But the mechanism of HDO-antimiR about the target-silencing is unknown. We here tried to elucidate the interaction mechanism of HDO-antimiR to miRNA using molecular dynamics (MD) simulation. When interaction of the conventional antimiR or HDO-antimiR and the target miRNA was simulated, they combined with each other in various forms. In the hydrogen bond analyses, base site of the antimiR formed hydrogen bond with miRNA. On the other hand, phosphate site of the HDO-antimiR formed hydrogen bond with miRNA. These results suggested that there were differences about the binding mechanisms between antimiR and HDO-antimiR to the target miRNA. In particular, there was a difference in the binding site between antimiR and HDO-antimiR. Additionally, it was found that guanine in the miRNA is mainly involved in the binding to the antimiR or HDO-antimiR. MD simulation method is useful in understanding the mechanism of oligonucleotide therapeutics.
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Affiliation(s)
- Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
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28
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Qin Z, Zhang K, He P, Zhang X, Xie M, Fu Y, Gu C, Zhu Y, Tong A, Wei H, Zhang C, Xiang Y. Discovering covalent inhibitors of protein-protein interactions from trillions of sulfur(VI) fluoride exchange-modified oligonucleotides. Nat Chem 2023; 15:1705-1714. [PMID: 37653229 DOI: 10.1038/s41557-023-01304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Molecules that covalently engage target proteins are widely used as activity-based probes and covalent drugs. The performance of these covalent inhibitors is, however, often compromised by the paradox of efficacy and risk, which demands a balance between reactivity and selectivity. The challenge is more evident when targeting protein-protein interactions owing to their low ligandability and undefined reactivity. Here we report sulfur(VI) fluoride exchange (SuFEx) in vitro selection, a general platform for high-throughput discovery of covalent inhibitors from trillions of SuFEx-modified oligonucleotides. With SuFEx in vitro selection, we identified covalent inhibitors that cross-link distinct residues of the SARS-CoV-2 spike protein at its protein-protein interaction interface with the human angiotensin-converting enzyme 2. A separate suite of covalent inhibitors was isolated for the human complement C5 protein. In both cases, we observed a clear disconnection between binding affinity and cross-linking reactivity, indicating that direct search for the aimed reactivity-as enabled by SuFEx in vitro selection-is vital for discovering covalent inhibitors of high selectivity and potency.
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Affiliation(s)
- Zichen Qin
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Kaining Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Xie
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunmei Gu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
- Beijing Institute of Collaborative Innovation (BICI), Beijing, China
| | - Yiying Zhu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Aijun Tong
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Xiang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China.
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29
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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30
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Wang C, Yang Q, Dai YH, Xiong J, Zheng Y, Duan WL. Nickel-Catalyzed Asymmetric Synthesis of P-Stereogenic Phosphanyl Hydrazine Building Blocks. Angew Chem Int Ed Engl 2023; 62:e202313112. [PMID: 37770407 DOI: 10.1002/anie.202313112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Catalytic asymmetric methods for the synthesis of synthetically versatile P-stereogenic building blocks offer an efficient and practical approach for the diversity-oriented preparation of P-chiral phosphorus compounds. Herein, we report the first nickel-catalyzed synthesis of P-stereogenic secondary aminophosphine-boranes by the asymmetric addition of primary phosphines to azo compounds. We further demonstrate that the P-H and P-N bonds on these phosphanyl hydrazine building blocks can be reacted sequentially and stereospecifically to access various P-stereogenic compounds with structural diversity.
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Affiliation(s)
- Chuanyong Wang
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, 225002, Yangzhou, China
| | - Qingliang Yang
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, 225002, Yangzhou, China
| | - Yuan-Hao Dai
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, 225002, Yangzhou, China
| | - Jianqi Xiong
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, 225002, Yangzhou, China
| | - Yu Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, 210037, Nanjing, P. R. China
| | - Wei-Liang Duan
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, 225002, Yangzhou, China
- College of Chemistry and Chemical Engineering, Inner Mongolia University, 235 West University Street, 010021, Hohhot, China
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31
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Pfeiffer LS, Stafforst T. Precision RNA base editing with engineered and endogenous effectors. Nat Biotechnol 2023; 41:1526-1542. [PMID: 37735261 DOI: 10.1038/s41587-023-01927-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
RNA base editing refers to the rewriting of genetic information within an intact RNA molecule and serves various functions, such as evasion of the endogenous immune system and regulation of protein function. To achieve this, certain enzymes have been discovered in human cells that catalyze the conversion of one nucleobase into another. This natural process could be exploited to manipulate and recode any base in a target transcript. In contrast to DNA base editing, analogous changes introduced in RNA are not permanent or inheritable but rather allow reversible and doseable effects that appeal to various therapeutic applications. The current practice of RNA base editing involves the deamination of adenosines and cytidines, which are converted to inosines and uridines, respectively. In this Review, we summarize current site-directed RNA base-editing strategies and highlight recent achievements to improve editing efficiency, precision, codon-targeting scope and in vivo delivery into disease-relevant tissues. Besides engineered editing effectors, we focus on strategies to harness endogenous adenosine deaminases acting on RNA (ADAR) enzymes and discuss limitations and future perspectives to apply the tools in basic research and as a therapeutic modality. We expect the field to realize the first RNA base-editing drug soon, likely on a well-defined genetic disease. However, the long-term challenge will be to carve out the sweet spot of the technology where its unique ability is exploited to modulate signaling cues, metabolism or other clinically relevant processes in a safe and doseable manner.
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Affiliation(s)
- Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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32
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Roberts TC, Wood MJA, Davies KE. Therapeutic approaches for Duchenne muscular dystrophy. Nat Rev Drug Discov 2023; 22:917-934. [PMID: 37652974 DOI: 10.1038/s41573-023-00775-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a monogenic muscle-wasting disorder and a priority candidate for molecular and cellular therapeutics. Although rare, it is the most common inherited myopathy affecting children and so has been the focus of intense research activity. It is caused by mutations that disrupt production of the dystrophin protein, and a plethora of drug development approaches are under way that aim to restore dystrophin function, including exon skipping, stop codon readthrough, gene replacement, cell therapy and gene editing. These efforts have led to the clinical approval of four exon skipping antisense oligonucleotides, one stop codon readthrough drug and one gene therapy product, with other approvals likely soon. Here, we discuss the latest therapeutic strategies that are under development and being deployed to treat DMD. Lessons from these drug development programmes are likely to have a major impact on the DMD field, but also on molecular and cellular medicine more generally. Thus, DMD is a pioneer disease at the forefront of future drug discovery efforts, with these experimental treatments paving the way for therapies using similar mechanisms of action being developed for other genetic diseases.
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Affiliation(s)
- Thomas C Roberts
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- MDUK Oxford Neuromuscular Centre, Oxford, UK.
| | - Matthew J A Wood
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Kay E Davies
- MDUK Oxford Neuromuscular Centre, Oxford, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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33
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Tsurusaki T, Sato K, Wada T. Internucleotidic bond formation using H-phosphonamidate derivatives and acidic activators. RSC Adv 2023; 13:31674-31686. [PMID: 37908660 PMCID: PMC10614043 DOI: 10.1039/d3ra06193k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023] Open
Abstract
We previously developed a synthesis method for oligodeoxynucleotides using H-phosphonamidate derivatives as monomers. In this synthesis method, H-phosphonamidate monomers having a heterocyclic amino group as a leaving group reacts with an alcohol to form an internucleotidic H-phosphonate diester in pyridine without any additives upon heating. In this study, H-phosphonamidate reacted to form an internucleotidic linkage in the presence of acidic activators at room temperature. This finding is the first example of the activation of an amino group of an H-phosphonamidate derivative in the presence of acidic activators. In addition, the condensation reaction with acidic activators was accelerated with the use of pyridine as a solvent. Moreover, heterocyclic amino groups that have an electronegative atom, such as S and O, effectively served as a leaving group of the H-phosphonamidate monomer. From the results, we hypothesized that the tautomerization to the phosphite-form of the H-phosphonamidate monomer is an important step of the condensation reaction using acidic activators, and such process is accelerated when using pyridine as the solvent and heterocyclic amino groups as the leaving groups of the H-phosphonamidate monomer. Molecular orbital calculations also support our hypothesis. We optimized the condensation reaction conditions and synthesized dinucleoside phosphorothioate derivatives bearing all nucleobases.
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Affiliation(s)
- Taiki Tsurusaki
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki, Noda Chiba 278-8510 Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki, Noda Chiba 278-8510 Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki, Noda Chiba 278-8510 Japan
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34
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Li Z, Tong F, Xiao L, Larson NR, Zhou X, Zhang Y, Immel-Brown JP, Bou-Assaf GM. Establishing stereochemical comparability in phosphorothioate oligonucleotides with nuclease P1 digestion coupled with LCMS analysis. Analyst 2023; 148:5361-5365. [PMID: 37755232 DOI: 10.1039/d3an01392h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Stereochemical comparability is critical for ensuring manufacturing consistency in therapeutic phosphorothioate oligonucleotides. Currently, analytical methods for this assessment are limited. We hereby report on a novel protocol capable of detecting a stereochemistry change in a single phosphorothioate linkage by employing nuclease P1 digestion of the oligonucleotide with subsequent LCMS analysis of the resulting fragments. The method proves valuable for establishing stereochemical comparability and for ensuring manufacturing consistency of oligonucleotide therapeutics.
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Affiliation(s)
- Zifan Li
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Fei Tong
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Li Xiao
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Nicholas R Larson
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Xuan Zhou
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Yueheng Zhang
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - Jonas P Immel-Brown
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | - George M Bou-Assaf
- Pharmaceutical Operations & Technology, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
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35
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Goyon A, Blevins MS, Napolitano JG, Nguyen D, Goel M, Scott B, Wang J, Koenig SG, Chen T, Zhang K. Characterization of antisense oligonucleotide and guide ribonucleic acid diastereomers by hydrophilic interaction liquid chromatography coupled to mass spectrometry. J Chromatogr A 2023; 1708:464327. [PMID: 37660562 DOI: 10.1016/j.chroma.2023.464327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
Oligonucleotides have become an essential modality for a variety of therapeutic approaches, including cell and gene therapies. Rapid progress in the field has attracted significant research in designing novel oligonucleotide chemistries and structures. Beyond their polar nature, the length of large RNAs and presence of numerous diastereomers for phosphorothioate (PS)-modified RNAs pose heightened challenges for their characterization. In this study, the stereochemistry of a fully-modified antisense oligonucleotide (ASO) and partially-modified guide RNAs (gRNAs) was investigated using HILIC and orthogonal techniques. The profiles of three lots of a fully-modified ASO with PS linkages were compared using ion-pairing RPLC (IPRP) and HILIC. Interestingly, three isomer peaks were partially resolved by HILIC for two lots while only one peak was observed on the IPRP profile. Model oligonucleotides having the same sequence of the five nucleotides incorporated to the 3'-end of the gRNA but differing in their number and position of PS linkages were investigated by HILIC, IPRP, ion mobility spectrometry-mass spectrometry (IM-MS) and nuclear magnetic resonance (NMR). An strategy was ultimately designed to aid in the characterization of gRNA stereochemistry. Ribonuclease (RNase) T1 digestion enabled the characterization of gRNA diastereomers by reducing their number from 32 at the gRNA intact level to 4 or 8 at the fragment level. To our knowledge, this is the first time that HILIC has successfully been utilized for the profiling of diastereomers for various oligonucleotide formats and chemical modifications.
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Affiliation(s)
- Alexandre Goyon
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Molly S Blevins
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - José G Napolitano
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daniel Nguyen
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Meenakshi Goel
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brandon Scott
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jenny Wang
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Stefan G Koenig
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tao Chen
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Synthetic Molecule Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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36
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Wang J, Tan M, Wang Y, Liu X, Lin A. Advances in modification and delivery of nucleic acid drugs. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:417-428. [PMID: 37643976 PMCID: PMC10495244 DOI: 10.3724/zdxbyxb-2023-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/14/2023] [Indexed: 08/18/2023]
Abstract
Nucleic acid-based drugs, such as RNA and DNA drugs, exert their effects at the genetic level. Currently, widely utilized nucleic acid-based drugs include nucleic acid aptamers, antisense oligonucleotides, mRNA, miRNA, siRNA and saRNA. However, these drugs frequently encounter challenges during clinical application, such as poor stability, weak targeting specificity, and difficulties in traversing physiological barriers. By employing chemical modifications of nucleic acid structures, it is possible to enhance the stability and targeting specificity of certain nucleic acid drugs within the body, thereby improving delivery efficiency and reducing immunogenicity. Moreover, utilizing nucleic acid drug carriers can facilitate the transportation of drugs to lesion sites, thereby aiding efficient intracellular escape and promoting drug efficacy within the body. Currently, commonly employed delivery carriers include virus vectors, lipid nanoparticles, polymer nanoparticles, inorganic nanoparticles, protein carriers and extracellular vesicles. Nevertheless, individual modifications or delivery carriers alone are insufficient to overcome numerous obstacles. The integration of nucleic acid chemical modifications with drug delivery systems holds promise for achieving enhanced therapeutic effects. However, this approach also presents increased technical complexity and clinical translation costs. Therefore, the development of nucleic acid drug carriers and nucleic acid chemical modifications that are both practical and simple, while maintaining high efficacy, low toxicity, and precise nucleic acid delivery, has become a prominent research focus in the field of nucleic acid drug development. This review comprehensively summarizes the advancements in nucleic acid-based drug modifica-tions and delivery systems. Additionally, strategies to enhance nucleic acid drug delivery efficiency are discussed, with the aim of providing valuable insights for the translational application of nucleic acid drugs.
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Affiliation(s)
- Junfeng Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
| | - Manman Tan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Ying Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Xiangrui Liu
- Zhejiang University Cancer Center, Hangzhou 310058, China.
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Center for RNA Medicine, International Institutes of Medicine, Zhejiang University, Jinhua 322000, Zhejiang Province, China.
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37
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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38
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Rosenqvist P, Saari V, Pajuniemi E, Gimenez Molina A, Ora M, Horvath A, Virta P. Stereo-Controlled Liquid Phase Synthesis of Phosphorothioate Oligonucleotides on a Soluble Support. J Org Chem 2023. [PMID: 37428953 PMCID: PMC10367069 DOI: 10.1021/acs.joc.3c01006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
5'-O-(2-Methoxyisopropyl) (MIP)-protected 2'-deoxynucleosides as chiral P(V)-building blocks, based on the limonene-derived oxathiaphospholane sulfide, were synthesized and used for the assembly of di-, tri-, and tetranucleotide phosphorothioates on a tetrapodal pentaerythritol-derived soluble support. The synthesis cycle consisted of two reactions and two precipitations: (1) the coupling under basic conditions, followed by neutralization and precipitation and (2) an acid catalyzed 5'-O-deacetalization, followed by neutralization and precipitation. The simple P(V) chemistry together with the facile 5'-O-MIP deprotection proved efficient in the liquid phase oligonucleotide synthesis (LPOS). Ammonolysis released nearly homogeneous Rp or Sp phosphorothioate diastereomers in ca. 80% yield/synthesis cycle.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Ella Pajuniemi
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Alejandro Gimenez Molina
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Andras Horvath
- Chemical Process Research & Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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39
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Zhang Y, Zhao P, Sun S, Wu Q, Shi E, Xiao J. Universal and divergent P-stereogenic building with camphor-derived 2,3-diols. Commun Chem 2023; 6:133. [PMID: 37369718 DOI: 10.1038/s42004-023-00935-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The access to P-stereogenic motifs has always been considered a very challenging and high attractive mission in modern organic synthesis. While several chiral auxiliaries employed by the practical Jugé-Stephan-like methodology have been developed, new type of readily accessible bifunctional ligands toward P-stereogenic building still remain much desirable. Herein, we present a powerful chiral template, camphor-derived 2,3-diols named CAMDOL, which were designed and synthesized from the commercially cheap camphorquinone in high yields at 50 grams scale with a column-free purification. Diverse P(III)-chiral compounds and their borane forms including phosphinous acids, phosphinites, and phosphines, as well as the corresponding P(V)-chiral compounds including phosphinates, phosphine oxides, phosphinothioates, phosphine sulfides, and secondary phosphine oxides were afforded in high yields and ee values through the optimal 2,3-diphenyl CAMDOL platform. An unusual C3-OP bond cleavage following the first P-OC2 bond breaking was observed during the ring-opening process when quenching by NH4Cl solution, which generates a unique but valuable camphor-epoxide scaffold as by-product.
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Affiliation(s)
- Yulong Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Peichao Zhao
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Shengnan Sun
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Qian Wu
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Enxue Shi
- State Key Laboratory of NBC Protection for Civilian, Beijing, China.
| | - Junhua Xiao
- State Key Laboratory of NBC Protection for Civilian, Beijing, China.
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40
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Dowerah D, V. N. Uppuladinne M, Sarma PJ, Biswakarma N, Sonavane UB, Joshi RR, Ray SK, Namsa ND, Deka RC. Design of LNA Analogues Using a Combined Density Functional Theory and Molecular Dynamics Approach for RNA Therapeutics. ACS OMEGA 2023; 8:22382-22405. [PMID: 37396274 PMCID: PMC10308574 DOI: 10.1021/acsomega.2c07860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/17/2023] [Indexed: 07/04/2023]
Abstract
Antisense therapeutics treat a wide spectrum of diseases, many of which cannot be addressed with the current drug technologies. In the quest to design better antisense oligonucleotide drugs, we propose five novel LNA analogues (A1-A5) for modifying antisense oligonucleotides and establishing each with the five standard nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). Monomer nucleotides of these modifications were considered for a detailed Density Functional Theory (DFT)-based quantum chemical analysis to determine their molecular-level structural and electronic properties. A detailed MD simulation study was done on a 14-mer ASO (5'-CTTAGCACTGGCCT-3') containing these modifications targeting PTEN mRNA. Results from both molecular- and oligomer-level analysis clearly depicted LNA-level stability of the modifications, the ASO/RNA duplexes maintaining stable Watson-Crick base pairing preferring RNA-mimicking A-form duplexes. Notably, monomer MO isosurfaces for both purines and pyrimidines were majorly distributed on the nucleobase region in modifications A1 and A2 and in the bridging unit in modifications A3, A4, and A5, suggesting that A3/RNA, A4/RNA, and A5/RNA duplexes interact more with the RNase H and solvent environment. Accordingly, solvation of A3/RNA, A4/RNA, and A5/RNA duplexes was higher compared to that of LNA/RNA, A1/RNA, and A2/RNA duplexes. This study has resulted in a successful archetype for creating advantageous nucleic acid modifications tailored for particular needs, fulfilling a useful purpose of designing novel antisense modifications, which may overcome the drawbacks and improve the pharmacokinetics of existing LNA antisense modifications.
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Affiliation(s)
- Dikshita Dowerah
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
| | - Mallikarjunachari V. N. Uppuladinne
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Plaban J. Sarma
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
- Department
of Chemistry, Gargaon College, Sivasagar, Assam 785685, India
| | - Nishant Biswakarma
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
| | - Uddhavesh B. Sonavane
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Rajendra R. Joshi
- HPC—Medical
& Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune 411008, India
| | - Suvendra K. Ray
- Department
of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Nima D. Namsa
- Department
of Molecular Biology and Biotechnology, Tezpur University, Napaam, Sonitpur, Assam 784028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
| | - Ramesh Ch. Deka
- CMML—Catalysis
and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam, Sonitpur, Assam 784 028, India
- Center
for Multidisciplinary Research, Tezpur University, Napaam, Sonitpur, Assam 784028, India
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41
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Yan A, Chen X, He J, Ge Y, Liu Q, Men D, Xu K, Li D. Phosphorothioated DNA Engineered Liposomes as a General Platform for Stimuli-Responsive Cell-Specific Intracellular Delivery and Genome Editing. Angew Chem Int Ed Engl 2023; 62:e202303973. [PMID: 37100742 DOI: 10.1002/anie.202303973] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 04/28/2023]
Abstract
Intracellular protein delivery is highly desirable for protein drug-based cell therapy. Established technologies suffer from poor cell-specific cytosolic protein delivery, which hampers the targeting therapy of specific cell populations. A fusogenic liposome system enables cytosolic delivery, but its ability of cell-specific and controllable delivery is quite limited. Inspired by the kinetics of viral fusion, we designed a phosphorothioated DNA coatings-modified fusogenic liposome to mimic the function of viral hemagglutinin. The macromolecular fusion machine docks cargo-loaded liposomes at the membrane of target cells, triggers membrane fusion upon pH or UV light stimuli, and facilitates cytosolic protein delivery. Our results showed efficient cell-targeted delivery of proteins of various sizes and charges, indicating the phosphorothioated DNA plug-in unit on liposomes could be a general strategy for spatial-temporally controllable protein delivery both in vitro and in vivo.
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Affiliation(s)
- An Yan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xiaoqing Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Jie He
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Yifan Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Qing Liu
- Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Dong Men
- Guangzhou Laboratory, Guangzhou, 510005, China
| | - Ke Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
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42
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Moody ER, Obexer R, Nickl F, Spiess R, Lovelock SL. An enzyme cascade enables production of therapeutic oligonucleotides in a single operation. Science 2023; 380:1150-1154. [PMID: 37319201 DOI: 10.1126/science.add5892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Therapeutic oligonucleotides have emerged as a powerful drug modality with the potential to treat a wide range of diseases; however, the rising number of therapies poses a manufacturing challenge. Existing synthetic methods use stepwise extension of sequences immobilized on solid supports and are limited by their scalability and sustainability. We report a biocatalytic approach to efficiently produce oligonucleotides in a single operation where polymerases and endonucleases work in synergy to amplify complementary sequences embedded within catalytic self-priming templates. This approach uses unprotected building blocks and aqueous conditions. We demonstrate the versatility of this methodology through the synthesis of clinically relevant oligonucleotide sequences containing diverse modifications.
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Affiliation(s)
- E R Moody
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Obexer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - F Nickl
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - S L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
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43
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Genna V, Iglesias-Fernández J, Reyes-Fraile L, Villegas N, Guckian K, Seth P, Wan B, Cabrero C, Terrazas M, Brun-Heath I, González C, Sciabola S, Villalobos A, Orozco M. Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides. Nucleic Acids Res 2023; 51:4713-4725. [PMID: 37099382 PMCID: PMC10250214 DOI: 10.1093/nar/gkad309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 04/27/2023] Open
Abstract
Phosphorothioates (PS) have proven their effectiveness in the area of therapeutic oligonucleotides with applications spanning from cancer treatment to neurodegenerative disorders. Initially, PS substitution was introduced for the antisense oligonucleotides (PS ASOs) because it confers an increased nuclease resistance meanwhile ameliorates cellular uptake and in-vivo bioavailability. Thus, PS oligonucleotides have been elevated to a fundamental asset in the realm of gene silencing therapeutic methodologies. But, despite their wide use, little is known on the possibly different structural changes PS-substitutions may provoke in DNA·RNA hybrids. Additionally, scarce information and significant controversy exists on the role of phosphorothioate chirality in modulating PS properties. Here, through comprehensive computational investigations and experimental measurements, we shed light on the impact of PS chirality in DNA-based antisense oligonucleotides; how the different phosphorothioate diastereomers impact DNA topology, stability and flexibility to ultimately disclose pro-Sp S and pro-Rp S roles at the catalytic core of DNA Exonuclease and Human Ribonuclease H; two major obstacles in ASOs-based therapies. Altogether, our results provide full-atom and mechanistic insights on the structural aberrations PS-substitutions provoke and explain the origin of nuclease resistance PS-linkages confer to DNA·RNA hybrids; crucial information to improve current ASOs-based therapies.
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Affiliation(s)
- Vito Genna
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- NBD | Nostrum Biodiscovery, Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Laura Reyes-Fraile
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Nuria Villegas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | | | - Punit Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cristina Cabrero
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | - Montserrat Terrazas
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, C/ Serrano 119, Madrid 28006, Spain
| | | | | | - Modesto Orozco
- Mechanisms of Diseases, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain
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44
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Becette OB, Marino JP, Brinson RG. Structural Fingerprinting of Antisense Oligonucleotide Therapeutics by Solution NMR Spectroscopy. Pharm Res 2023; 40:1373-1382. [PMID: 36195820 DOI: 10.1007/s11095-022-03403-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 10/10/2022]
Abstract
PURPOSE Antisense oligonucleotide (ASO) therapeutics are an emerging class of biopharmaceuticals to treat and prevent diseases, particularly those involving "undruggable" protein targets. Impurities generated throughout the ASO drug manufacturing and formulation pipeline can be detrimental to drug safety and efficacy. Therefore, analytical techniques are needed to rigorously characterize these molecules for quality assurance purposes. METHODS We demonstrate 1D and 2D nuclear magnetic resonance (NMR) spectroscopy methods that can generate high-resolution structural "fingerprints" of ASOs. RESULTS AND CONCLUSIONS 1D 1H and 31P measurements are shown to provide rapid initial assessment of the ASO integrity. In particular, a well-resolved pair of 31P signals arising from the 5´-end of the phosphorodiamidate morpholino oligomer (PMO) are sensitive to complex formation and oligomerization state. 2D 1H-1H, 1H-13C, and 1H-15 N experiments, although less sensitive, are further shown to enable resonance assignment, which will allow the tracking of structural changes at high-resolution during the drug development and manufacturing processes. We further anticipate that the described NMR approaches will be broadly applicable to fully formulated ASO therapeutics, including modalities other than PMOs.
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Affiliation(s)
- Owen B Becette
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA
| | - Robert G Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland, 20850, USA.
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45
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Li Y, Zhu S, Chen Y, Ma Q, Kan D, Yu W, Zhang B, Chen X, Wei W, Shao Y, Wang K, Zhang M, Deng S, Niu Y, Shang Z. Post-transcriptional modification of m 6A methylase METTL3 regulates ERK-induced androgen-deprived treatment resistance prostate cancer. Cell Death Dis 2023; 14:289. [PMID: 37095108 PMCID: PMC10126012 DOI: 10.1038/s41419-023-05773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 04/26/2023]
Abstract
As the most common modification of RNA, N6-methyladenosin (m6A) has been confirmed to be involved in the occurrence and development of various cancers. However, the relationship between m6A and castration resistance prostate cancer (CRPC), has not been fully studied. By m6A-sequencing of patient cancer tissues, we identified that the overall level of m6A in CRPC was up-regulated than castration sensitive prostate cancer (CSPC). Based on the analysis of m6A-sequencing data, we found m6A modification level of HRas proto-oncogene, GTPase (HRAS) and mitogen-activated protein kinase kinase 2 (MEK2 or MAP2K2) were enhanced in CRPC. Specifically, tissue microarray analysis and molecular biology experiments confirmed that METTL3, an m6A "writer" up-regulated after castration, activated the ERK pathway to contribute to malignant phenotype including ADT resistance, cell proliferation and invasion. We revealed that METTL3-mediated ERK phosphorylation by stabilizing the transcription of HRAS and positively regulating the translation of MEK2. In the Enzalutamide-resistant (Enz-R) C4-2 and LNCap cell line (C4-2R, LNCapR) established in the current study, the ERK pathway was confirmed to be regulated by METTL3. We also found that applying antisense oligonucleotides (ASOs) to target the METTL3/ERK axis can restore Enzalutamide resistance in vitro and in vivo. In conclusion, METTL3 activated the ERK pathway and induced the resistance to Enzalutamide by regulating the m6A level of critical gene transcription in the ERK pathway.
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Affiliation(s)
- Yang Li
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shimiao Zhu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yutong Chen
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Qianwang Ma
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Duo Kan
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wenyue Yu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Boya Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xuanrong Chen
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wanqing Wei
- Lianshui People's Hospital of Kangda College affiliated with Nanjing Medical University, Huai'an, China
| | - Yi Shao
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Keruo Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Mingpeng Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shu Deng
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuanjie Niu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
| | - Zhiqun Shang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
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46
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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48
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Tsurusaki T, Sato K, Wada T. Development of a new synthetic method for oligodeoxynucleotides using 3'- H-phosphonamidate derivatives. Org Biomol Chem 2023; 21:2486-2492. [PMID: 36688350 DOI: 10.1039/d2ob02292c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this study, we developed a new approach for the solution-phase synthesis of oligodeoxynucleotides (ODNs) using nucleoside 3'-H-phosphonamidate derivatives as monomers. The H-phosphonamidate monomers having a heterocyclic amino group as the leaving group reacted with an alcohol to form an internucleotidic H-phosphonate diester under mild basic conditions without using additives. The resultant internucleotidic linkage was converted into a more stable linkage, such as an S-cyanoethyl phosphorothioate diester. Moreover, under the conditions for detritylation, the unreacted H-phosphonamidate monomer was converted into a water-soluble compound, which was easily removed by extraction. Thus, only simple extractions were required to purify intermediates, and the solution-phase synthesis of trithymidine diphosphorothioate from the monomer was achieved with only one silica gel column chromatography purification. This method was applied to deoxyadenosine, deoxycytidine, and deoxyguanosine derivatives. This strategy enables us to reduce the number of reagents and simplify the purification process.
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Affiliation(s)
- Taiki Tsurusaki
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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Xian H, Zhang Y, Yu C, Wang Y. Nanobiotechnology-Enabled mRNA Stabilization. Pharmaceutics 2023; 15:pharmaceutics15020620. [PMID: 36839942 PMCID: PMC9965532 DOI: 10.3390/pharmaceutics15020620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
mRNA technology has attracted enormous interest due to its great therapeutic potential. Strategies that can stabilize fragile mRNA molecules are crucial for their widespread applications. There are numerous reviews on mRNA delivery, but few focus on the underlying causes of mRNA instability and how to tackle the instability issues. Herein, the recent progress in nanobiotechnology-enabled strategies for stabilizing mRNA and better delivery is reviewed. First, factors that destabilize mRNA are introduced. Second, nanobiotechnology-enabled strategies to stabilize mRNA molecules are reviewed, including molecular and nanotechnology approaches. The impact of formulation processing on mRNA stability and shelf-life, including freezing and lyophilization, are also briefly discussed. Lastly, our perspectives on challenges and future directions are presented. This review may provide useful guidelines for understanding the structure-function relationship and the rational design of nanobiotechnology for mRNA stability enhancement and mRNA technology development.
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50
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Das A, Ghosh A, Sinha S. C5-pyrimidine-functionalized morpholino oligonucleotides exhibit differential binding affinity, target specificity and lipophilicity. Org Biomol Chem 2023; 21:1242-1253. [PMID: 36633261 DOI: 10.1039/d2ob01759h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
C5-substituted uridine and cytidine morpholino chlorophosphoramidate monomers were synthesized and incorporated into a 12-mer Phosphorodiamidate Morpholino Oligonucleotide (PMO) using semi-automated solid phase synthesis. PMOs with most of the tested pyrimidine C5-substitutions have significantly increased thermal stability when bound to the complementary RNA strand relative to the PMO. They exhibit higher binding with RNA than DNA. CD-spectra show B-type helical conformation of duplexes. HPLC analysis indicates their greater lipophilicity compared to regular PMOs. These chemical modifications have significant potential towards the development of better antisense technologies.
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Affiliation(s)
- Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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