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Das A, Gupta S, Shaw P, Sinha S. Synthesis of Self Permeable Antisense PMO Using C5-Guanidino-Functionalized Pyrimidines at the 5'-End Enables Sox2 Downregulation in Triple Negative Breast Cancer Cells. Mol Pharm 2024; 21:1256-1271. [PMID: 38324380 DOI: 10.1021/acs.molpharmaceut.3c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Delivery of macromolecular drugs inside cells has been a huge challenge in the field of oligonucleotide therapeutics for the past few decades. Earliest natural inspirations included the arginine rich stretch of cell permeable HIV-TAT peptide, which led to the design of several molecular transporters with varying numbers of rigid or flexible guanidinium units with different tethering groups. These transporters have been shown to efficiently deliver phosphorodiamidate morpholino oligonucleotides, which have a neutral backbone and cannot form lipoplexes. In this report, PMO based delivery agents having 3 or 4 guanidinium groups at the C5 position of the nucleobases of cytosine and uracil have been explored, which can be assimilated within the desired stretch of the antisense oligonucleotide. Guanidinium units have been connected by varying the flexibility with either a saturated (propyl) or an unsaturated (propargyl) spacer, which showed different serum dependency along with varied cytoplasmic distribution. The effect of cholesterol conjugation in the delivery agent as well as at the 5'-end of full length PMO in cellular delivery has also been studied. Finally, the efficacy of the delivery has been studied by the PMO mediated downregulation of the stemness marker Sox2 in the triple-negative breast cancer cell line MDA-MB 231. These results have validated the use of this class of delivery agents, which permit at a stretch PMO synthesis where the modified bases can also participate in Watson-Crick-Franklin base pairing for enhanced mRNA binding and protein downregulation and could solve the delivery problem of PMO.
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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
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Pallab Shaw
- 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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2
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Banerjee A, Das A, Ghosh A, Gupta A, Sinha S. Synthesis and Biophysical Properties of Triazole-Incorporated PMOs (TzPMOs): A Convergent, Click Ligation Approach. J Org Chem 2024; 89:2895-2903. [PMID: 38344977 DOI: 10.1021/acs.joc.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The synthesis of phosphorodiamidate morpholino oligonucleotides (PMOs) incorporating single or double triazole rings in the backbone has been achieved via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The synthetic approach implemented is fundamentally convergent, involving the ligation of a 5'-azide PMO fragment to a 3'-alkyne fragment both in solution and on solid support. To access the 3'-alkyne PMO fragment, we synthesized 3'-N-propargyl chlorophosphoramidate morpholino monomers for all four nucleobases. The resulting triazole-incorporated PMOs (TzPMOs) have exhibited comparable or improved binding affinity toward complementary deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) strands compared to its regular analogues. Finally, a full-length TzPMO was designed to target the Nanog gene, demonstrating almost identical hybridization properties when compared to its regular version. Circular dichroism studies revealed a B-type helical conformation for the duplexes formed by TzPMOs.
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Affiliation(s)
- Arpan Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Abhishek Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700 032, India
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3
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Das U, Kundu J, Shaw P, Bose C, Ghosh A, Gupta S, Sarkar S, Bhadra J, Sinha S. Self-transfecting GMO-PMO chimera targeting Nanog enable gene silencing in vitro and suppresses tumor growth in 4T1 allografts in mouse. MOLECULAR THERAPY - NUCLEIC ACIDS 2023; 32:203-228. [PMID: 37078062 PMCID: PMC10106836 DOI: 10.1016/j.omtn.2023.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotide (PMO)-based antisense reagents cannot enter cells without the help of a delivery technique, which limits their clinical applications. To overcome this problem, self-transfecting guanidinium-linked morpholino (GMO)-PMO or PMO-GMO chimeras have been explored as antisense agents. GMO facilitates cellular internalization and participates in Watson-Crick base pairing. Targeting NANOG in MCF7 cells resulted in decline of the whole epithelial to mesenchymal transition (EMT) and stemness pathway, evident through its phenotypic manifestations, all of which were promulgated in combination with Taxol due to downregulation of MDR1 and ABCG2. GMO-PMO-mediated knockdown of no tail gene resulted in desired phenotypes in zebrafish even upon delivery after 16-cell stages. In BALB/c mice, 4T1 allografts were found to regress via intra-tumoral administration of NANOG GMO-PMO antisense oligonucleotides (ASOs), which was associated with occurrence of necrotic regions. GMO-PMO-mediated tumor regression restored histopathological damage in liver, kidney, and spleen caused by 4T1 mammary carcinoma. Serum parameters of systemic toxicity indicated that GMO-PMO chimeras are safe. To the best of our knowledge, self-transfecting antisense reagent is the first report since the discovery of guanidinium-linked DNA (DNG), which could be useful as a combination cancer therapy and, in principle, can render inhibition of any target gene without using any delivery vehicle.
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Ghosh A, Akabane-Nakata M, Kundu J, Harp JM, Madaoui M, Egli M, Manoharan M, Sinha S. Synthesis and Biophysical Properties of Phosphorodiamidate Piperidino Oligomers. Org Lett 2023; 25:901-906. [PMID: 36734846 DOI: 10.1021/acs.orglett.2c04067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the synthesis of piperidino nucleoside phosphoramidates functionalized with uracil, cytosine, guanine, and adenine and their incorporation into oligomers. High-performance liquid chromatography analyses demonstrated that a phosphorodiamidate piperidino oligomer (PPO) is more lipophilic than a phosphorodiamidate morpholino oligomer (PMO) of the same tetrameric sequence. A PMO containing piperidino residues formed duplexes with both DNA and RNA, and the PPO had higher stability at endosomolytic pH and higher hydrophobicity than the PMO.
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Affiliation(s)
- Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Kundu J, Ghosh U, Ghosh A, Pattanayak S, Das A, Sinha S. Synthesis of Chlorophosphoramidate Monomer Morpholinos and PMOs. Curr Protoc 2023; 3:e686. [PMID: 36802170 DOI: 10.1002/cpz1.686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) are a successful class of antisense reagents that efficiently modulate gene expression. Because PMOs do not follow standard phosphoramidite chemistry, optimized synthetic protocols for these compounds are relatively scarce in the literature. This paper presents detailed protocols for synthesizing full-length PMOs using chlorophosphoramidate chemistry by manual solid-phase synthesis. We first describe the synthesis of Fmoc-protected morpholino hydroxyl monomers, and the corresponding chlorophosphoramidate monomers, from commercially available protected ribonucleosides. The new Fmoc chemistry necessitates the use of a milder base, such as N-ethylmorpholine (NEM), and coupling reagent, such as 5-(ethylthio)-1H-tetrazole (ETT), which are also tolerated for acid-sensitive trityl chemistry. These chlorophosphoramidate monomers are then employed for PMO synthesis in a manual solid-phase procedure using four sequential steps. The synthetic cycle for each nucleotide incorporation consists of (a) deblocking of the 3'-N protecting group using an acidic deblocking cocktail for trityl and base deblocking for Fmoc, (b) neutralization, (c) coupling in the presence of ETT and NEM, and (d) capping of the unreacted morpholine ring-amine. The method uses safe, stable, and inexpensive reagents, and the process is expected to be scalable. After full-length PMO synthesis and ammonia-mediated cleavage from the solid support and deprotection, a range of PMOs with different lengths can be obtained conveniently and efficiently with reproducible good yields. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the novel Fmoc-protected morpholino monomers Basic Protocol 2: Synthesis of the phosphorylating reagent (N,N-dimethylphosphoramic dichloride) required for chlorophosphoramidate monomer synthesis Basic Protocol 3: Synthesis of chlorophosphoramidate monomers of Fmoc-protected morpholino monomers Basic Protocol 4: Solution-phase standardization of dimer and trimer PMO synthesis using Fmoc chemistry Basic Protocol 5: Solid-phase synthesis, purification, and characterization of full-length (25-mer) no-tail PMO using both trityl and Fmoc chemistry.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
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Ghosh U, Gupta S, Sinha S. Synthesis of 5'-Thiol Functionalized Morpholino Oligo-Nucleotide and Subsequent Conjugation with IGT to Improve Delivery and Antisense Efficacy In Vitro. Bioconjug Chem 2023; 34:174-180. [PMID: 36538654 DOI: 10.1021/acs.bioconjchem.2c00587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thiol functionalized oligonucleotides are useful intermediates for a wide range of applications including DNA nanobiotechnology field through conjugation with various types of probes and cargos. Due to the limitation of synthetic process, phosphorodiamidate morpholino oligonucleotides (PMOs) have not been explored like other oligonucleotides through SH conjugation as mentioned above. In this paper, we report the synthesis of 5'-SH functionalized PMO using a solid support synthesis protocol with an optimized cysteine derived linker so that loading and coupling efficiency of morpholino monomers were effective enough to get a 25-mer 5'-SH functionalized PMO against human Nanog. The PMO with SH functionality was subsequently conjugated with our previously reported Internal Oligo-guanidinium Transporter (IGT) in solution phase to obtain the IGT-PMO conjugate. Interestingly, 5'-conjugated PMO (IGT-PMO) showed 2.5 times better antisense efficacy than 3'-conjugated PMO with IGT (PMO-IGT). 5'-Conjugation enables us to use IGT-PMO for further conjugation at the 3'-N terminal of PMO which was not possible earlier with 5'-OH-PMO-IGT. PMO has become an important class of antisense reagents because four PMO-based drugs have been approved for the treatment of Duchenne muscular dystrophy; hence such an improved result with 5'-modified PMO could be useful for enhancing the therapeutic efficacy of DMD drugs. Similarly, thiol-modified PMO could also be explored like other thiol-containing oligonucleotides for various other applications.
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Affiliation(s)
- Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
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Bege M, Borbás A. The Medicinal Chemistry of Artificial Nucleic Acids and Therapeutic Oligonucleotides. Pharmaceuticals (Basel) 2022; 15:ph15080909. [PMID: 35893733 PMCID: PMC9330994 DOI: 10.3390/ph15080909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Nucleic acids play a central role in human biology, making them suitable and attractive tools for therapeutic applications. While conventional drugs generally target proteins and induce transient therapeutic effects, nucleic acid medicines can achieve long-lasting or curative effects by targeting the genetic bases of diseases. However, native oligonucleotides are characterized by low in vivo stability due to nuclease sensitivity and unfavourable physicochemical properties due to their polyanionic nature, which are obstacles to their therapeutic use. A myriad of synthetic oligonucleotides have been prepared in the last few decades and it has been shown that proper chemical modifications to either the nucleobase, the ribofuranose unit or the phosphate backbone can protect the nucleic acids from degradation, enable efficient cellular uptake and target localization ensuring the efficiency of the oligonucleotide-based therapy. In this review, we present a summary of structure and properties of artificial nucleic acids containing nucleobase, sugar or backbone modifications, and provide an overview of the structure and mechanism of action of approved oligonucleotide drugs including gene silencing agents, aptamers and mRNA vaccines.
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Affiliation(s)
- Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- Institute of Healthcare Industry, University of Debrecen, Nagyerdei körút 98, 4032 Debrecen, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary;
- National Laboratory of Virology, University of Pécs, Ifjúság útja 20, 7624 Pécs, Hungary
- Correspondence:
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Kundu J, Ghosh A, Ghosh U, Das A, Nagar D, Pattanayak S, Ghose A, Sinha S. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides Using Trityl and Fmoc Chemistry in an Automated Oligo Synthesizer. J Org Chem 2022; 87:9466-9478. [PMID: 35839125 DOI: 10.1021/acs.joc.2c00265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphorodiamidate morpholino oligonucleotides (PMOs) constitute 3 out of the 11 FDA-approved oligonucleotide-based drugs in the last 6 years. PMOs can effectively silence disease-causing genes and modify splicing. However, PMO synthesis has remained challenging for a variety of reasons: inefficient deprotection and coupling methods and instability of monomers. Here, we report the development of a suitable combination of resin supports, deblocking and coupling reagents for synthesizing PMOs using either trityl or Fmoc-protected chlorophosphoramidate monomers. The synthesized PMOs using both the methods on a solid support have been validated for gene silencing in a zebrafish model. The protocol was successfully transferred into an automated DNA synthesizer to make several sequences of PMOs, demonstrating for the first time the adaptation of regular PMOs in a commercial DNA synthesizer. Moreover, PMOs with longer than 20-mer sequences, including FDA-approved Eteplirsen (30-mer), were achieved in >20% overall yield that is superior to previous reports. Hybridization study shows that PMOs exhibit a higher binding affinity toward complementary DNA relative to the DNA/DNA duplex (>6 °C). Additionally, the introduction of Fmoc chemistry into PMOs opens up the possibility for PMO synthesis in commercial peptide synthesizers for future development.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arnab Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Dhriti Nagar
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Sankha Pattanayak
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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9
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Debreczeni N, Bege M, Herczeg M, Bereczki I, Batta G, Herczegh P, Borbás A. Tightly linked morpholino-nucleoside chimeras: new, compact cationic oligonucleotide analogues. Org Biomol Chem 2021; 19:8711-8721. [PMID: 34586122 DOI: 10.1039/d1ob01174j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The polyanionic phosphodiester backbone of nucleic acids contributes to high nuclease sensitivity and low cellular uptake and is therefore a major obstacle to the biological application of native oligonucleotides. Backbone modifications, particularly charge alterations is a proven strategy to provide artificial oligonucleotides with improved properties. Here, we describe the synthesis of a new type of oligonucleotide analogues consisting of a morpholino and a ribo- or deoxyribonucleoside in which the 5'-amino group of the nucleoside unit provides the nitrogen of the morpholine ring. The synthetic protocol is compatible with trityl and dimethoxytrityl protecting groups and azido functionality, and was extended to the synthesis of higher oligomers. The chimeras are positively charged in aqueous medium, due to the N-alkylated tertiary amine structure of the morpholino unit.
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Affiliation(s)
- Nóra Debreczeni
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Doctoral School of Chemistry, University of Debrecen, Hungary
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
| | - Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Institute of Healthcare Industry, University of Debrecen, H-4032, Debrecen, Nagyerdei körút 98, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, UD, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- Research Group for Oligosaccharide Chemistry of HAS, UD, H-4032, Debrecen, Egyetem tér 1, Hungary
| | - Ilona Bereczki
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, H-4032, Debrecen, Hungary
| | - Pál Herczegh
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, H-4032, Debrecen, Egyetem tér 1, Hungary.
- National Virology Laboratory, Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary
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Novel Lipid-Oligonucleotide Conjugates Containing Long-Chain Sulfonyl Phosphoramidate Groups: Synthesis and Biological Properties. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11031174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New lipid conjugates of DNA and RNA incorporating one to four [(4-dodecylphenyl)sulfonyl]phosphoramidate or (hexadecylsulfonyl)phosphoramidate groups at internucleotidic positions near the 3′ or 5′-end were synthesized and characterized. Low cytotoxicity of the conjugates and their ability to be taken up into cells without transfection agents were demonstrated. Lipid-conjugated siRNAs targeting repulsive guidance molecules a (RGMa) have shown a comparable gene silencing activity in PK-59 cells to unmodified control siRNA when delivered into the cells via Lipofectamine mediated transfection.
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Kundu J, Banerjee P, Bose C, Das U, Ghosh U, Sinha S. Internal Oligoguanidinium Transporter: Mercury-Free Scalable Synthesis, Improvement of Cellular Localization, Endosomal Escape, Mitochondrial Localization, and Conjugation with Antisense Morpholino for NANOG Inhibition to Induce Chemosensitization of Taxol in MCF-7 Cells. Bioconjug Chem 2020; 31:2367-2382. [PMID: 32986398 DOI: 10.1021/acs.bioconjchem.0c00444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A nontoxic delivery vehicle is essential for the therapeutic applications of antisense phosphorodiamidate morpholino oligonucleotides (PMOs). Though guanidinium-rich or arginine-rich cellular transporter conjugated Vivo-PMO or PPMO has been developed for in vivo application, however, either their toxicity or stability has become an issue. Previously, we reported nonpeptidic internal guanidinium transporter (IGT) mediated delivery of PMO for gene silencing and got encouraging results. In this paper, we report the synthesis of IGT using a Hg-free method for scale up and N-terminal modification of IGT with a suitable hydrophobic or lipophilic group to improve the cell permeability, endosomal escape, and mitochondrial localization and to reduce toxicity in the MTT assay. For the delivery of PMO, IGT-PMO conjugate was synthesized to target NANOG in cells, a transcription factor required for cancer stem cell proliferation and embryonic development and is involved in many cancers. Our data shows IGT-PMO-facilitated NANOG inhibition, and thereby the prevention of EpCAM-N-Cadherin-Vimentin axis mediated epithelial to mesenchymal transition (EMT) in MCF-7 cells. Moreover, unlike taxol, NANOG inhibition influences the expression of stemness factor c-Myc, Hh-Gli signaling proteins, other cancer related factors, and their respective phenotypes in cancer cells. To the best of our knowledge, this is the first report to illustrate that the IGT-PMO-mediated NANOG inhibition increases the therapeutic potential of taxol and induces G0-G1 arrest in cancer cells to prevent cancer progression. However, it warrants further investigation in other cancer cells and preclinical platforms.
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Affiliation(s)
- Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Priyanjalee Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chandra Bose
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Ujjal Das
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
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12
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Khatra H, Khan PP, Pattanayak S, Bhadra J, Rather B, Chakrabarti S, Saha T, Sinha S. Hedgehog Antagonist Pyrimidine-Indole Hybrid Molecule Inhibits Ciliogenesis through Microtubule Destabilisation. Chembiochem 2018; 19:723-735. [PMID: 29363254 DOI: 10.1002/cbic.201700631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 12/12/2022]
Abstract
One of the crucial regulators of embryonic patterning and tissue development is the Hedgehog-glioma (Hh-Gli) signalling pathway; its uncontrolled activation has been implicated in different types of cancer in adult tissues. Primary cilium is one of the important factors required for the activation of Hh signalling, as it brings the critical components together for key protein-protein interactions required for Hh pathway regulation. Most of the synthetic and natural small molecule modulators of the pathway primarily antagonise Smoothened (Smo) or other effectors like Hh ligand or Gli. Here, we report a previously described Hh antagonist, with a pyrimidine-indole hybrid (PIH) core structure, as an inhibitor of ciliogenesis. The compound is unique in its mode of action, as it shows perturbation of microtubule dynamics in both cell-based assays and in vivo systems (zebrafish embryos). Further studies revealed that the probable targets are α-tubulin and its acetylated form, found in the cytoplasm and primary cilia. PIH also showed axonal defasiculation in developing zebrafish embryos. We thus propose that PIH antagonises Hh signalling by repressing cilia biogenesis and disassembling α-tubulin from its stabilised form.
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Affiliation(s)
- Harleen Khatra
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Pragya Paramita Khan
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Sankha Pattanayak
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Jhuma Bhadra
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
| | - Bilal Rather
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, 700 032, India
| | - Saikat Chakrabarti
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, 700 032, India
| | - Taniya Saha
- Division of Molecular Medicine, Bose Institute, Kolkata, 700 009, India
| | - Surajit Sinha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, India
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Nandi B, Khatra H, Khan PP, Bhadra J, Pattanayak S, Sinha S. Cationic Cytosine Morpholino-Based Transporters: Synthesis and Regulation of Intracellular Localization. ChemistrySelect 2017. [DOI: 10.1002/slct.201700238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bappaditya Nandi
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Harleen Khatra
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Pragya Paramita Khan
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Jhuma Bhadra
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Sankha Pattanayak
- Department of Chemical and Systems Biology; Stanford University; Stanford, California, CA 94305-5174
| | - Surajit Sinha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
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Bhadra J, Pattanayak S, Khan PP, Kundu J, Sinha S. Internal Oligoguanidinium-Based Cellular Transporter Enhances Antisense Efficacy of Morpholinos in In Vitro and Zebrafish Model. Bioconjug Chem 2016; 27:2254-2259. [PMID: 27625020 DOI: 10.1021/acs.bioconjchem.6b00252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient cellular transporter is highly desirable for the therapeutic applications of antisense phosphorodiamidate morpholino oligonucleotides (PMOs) as Vivo-PMO and PPMO have limitations for in vivo study. We report here a novel internally tetraguanidinium-linked nonpeptidic cellular transporter having a conformationally rigid backbone composed of pharmacologically compatible heterocyclic six-membered rings which internalizes efficiently into cells in full growth medium and ubiquitously distributed into zebrafish embryos. It efficiently transports antisense PMO in vitro and in vivo zebrafish embryos. Comparative study with Gene Tools Vivo-PMO revealed that our cellular-transporter conjugated PMO shows better antisense efficacy.
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Affiliation(s)
- Jhuma Bhadra
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Sankha Pattanayak
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Pragya Paramita Khan
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Jayanta Kundu
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Surajit Sinha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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Bhadra J, Pattanayak S, Sinha S. Synthesis of Morpholino Monomers, Chlorophosphoramidate Monomers, and Solid-Phase Synthesis of Short Morpholino Oligomers. ACTA ACUST UNITED AC 2015; 62:4.65.1-4.65.26. [PMID: 26380905 DOI: 10.1002/0471142700.nc0465s62] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phosphorodiamidate morpholino oligomers (PMOs) are a highly capable class of synthetic antisense oligonucleotides that are used to study gene functions in in vitro and in vivo models. This unit describes the synthesis of exocyclic-amine-protected 7'-hydroxy and 7'-chlorophosphoramidate-activated morpholino monomers of A, T, G, and C, together with their incorporation into short PMO oligomers by solid-phase synthesis. Starting from ribonucleosides, the exocyclic-amine-protected 7'-hydroxy monomers are prepared following a modified Summerton protocol, which consists of a periodate cleavage/Schiff base formation/reduction cycle. The exocyclic amine protections are installed at a later stage (except G) to avoid the use of costly exocyclic-amine-protected counterparts that give control over protecting group manipulation. The 7'-hydroxy monomers with N-Trit/N-MMTr are then converted to the 7'-chlorophosphoramidate morpholino monomers in one step employing a combination of lithium bromide and DBU. These chlorophosphoramidate monomers are finally assembled by solid-support synthesis to obtain the short PMO oligomers.
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Affiliation(s)
- Jhuma Bhadra
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India.,These authors contributed equally
| | - Sankha Pattanayak
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India.,These authors contributed equally
| | - Surajit Sinha
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
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Abramova TV, Belov SS, Tarasenko YV, Silnikov VN. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics. Beilstein J Org Chem 2014; 10:1151-8. [PMID: 24991266 PMCID: PMC4077379 DOI: 10.3762/bjoc.10.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 12/14/2022] Open
Abstract
An efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.
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Affiliation(s)
- Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Sergey S Belov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia ; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Yulia V Tarasenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
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Paul S, Pattanayak S, Sinha S. Synthesis and cell transfection properties of cationic uracil-morpholino tetramer. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2013.12.087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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