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Spriha SE, Rahman FI, Rahman SMA. Synthesis, in vivo and in silico analgesic and anti-inflammatory studies of α-D-ribofuranose derivatives. Saudi Pharm J 2021; 29:981-991. [PMID: 34588844 PMCID: PMC8463446 DOI: 10.1016/j.jsps.2021.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/16/2021] [Indexed: 11/29/2022] Open
Abstract
Five α-D-ribofuranose analogues (2, 3, 4, 5 and 6) were synthesized in good yields from 3-O-benzyl-4-C-(hydroxymethyl)-1, 2-O-isopropylidene-α-D-ribofuranose (1). The synthesized compounds were then subjected to analgesic, anti-inflammatory, antimicrobial and antioxidant assays. Compound 3 demonstrated 79.74% (P < 0.001) writhing inhibition and highest reaction time of 2.55 ± 0.13 min (P < 0.001) after 30 min of oral administration in peripheral and central analgesic assay, respectively, at 50 mg/kg dose. Compound 2 and 6 exhibited significant anti-inflammatory activity at 100 mg/kg dose with paw edema inhibition of 91.15% (P < 0.001) and 95.13% (P < 0.001), respectively, in 4th hour. The synthesized analogues did not show notable antioxidant and antibacterial properties. Molecular docking study revealed higher binding affinity of −8.1 kcal/mol and −8.9 kcal/mol of compound 3 towards cyclooxygenase-1 and phospholipase A2, respectively, compared to −7.7 and −7.6 kcal/mol respectively for corresponding native ligands. Compound 2 demonstrated binding affinity of −9.1 kcal/mol towards interleukin-1 receptor-associated kinase-4 compared to −8.7 kcal/mol of the native ligand. The molecular properties related to drug likeness of compounds were found to be within acceptable range. Synthesized D-ribofuranose analogues demonstrated promising analgesic and anti-inflammatory activities and further development may lead to new potent analgesic and anti-inflammatory agents.
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Affiliation(s)
- Sabiha Enam Spriha
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad Imtiaz Rahman
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - S M Abdur Rahman
- Department of Clinical Pharmacy & Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
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2
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Ejlersen M, Christensen NJ, Sørensen KK, Jensen KJ, Wengel J, Lou C. Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA. Bioconjug Chem 2018; 29:1025-1029. [PMID: 29505242 DOI: 10.1021/acs.bioconjchem.8b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.
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Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
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3
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Hari Y, Obika S. Synthesis and Properties of 2’,4’-Bridged Nucleic Acids Containing Multiple Heteroatoms in the Bridges. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
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4
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Shirato W, Chiba J, Inouye M. A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate. Chem Commun (Camb) 2015; 51:7043-6. [PMID: 25806487 DOI: 10.1039/c4cc09486g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe artificial DNA molecules exclusively consisting of four types of alkynyl C-nucleotides with nonnatural bases. The artificial DNA exhibited almost the same characteristics as natural DNA, such as in regard to the stepwise duplex and triplex formation and the right-handed higher-order structure with an antiparallel alignment fashion.
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Affiliation(s)
- Wataru Shirato
- Graduate School of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan.
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5
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Mori K, Kodama T, Obika S. Synthesis and hybridization property of a boat-shaped pyranosyl nucleic acid containing an exocyclic methylene group in the sugar moiety. Bioorg Med Chem 2014; 23:33-7. [PMID: 25496806 DOI: 10.1016/j.bmc.2014.11.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 12/29/2022]
Abstract
A boat-shaped pyranosyl nucleic acid (BsNA) having an exocyclic methylene group in the sugar moiety was synthesized to investigate the possibility that the axial H3' of original BsNA is the cause of its duplex destabilization. The synthesized BsNA analog was chemically stable against various nucleophiles. From the thermal stability of duplex oligonucleotides including the BsNA analog, it was found that the duplex-forming ability can be sensitive to the size of functional groups at the 3'-position.
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Affiliation(s)
- Kazuto Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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6
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Shrestha AR, Hari Y, Yahara A, Osawa T, Obika S. Synthesis and properties of a bridged nucleic acid with a perhydro-1,2-oxazin-3-one ring. J Org Chem 2011; 76:9891-9. [PMID: 22059648 DOI: 10.1021/jo201597e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A novel derivative of 2',4'-bridged nucleic acid, named hydroxamate-bridged nucleic acid (HxNA), containing a six-membered perhydro-1,2-oxazin-3-one ring, was designed and synthesized. The introduction of a carbonyl function along with an N-O linkage in the six-membered bridged structure is the unique structural feature of the novel 2',4'-bridged nucleic acid analogue. The design was carried out to restrict the flexibility of the sugar moiety through the trigonal planarity of carbonyl function, which would improve the properties of the modification. The synthesized monomer was incorporated into oligonucleotides, and their properties were examined. The HxNA-modified oligonucleotides exhibited selectively high affinity toward complementary ssRNA. Furthermore, the nuclease resistance of the HxNA-modified oligonucleotide was found to be higher than that of the corresponding natural and 2',4'-BNA/LNA-modified oligonucleotides. Interestingly, exposure of HxNA modified oligonucleotide to 3'-exonuclease resulted in gradual opening of the bridge, which stopped further digestion. Moreover, ring-opening of only one modification at the 3'-end of the oligonucleotides was observed, even if two or three HxNA modifications were present in the sequence. The results demonstrate the strong potential of the HxNA modification as a switch for the generation of highly nuclease-resistant RNA selective oligonucleotide in situ, which could have potential applications in antisense technology.
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Affiliation(s)
- Ajaya R Shrestha
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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7
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Nicolaou KC, Ellery SP, Rivas F, Saye K, Rogers E, Workinger TJ, Schallenberger M, Tawatao R, Montero A, Hessell A, Romesberg F, Carson D, Burton D. Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues. Bioorg Med Chem 2011; 19:5648-69. [PMID: 21840722 PMCID: PMC3348725 DOI: 10.1016/j.bmc.2011.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 μM) and HxB2 (IC(50)=2.4 μM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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8
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Mori K, Kodama T, Baba T, Obika S. Bridged nucleic acid conjugates at 6'-thiol: synthesis, hybridization properties and nuclease resistances. Org Biomol Chem 2011; 9:5272-9. [PMID: 21643564 DOI: 10.1039/c1ob05469d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The bridged nucleic acid (BNA) containing a thiol at the 6'-position in the bridged structure was synthesized from the disulfide-type BNA and conjugated with various functional molecules via the thioether or the disulfide linkage post-synthetically and efficiently in solution phase. The disulfide-linked conjugate was cleaved under reductive conditions derived from glutathione and an oligonucleotide bearing a free thiol was released smoothly. Conjugated functional molecules had great effects on duplex stability with the DNA complement. In contrast, the molecules little influenced the stability with the RNA complement. Moreover, the oligonucleotides with functional groups at the 6'-position had as high or higher resistances against 3'-exonuclease than phosphorothioate oligonucleotide (S-oligo).
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Affiliation(s)
- Kazuto Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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9
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Kodama T. [Design, syntheses and properties of nucleic Acid switch in response to external stimuli]. YAKUGAKU ZASSHI 2011; 131:101-11. [PMID: 21212620 DOI: 10.1248/yakushi.131.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The control of molecular properties using external stimuli is an attractive research area that offers the potential for regulation of various biological phenomena. This review summarizes the concept, design, syntheses and properties of nucleic acid switches in response to external stimuli, namely, "external-stimuli-responsive bridged nucleic acids monomer". From (1)H-NMR experiments, every external-stimuli-responsive bridged nucleic acid monomer was found to have an N-conformation, while an S-conformation was predominantly observed after exposure to a proper stimulus. Each bridged nucleic acid monomer was effectively introduced into oligodeoxynucleotides using an automated DNA synthesizer. Moreover, oligonucleotides modified with these bridged nucleic acid monomer were changed in their hybridization property and tolerance to enzymatic digestion in response to each stimulus. These results clearly showed that external-stimuli-responsive bridged nucleic acids monomers should work as a nucleic acid switch, and have the potential for regulation of various biological phenomena.
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Affiliation(s)
- Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
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10
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Nishida M, Baba T, Kodama T, Yahara A, Imanishi T, Obika S. Synthesis, RNA selective hybridization and high nuclease resistance of an oligonucleotide containing novel bridged nucleic acid with cyclic urea structure. Chem Commun (Camb) 2010; 46:5283-5. [PMID: 20567794 DOI: 10.1039/c0cc00154f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A novel bridged nucleic acid bearing cyclic urea structure was successfully synthesized and introduced into oligonucleotide, displaying attractive characteristics of highly RNA selective hybridization ability and excellent resistance towards nuclease degradation.
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Affiliation(s)
- Masaru Nishida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
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11
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Obika S, Imanishi T, Kawada Y, Baba T, Fujisaka A. Bridged Nucleic Acids: Development, Synthesis and Properties. HETEROCYCLES 2010. [DOI: 10.3987/rev-10-667] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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