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Ramesh NG. From Glycals to Nitrogen Heterocycles and Carbocycles via "Cleavage-Intramolecular Recombination Strategy". CHEM REC 2021; 21:2930-2957. [PMID: 34472196 DOI: 10.1002/tcr.202100187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022]
Abstract
Glycals (carbohydrate enol-ethers) have enjoyed profound applications in organic synthesis for more than a century. They not only serve as versatile glycosyl donors or as substrates for Ferrier rearrangement, but also find extensive synthetic applications especially as a "chiral pool" for accomplishing the synthesis of a variety of natural and biologically important compounds. As cyclic enol ethers, they demonstrate high reactivity and are among the most and variously transformable monosaccharide derivatives. The uniqueness of the reactivity of glycals is that they can be synthetically tuned to get a library of derivatives through stereo- and regioselective introduction of a variety of functional groups at C1, C2, C3 as well as C4 carbons of the sugar. We have developed a practical approach for stereoselective mono- and diamination of glycals and over the years utilized these scaffolds for the synthesis of a variety of biologically important nitrogen heterocycles and carbocycles through a "Diversity Oriented Approach". Our synthetic strategy in this direction mainly relied on the cleavage of ring O-C bond of the sugar followed by an "intramolecular recombination" reaction. Utilizing this strategy, we have accomplished the synthesis of several biologically important natural products, their analogues and related unnatural derivatives. Examples of such compounds reported from our group include polyhydroxypyrrolidines, DMDP, anisomycin, steviamine, pochonicine, conduramines, bulgecinine, aminocyclitols, azepanes, 4-hydroxy-D-proline, azanucleosides and their analogues. A personal account highlighting these syntheses is presented here.
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Affiliation(s)
- Namakkal G Ramesh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Verma V, Maity J, Maikhuri VK, Sharma R, Ganguly HK, Prasad AK. Double-headed nucleosides: Synthesis and applications. Beilstein J Org Chem 2021; 17:1392-1439. [PMID: 34194579 PMCID: PMC8204177 DOI: 10.3762/bjoc.17.98] [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: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.
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Affiliation(s)
- Vineet Verma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen’s College, University of Delhi, Delhi-110 007, India
| | - Vipin K Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Ritika Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata-700 054, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
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Mishra UK, Sanghvi YS, Egli M, Ramesh NG. Supramolecular Architecture through Self-Organization of Janus-Faced Homoazanucleosides. J Org Chem 2021; 86:367-378. [PMID: 33284627 DOI: 10.1021/acs.joc.0c02140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Design of Janus-faced or double-headed homoazanucleosides with the possibility to undergo self-organization through base pairing has been conceptualized and accomplished. The synthetic strategy demonstrates the unique ability to introduce two similar or complementary nucleobases on opposite arms of a chiral polyhydroxypyrrolidine while also ensuring that their faces are anti to each other to allow only intermolecular interactions between the nucleobases, an essential requisite for self-assembly. Single-crystal X-ray structures were determined for all three types of homoazanucleosides, one possessing two adenine molecules, the other with two thymine moieties, and the third containing both adenine and thymine. The crystal structures of all three display noncovalent interactions, including Watson-Crick base pairing, Hoogsteen H-bonding, and π-π stacking, resulting in unusual supramolecular patterns. The most striking supramolecular motif among them, which emerged from the crystal structure of the homoazanucleoside containing both adenine and thymine, is a left-handed helix formed through Watson-Crick pairing between nucleobases. The present study thus forms a prelude to the design of Janus-faced building blocks to establish helical pillars as well as lateral branches that together define a three-dimensional (3D) lattice. The ready accessibility of these molecules is expected to spur the next generation of discoveries in the design of functional nanomaterials.
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Affiliation(s)
- Umesh K Mishra
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Namakkal G Ramesh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Verma V, Maikhuri VK, Khatri V, Singh A, Prasad AK. Synthesis of hexopyranosyl pyrimidine homonucleosides. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1836224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Vineet Verma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Vipin K. Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Vinod Khatri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Pt. Neki Ram Sharma Govt. College, Rohtak, India
| | - Ankita Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Ashok K. Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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The chemistry of the carbon-transition metal double and triple bond: Annual survey covering the year 2014. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kumar R, Kumar M, Maity J, Prasad AK. Chemo-enzymatic synthesis of 3′-O,4′-C-methylene-linked α-l-arabinonucleosides. RSC Adv 2016. [DOI: 10.1039/c6ra17218k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biocatalytic methodology has been developed for the efficient and environment friendly synthesis of 3′-O,4′-C-methylene-linked α-l-arabinonucleosides.
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Affiliation(s)
- Rajesh Kumar
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Manish Kumar
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Jyotirmoy Maity
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
| | - Ashok K. Prasad
- Bioorganic Laboratory
- Department of Chemistry
- University of Delhi
- Delhi-110007
- India
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Kaura M, Hrdlicka PJ. Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers. Org Biomol Chem 2015; 13:7236-47. [PMID: 26055658 DOI: 10.1039/c5ob00860c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
LNA and nucleobase-modified DNA monomers are two types of building blocks that are used extensively in oligonucleotide chemistry. However, there are only very few reports in which these two monomer families are used alongside each other. In the present study we set out to characterize the biophysical properties of oligodeoxyribonucleotides in which C5-modified 2'-deoxyuridine or C8-modified 2'-deoxyadenosine monomers are flanked by LNA nucleotides. We hypothesized that the LNA monomers would alter the sugar rings of the modified DNA monomers toward more RNA-like North-type conformations for maximal DNA/RNA affinity and specificity. Indeed, the incorporation of LNA monomers almost invariably results in increased target affinity and specificity relative to the corresponding LNA-free ONs, but the magnitude of the stabilization varies greatly. Introduction of LNA nucleotides as direct neighbors into C5-pyrene-functionalized pyrimidine DNA monomers yields oligonucleotide probes with more desirable photophysical properties as compared to the corresponding LNA-free probes, including more intense fluorescence emission upon target binding and improved discrimination of single nucleotide polymorphisms (SNPs). These hybrid oligonucleotides are therefore promising probes for diagnostic applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
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Dalager M, Andersen NK, Kumar P, Nielsen P, Sharma PK. Double-headed nucleotides introducing thymine nucleobases in the major groove of nucleic acid duplexes. Org Biomol Chem 2015; 13:7040-9. [PMID: 26053231 DOI: 10.1039/c5ob00872g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Four different double-headed nucleosides each combining two thymine nucleobases with different linkers were synthesised. The 5-position of 2'-deoxyuridine was connected to the N1-position of a thymine through either m- or p-disubstituted phenyl or phenylacetylene linkers by the use of Suzuki or Sonogashira couplings. When introduced into oligonucleotides, the thermal stability of dsDNA and DNA : RNA duplexes were determined and structural information was obtained from CD- and fluorescence spectroscopy. Also the recognition of abasic sites was studied. In general, the more stable duplexes were obtained with m- rather than p-substitution and with phenylacetylene rather than phenyl linkers.
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Affiliation(s)
- Michael Dalager
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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Kumar P, Sharma PK, Nielsen P. Double-headed nucleotides with arabino configuration: synthesis and hybridization properties. J Org Chem 2014; 79:11534-40. [PMID: 25375974 DOI: 10.1021/jo502189h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The formation of new nucleic acid motifs by using double-headed nucleotides is reported. Modified phosphoramidites carrying additional thymine or adenine attached to the 2'-position of arabinouridine through a methylene linker are conveniently prepared and incorporated into oligonucleotides to obtain the modified nucleotide monomers (a)U(T) and (a)U(A), respectively. The extension of a DNA double helix by one or two additional A:T base pairs is achieved by placing these modified monomers in the opposite strands in a so-called (+1)-zipper arrangement. Hence, 12 basepairs can be presented in an 11-mer or even a 10-mer duplex. The modified nucleotide monomers also behave as dinucleotides when base-paired with two complementary nucleotides from the opposite strand. A new nucleic acid motif is introduced when two (a)U(A) monomers recognize each other in the center of a duplex.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense M, Denmark
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