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Fàbrega C, Clua A, Eritja R, Aviñó A. Oligonucleotides Carrying Nucleoside Antimetabolites as Potential Prodrugs. Curr Med Chem 2023; 30:1304-1319. [PMID: 34844535 DOI: 10.2174/0929867328666211129124039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleoside and nucleobase antimetabolites are an important class of chemotherapeutic agents for the treatment of cancer as well as other diseases. INTRODUCTION In order to avoid undesirable side effects, several prodrug strategies have been developed. In the present review, we describe a relatively unknown strategy that consists of using oligonucleotides modified with nucleoside antimetabolites as prodrugs. METHODS The active nucleotides are generated by enzymatic degradation once incorporated into cells. This strategy has attracted large interest and is widely utilized at present due to the continuous developments made in therapeutic oligonucleotides and the recent advances in nanomaterials and nanomedicine. RESULTS A large research effort was made mainly in the improvement of the antiproliferative properties of nucleoside homopolymers, but recently, chemically modified aptamers, antisense oligonucleotides and/or siRNA carrying antiproliferative nucleotides have demonstrated a great potential due to the synergetic effect of both therapeutic entities. In addition, DNA nanostructures with interesting properties have been built to combine antimetabolites and enhancers of cellular uptake in the same scaffold. Finally, protein nanoparticles functionalized with receptor-binders and antiproliferative oligomers represent a new avenue for a more effective treatment in cancer therapy. CONCLUSION It is expected that oligonucleotides carrying nucleoside antimetabolites will be considered as potential drugs in the near future for biomedical applications.
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Affiliation(s)
- Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Clua
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
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2
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Écija P, Uriarte I, Spada L, Davis BG, Caminati W, Basterretxea FJ, Lesarri A, Cocinero EJ. Furanosic forms of sugars: conformational equilibrium of methyl β-d-ribofuranoside. Chem Commun (Camb) 2016; 52:6241-4. [DOI: 10.1039/c6cc01180b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rotational spectrum of the isolated ribofuranoside unit, the biologically active sugar form, revealed two structures with a similar puckering to the RNA units in crystals.
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Affiliation(s)
- Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Iciar Uriarte
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Lorenzo Spada
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | | | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 1-40126 Bologna
- Italy
| | - Francisco J. Basterretxea
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
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3
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Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and duplex-stabilizing properties of fluorinated N-methanocarbathymidine analogues locked in the C3'-endo conformation. Angew Chem Int Ed Engl 2014; 53:9893-7. [PMID: 25044699 DOI: 10.1002/anie.201405283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 11/11/2022]
Abstract
The efficient synthesis, antiviral activity, and duplex-stabilizing properties of both isomers of the 2'-fluoro analogue of Northern methanocarbathymidine (N-MCT), 2 and 3, are reported. We show that 2'-F incorporation on the N-MCT scaffold has a strong stabilizing effect on duplex thermal stability.
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Affiliation(s)
- Michael E Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA).
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4
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Jung ME, Dwight TA, Vigant F, Østergaard ME, Swayze EE, Seth PP. Synthesis and Duplex-Stabilizing Properties of FluorinatedN-Methanocarbathymidine Analogues Locked in the C3′-endoConformation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Nasr T, Taniguchi Y, Takaki T, Okamura H, Sasaki S. Properties of oligonucleotide with phenyl-substituted carbocyclic nucleoside analogs for the formation of duplex and triplex DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 31:841-60. [PMID: 23215548 DOI: 10.1080/15257770.2012.737970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
(1S,3S,4R)-1-Phenyl-1-thymidyl-3-hydroxy-4-hydroxymethylcyclopentane (10) and their analogs were synthesized, incorporated into the oligodeoxynucleotides, and their properties were evaluated for the formation of duplex and triplex DNA. The known chiral cyclopentanone derivative was converted into the corresponding ketimine sulfonamide derivative, which was subjected to a stereoselective PhLi addition. The formed sulfonamide was hydrolyzed to afford the primary amino group, on which the thymine moiety was built. The benzyl protecting groups were removed to form the nucleoside analog having a phenyl group and the thymine unit at the 1' position of a carbocyclic skeleton (10). In the estimation of the oligodeoxynucleotides incorporating 10 for duplex and triplex formation, the carbocyclic nucleoside analog 10 did not show the stabilizing effect for duplex formation; on the other hand, it stabilized the triplex. Therefore, the skeleton of the phenyl-substituted carbocyclic nucleoside analog 10 may be a platform for the formation of stable triplex DNA.
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Affiliation(s)
- Tamer Nasr
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan
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6
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Hon YS, Luo CZ, Hong BC, Liao JH. Development of the Ireland-Claisen Rearrangement of Allyl-2-alkoxyacetate Bearing an Allylic Amine and the Transformation to 3-Hydroxy-4-hydroxymethylpyrrolidine. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Obika S, Kodama T, Sugaya K, Baba T, Imanishi T. Synthesis of a Novel trans-3’,4’-BNA Monomer Bearing a 4,8-Dioxa-5-azabicyclo[5.3.0]decane Skeleton. HETEROCYCLES 2009. [DOI: 10.3987/com-08-s(d)58] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Huang H, Greenberg MM. Synthesis and analysis of oligonucleotides containing abasic site analogues. J Org Chem 2008; 73:2695-703. [PMID: 18324835 DOI: 10.1021/jo702614p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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9
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Maderia M, Shenoy S, Van QN, Marquez VE, Barchi JJ. Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates. Nucleic Acids Res 2007; 35:1978-91. [PMID: 17341464 PMCID: PMC1895885 DOI: 10.1093/nar/gkm025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Shilpa Shenoy
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Que N. Van
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
- *To whom correspondence should be addressed. +1 301 846 5905+1 301 846 6033
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10
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New Synthetic Approach to the Bicyclo[3.1.0]hexane Ring System from (+)-(1R,4R)-4-(Benzyloxymethyl)-4-(hydroxymethyl)cyclopent-2-enol. B KOREAN CHEM SOC 2005; 26:1503-1504. [DOI: 10.5012/bkcs.2005.26.10.1503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X. Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res 2004; 32:3877-86. [PMID: 15273274 PMCID: PMC506793 DOI: 10.1093/nar/gkh701] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some DNA/RNA-binding proteins. Here, we report the structure of HhaI methyltransferase in complex with DNA containing a south-constrained abasic carbocyclic sugar at the target site in the presence of the methyl donor byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be trapped in the middle of the flipping pathway via the DNA major groove, held in place primarily through Van der Waals contacts with a set of invariant amino acids. Molecular dynamics simulations indicate that the structural stabilization observed with the south-constrained pseudosugar will not occur with a north-constrained pseudosugar, which explains its lowered binding affinity. Moreover, comparison of structural transitions of the sugar and phosphodiester backbone observed during computational studies of base flipping in the M.HhaI-DNA-AdoHcy ternary complex indicate that the south-constrained pseudosugar induces a conformation on the phosphodiester backbone that corresponds to that of a discrete intermediate of the base-flipping pathway. As previous crystal structures of M.HhaI ternary complex with DNA displayed the flipped sugar moiety in the antipodal north conformation, we suggest that conversion of the sugar pucker from south to north beyond the middle of the pathway is an essential part of the mechanism through which flipping must proceed to reach its final destination. We also discuss the possibility of the south-constrained pseudosugar mimicking a transition state in the phosphodiester and sugar moieties that occurs during DNA base flipping in the presence of M.HhaI.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
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12
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Maier MA, Choi Y, Gaus H, Barchi JJ, Marquez VE, Manoharan M. Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs. Nucleic Acids Res 2004; 32:3642-50. [PMID: 15247346 PMCID: PMC484163 DOI: 10.1093/nar/gkh667] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oligodeoxyribonucleotides containing pseudorotationally locked sites derived from bicyclo[3.1.0]hexane pseudosugars have been synthesized using adenosine, thymidine and abasic versions of North- and South-methanocarba nucleosides. The reaction conditions for coupling and oxidation steps of oligonucleotide synthesis have been investigated and optimized to allow efficient and facile solid-phase synthesis using phosphoramidite chemistry. Our studies demonstrate that the use of iodine for P(III) to P(V) oxidation leads to strand cleavage at the sites where the pseudosugar is North. In contrast, the same cleavage reaction was not observed in the case of South pseudosugars. Iodine oxidation generates a 5'-phosphate oligonucleotide fragment on the resin and releases the North pseudosugar into the solution. This side reaction, which is responsible for the extremely low yields observed for the incorporation of the North pseudosugar analogs, has been studied in detail and can be easily overcome by replacing iodine with t-butylhydroperoxide as oxidant.
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Affiliation(s)
- Martin A Maier
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA
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13
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Obika S, Osaki T, Sekiguchi M, Somjing R, Harada Y, Imanishi T. Synthesis and conformation of a novel bridged nucleic acid having a trans -fused 3,5,8-trioxabicyclo[5.3.0]decane structure. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.04.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Houseknecht JB, Lowary TL, Hadad CM. Gas- and Solution-Phase Energetics of the Methyl α- and β-d-Aldopentofuranosides. J Phys Chem A 2003. [DOI: 10.1021/jp027716w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Todd L. Lowary
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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15
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Comin MJ, Rodriguez JB, Russ P, Marquez VE. Synthesis of conformationally locked carbocyclic nucleosides built on an oxabicyclo[3.1.0]hexane system. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(02)01528-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Yoshimura Y, Moon HR, Choi Y, Marquez VE. Enantioselective synthesis of bicyclo[3.1.0]hexane carbocyclic nucleosides via a lipase-catalyzed asymmetric acetylation. Characterization of an unusual acetal byproduct. J Org Chem 2002; 67:5938-45. [PMID: 12182625 DOI: 10.1021/jo020249u] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bicyclo[3.1.0]hexane scaffold can lock the conformation of a carbocyclic nucleoside into one of the two antipodal (north or south) conformations typical of conventional nucleosides that normally exist in a rapid, two-state equilibrium in solution. In a recent brief communication, we reported a practical method to access the requisite bicyclo[3.1.0]hexane pseudosugar for the north antipode via an intramolecular olefin-ketocarbene cycloaddition. The most attractive features of this synthesis was that a relatively complex synthon was obtained from simple and inexpensive starting materials and that the resulting racemic mixtures of purine nucleosides could be successfully resolved by adenosine deaminase (ADA) hydrolysis. In this work, we describe the development of a more general, lipase-catalyzed double-acetylation reaction, which could successfully resolve an earlier precursor, 4-(tert-butyldiphenylsilamethoxy)-1-(hydroxymethyl)bicyclo[3.1.0]hexan-2-ol [(+/-)-7], into enantiomerically pure (+)-diacetate 8 and (-)-monoacetate 9. The former diacetate was converted to the conformationally locked (north)-carbocyclic guanosine (+)-17 identical to the one obtained previously by ADA resolution. The present method represents a more general and efficient process applicable to the synthesis of all classes of (north) bicyclo[3.1.0]hexane nucleosides, including pyrimidine analogues. During the lipase-catalyzed resolution, we were able to demonstrate the presence of an unusual acetal-forming reaction that consumed small amounts of the unreactive monoacetate (-)-9. This side reaction was also enzyme-catalyzed and was triggered by the byproduct acetaldehyde generated during the reaction.
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Affiliation(s)
- Yuichi Yoshimura
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, 376 Boyles St., Frederick, Maryland 21702, USA
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17
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Banavali NK, MacKerell AD. Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol 2002; 319:141-60. [PMID: 12051942 DOI: 10.1016/s0022-2836(02)00194-8] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Structural distortions of DNA are essential for its biological function due to the genetic information of DNA not being physically accessible in the duplex state. Base flipping is one of the simplest structural distortions of DNA and may represent an initial event in strand separation required to access the genetic code. Flipping is also utilized by DNA-modifying and repair enzymes to access specific bases. It is typically thought that base flipping (or base-pair opening) occurs via the major groove whereas minor groove flipping is only possible when mediated by DNA-binding proteins. Here, umbrella sampling with a novel center-of-mass pseudodihedral reaction coordinate was used to calculate the individual potentials of mean force (PMF) for flipping of the Watson-Crick (WC) paired C and G bases in the CCATGCGCTGAC DNA dodecamer. The novel reaction coordinate allowed explicit investigation of the complete flipping process via both the minor and major groove pathways. The minor and major groove barriers to flipping are similar for C base flipping while the major groove barrier is slightly lower for G base flipping. Minor groove flipping requires distortion of the WC partner while the flipping base pulls away from its partner during major groove flipping. The flipped states are represented by relatively flat free energy surfaces, with a small, local minimum observed for the flipped G base. Conserved patterns of phosphodiester backbone dihedral distortions during flipping indicate their essential role in the flipping process. During flipping, the target base tracks along the respective grooves, leading to hydrogen-bonding interactions with neighboring base-pairs. Such hydrogen-bonding interactions with the neighboring sequence suggest a novel mechanism of sequence dependence in DNA dynamics.
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Affiliation(s)
- Nilesh K Banavali
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 North Pine Street, Baltimore, MD 21201, USA
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18
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Choi Y, George C, Strazewski P, Marquez VE. Synthesis of a conformationally locked version of puromycin amino nucleoside. Org Lett 2002; 4:589-92. [PMID: 11843598 DOI: 10.1021/ol010288c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A conformationally locked carbocyclic version of puromycin amino nucleoside was synthesized via Mitsunobu coupling of a 3-azido-substituted carbocyclic moiety with 6-chloropurine without interference from the azido group reacting with triphenylphosphine. The requisite 3-azido-substituted carbocyclic pseudosugar was prepared by a double inversion of configuration at C3' (nucleoside numbering) involving a nucleophilic displacement with azide.
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Affiliation(s)
- Yongseok Choi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, NCI, Frederick, Maryland 21702, USA
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