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Lakshman MK. Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond. CHEM REC 2023; 23:e202200182. [PMID: 36166699 DOI: 10.1002/tcr.202200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Indexed: 01/24/2023]
Abstract
Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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2
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Thomson PF, Lagisetty P, Balzarini J, De Clercq E, Lakshman MK. Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides. Adv Synth Catal 2010; 352:1728-1735. [PMID: 21818182 PMCID: PMC3148652 DOI: 10.1002/adsc.200900728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Palladium‐catalyzed C—N bond forming reactions of 6‐bromo‐ as well as 6‐chloropurine ribonucleosides and the 2′‐deoxy analogues with arylamines are described. Efficient conversions were observed with palladium(II) acetate/Xantphos/cesium carbonate, in toluene at 100 °C. Reactions of the bromonucleoside derivatives could be conducted at a lowered catalytic loading [5 mol% Pd(OAc)2/7.5 mol% Xantphos], whereas good product yields were obtained with a higher catalyst load [10 mol% Pd(OAc)2/15 mol% Xantphos] when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxy groups appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of arylamines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6‐chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates.
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Affiliation(s)
- Paul F Thomson
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, U.S.A
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Pratap R, Parrish D, Gunda P, Venkataraman D, Lakshman MK. Influence of Biaryl Phosphine Structure on C−N and C−C Bond Formation. J Am Chem Soc 2009; 131:12240-9. [DOI: 10.1021/ja902679b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramendra Pratap
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Damon Parrish
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Padmaja Gunda
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - D. Venkataraman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
| | - Mahesh K. Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, Naval Research Laboratory, Code 6030, 4555 Overlook Avenue, Washington, D.C. 20375, and Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003
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Jozak T, Fischer M, Thiel J, Sun Y, Kelm H, Thiel WR. A Series of NovelN,N-Donor Ligands with Binaphthyl Backbones. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801224] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ran C, Dai Q, Ruan Q, Penning TM, Blair IA, Harvey RG. Strategies for Synthesis of Adducts of o-Quinone Metabolites of Carcinogenic Polycyclic Aromatic Hydrocarbons with 2‘-Deoxyribonucleosides. J Org Chem 2008; 73:992-1003. [DOI: 10.1021/jo701667u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chongzhao Ran
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Qing Dai
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Qian Ruan
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Trevor M. Penning
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Ian A. Blair
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Ronald G. Harvey
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, and The Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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Liu Y, Bai Y, Zhang J, Li Y, Jiao J, Qi X. Optimization of the Conditions for Copper-MediatedN-Arylation of Heteroarylamines. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700577] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Champeil E, Pradhan P, Lakshman MK. Palladium-catalyzed synthesis of nucleoside adducts from bay- and fjord-region diol epoxides. J Org Chem 2007; 72:5035-45. [PMID: 17559269 PMCID: PMC2548296 DOI: 10.1021/jo070204z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Palladium-catalyzed C-N bond formation has been utilized to synthesize covalent 2'-deoxyadenosine (dA) and 2'-deoxyguanosine (dG) adducts of benzo[a]pyrene (BaP) series 1 (syn) and benzo[c]phenanthrene (BcPh) series 2 (anti) diol epoxides. For this, (+/-)-10 alpha-amino-7 beta,8 alpha,9 beta-trisbenzoyloxy-7,8,9,10-tetrahydro BaP and (+/-)-1 beta-amino-2 alpha,3 alpha,4 beta-trisbenzoyloxy-1,2,3,4-tetrahydro BcPh were coupled with 6-halo-9-[3,5-bis-O-(tert-butyldimethylsilyl)-beta-D-erythro-pentofuranosyl]purine and O6-benzyl-3',5'-bis-O-(tert-butyldimethylsilyl)-2-bromo-2'-deoxyinosine, using a (+/-)-BINAP-Pd complex and Cs2CO3. For the synthesis of the dA adducts, both the 6-chloro- as well as the 6-bromopurine nucleoside derivatives were analyzed for the C-N coupling reaction with the hydrocarbon amino tribenzoates. With the BaP amino tribenzoate, the 6-chloronucleoside provided satisfactory results, whereas the 6-bromo analogue proved to be superior with the BcPh amino tribenzoate. Overall, lower yields of the dA adducts were obtained with the more hindered fjord-region BcPh amino tribenzoate as compared to the bay-region BaP amino tribenzoate. In contrast to reactions leading to the dA adducts, the C-N reactions of both BaP and BcPh amino tribenzoates with the 2-bromo-2'-deoxyinosine derivative proceeded in comparable yields. This seems to indicate that such Pd-catalyzed adduct forming reactions at the C-6 position may be influenced by steric constraints of the amine component, whereas those at the C-2 position are less sensitive. Diastereomeric adduct pairs were separated and characterized by spectral methods and by comparisons to adducts produced by direct displacement reactions as well as those formed from DNA alkylation by diol epoxides.
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Affiliation(s)
| | | | - Mahesh K. Lakshman
- *Address correspondence to M.K.L. Tel: (212) 650-7835, fax: (212) 650-6107
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Takamura-Enya T, Enomoto S, Wakabayashi K. Palladium-catalyzed direct N-arylation of nucleosides, nucleotides, and oligonucleotides for efficient preparation of dG-N2 adducts with carcinogenic amino-/nitroarenes. J Org Chem 2007; 71:5599-606. [PMID: 16839139 DOI: 10.1021/jo0605243] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for direct palladium-catalyzed N-arylation reaction of nucleobases was developed for the convenient synthesis of DNA adducts with carcinogenic compounds. Using xantphos as the phosphine ligand and tetraethylammonium fluoride as the base in DMSO, several o-iodonitroarenes could be efficiently coupled with 2'-deoxyguanosine, 2'-deoxyadenosine, and 2'-deoxycytidine. The presence of a 3'-phosphate group in the deoxyribose moiety was found to be compatible with this N-arylation reaction; further, oligonucleotides could serve as substrates. The facile nitroreduction of the coupling compounds (12) yielded 2'-deoxyguanosin-N2-ylarylamine adducts, which are known to be biologically important. Compound 12 was easily converted to phosphoramidite derivatives, allowing the preparation of site-specific modified oligonucleotides with arylamine after the nitroreduction.
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Affiliation(s)
- Takeji Takamura-Enya
- Cancer Prevention Basic Research Project, National Cancer Centre Research Institute, Tokyo 104-0045, Japan.
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Liu J, Robins MJ. S(N)Ar displacements with 6-(fluoro, chloro, bromo, iodo, and alkylsulfonyl)purine nucleosides: synthesis, kinetics, and mechanism1. J Am Chem Soc 2007; 129:5962-8. [PMID: 17439120 DOI: 10.1021/ja070021u] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SNAr reactions with 6-(fluoro, chloro, bromo, iodo, and alkylsulfonyl)purine nucleosides and nitrogen, oxygen, and sulfur nucleophiles were studied. Pseudo-first-order kinetics were measured with 6-halopurine compounds, and comparative reactivities were determined versus a 6-(alkylsulfonyl)purine nucleoside. The displacement reactivity order was: F > Br > Cl > I (with BuNH2/MeCN), F > Cl approximately Br > I (with MeOH/1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)/MeCN), and F > Br > I > Cl [with K+ -SCOCH3/dimethyl sulfoxide (DMSO)]. The order of reactivity with a weakly basic arylamine (aniline) was: I > Br > Cl > F (with 5 equiv of aniline in MeCN at 70 degrees C). However, those reactions with aniline were autocatalytic and had significant induction periods ( approximately 50 min for the iodo compound and approximately 6 h for the fluoro analogue). Addition of trifluoroacetic acid (TFA) eliminated the induction period, and the order then was F > I > Br > Cl (with 5 equiv of aniline and 2 equiv of TFA in MeCN at 50 degrees C). The 6-(alkylsulfonyl)purine nucleoside analogue was more reactive than the 6-fluoropurine compound with both MeOH/DBU/MeCN and iPentSH/DBU/MeCN and was more reactive than the Cl, Br, and I compounds with BuNH2 and aniline/TFA. Titration of the 6-halopurine nucleosides in CDCl3 with TFA showed progressive downfield 1H NMR chemical shifts for H8 (larger) and H2 (smaller). The major site of protonation as N7 for both the 6-fluoro and 6-bromo analogues was confirmed by large upfield shifts ( approximately 16 ppm) of the 15N NMR signal for N7 upon addition of TFA (1.6 equiv). Mechanistic considerations and resolution of prior conflicting results are presented.
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Affiliation(s)
- Jiangqiong Liu
- Contribution from the Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
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Ngassa FN, Dekorver KA, Melistas TS, Yeh EAH, Lakshman MK. Pd−Xantphos-Catalyzed Direct Arylation of Nucleosides. Org Lett 2006; 8:4613-6. [PMID: 16986963 DOI: 10.1021/ol0619516] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Direct arylation of the exocyclic amino groups of nucleosides represents a simple approach to N-aryl nucleoside derivatives. To date, one limitation has been that only electron-deficient aryl bromides and triflates possessed adequate reactivity for efficient, direct N-arylation of nucleosides. We demonstrate herein that Pd-Xantphos catalytic systems lead to successful N-arylation of suitably protected 2'-deoxyadenosine and 2'-deoxyguanosine with a wide range of aryl bromides.
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Affiliation(s)
- Felix N Ngassa
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, USA.
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Abstract
[structure: see text] After bioactivation, the potent dietary mutagen 2-amino-3-methylimidazo[4,5-f]-quinoline (IQ) reacts with DNA to give two regioisomeric adducts of deoxyguanosine. The synthesis of the minor N2-adduct has been achieved utilizing the Buchwald-Hartwig palladium-catalyzed N-arylation reaction as the key step.
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Affiliation(s)
- James S Stover
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, Tennessee 37235-1822, USA
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Dai Q, Ran C, Harvey RG. Regioselective arylation of 2′-deoxyribonucleosides on amido or imino sites by copper(II)-mediated direct coupling with arylboronic acids. Tetrahedron 2006. [DOI: 10.1016/j.tet.2005.11.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Western EC, Shaughnessy KH. Inhibitory effects of the guanine moiety on Suzuki couplings of unprotected halonucleosides in aqueous media. J Org Chem 2005; 70:6378-88. [PMID: 16050700 DOI: 10.1021/jo050832l] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In the Suzuki arylations of unprotected halonucleosides in aqueous media, 8-bromo-2'-deoxyguanosine (8BrdG) couplings were slower to reach completion than the corresponding 8-bromo-2'-deoxyadenosine (8BrdA) couplings. The guanine moiety has an acidic proton, which under our Suzuki conditions (pH congruent with 10) may be deprotonated to give an anion that can coordinate to palladium. The possibility that guanine coordination was responsible for the observed slower rates was explored using additive experiments in which nonhalogenated nucleosides were added to the Suzuki coupling reaction of 8BrdA or 4-bromotoluene and PhB(OH)2 and the reaction progress monitored by HPLC or GC. Adding dG slowed these reactions, and an induction period was observed. The addition of dA or 1-methyl-2'-deoxyguanosine (1MedG) to these couplings did not affect the rate of conversion to product. Guanine coordination was further explored using 13C and 31P NMR spectroscopy, which implies that guanine is coordinating to palladium through N-1 or O-6, or both. Furthermore, the presence of dG inhibited the formation of the active palladium(0) catalytic species, which may account for both the observed induction period and the sluggishness of reactions where guanine is involved.
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Affiliation(s)
- Elizabeth C Western
- Department of Chemistry and the Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, USA
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2004; 43:6372-7. [PMID: 15558680 DOI: 10.1002/anie.200460782] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Padmaja Gunda
- Department of Chemistry, The City College and The City University of New York, 138th Street at Convent Avenue, New York, NY 10031, USA
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Gunda P, Russon LM, Lakshman MK. Pd-Catalyzed Amination of Nucleoside Arylsulfonates to yieldN6-Aryl-2,6-Diaminopurine Nucleosides. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460782] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Terrazas M, Ariza X, Farràs J, Guisado-Yang JM, Vilarrasa J. A direct, efficient method for the preparation of n6-protected 15n-labeled adenosines. J Org Chem 2004; 69:5473-5. [PMID: 15287800 DOI: 10.1021/jo049490u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
N6-Protected adenosines have been prepared from inosines by activation of the C6 position and Pd-catalyzed coupling with amides. An efficient route to [6-15NH2]-N6-benzoyladenosine and [1-15N,6-15NH2]-N6-benzoyladenosine has been achieved.
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Affiliation(s)
- Montserrat Terrazas
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
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Okazaki T, Laali KK. Electrophilic and oxidative chemistry of pyrene and its non-alternant isomers: theoretical (DFT, GIAO-NMR, NICS) study of protonation carbocations and oxidation dications from pyrene, azupyrene (dicyclopenta[ef,kl]heptalene) and dicyclohepta[ed,gh]pentalene. Org Biomol Chem 2004; 2:2214-9. [PMID: 15280958 DOI: 10.1039/b405009f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mono- and diprotonated carbocations and the two-electron oxidation dications derived from parent pyrene and its nonalternant isomers "azupyrene"(dicyclopenta[ef,kl]heptalene)(DCPH) and dicyclohepta[ed,gh]pentalene (DCHP) were studied by DFT at the B3LYP/6-31G(d) level. The most likely site(s) for mono- and diprotonation were determined based on relative arenium ion energies and the structures of the energetically most favored carbocations were determined by geometry optimization. The NMR chemical shifts for the protonated mono- and dications and the oxidation dications were computed by GIAO-NMR at the B3LYP/6-31G(d)//B3LYP/6-31G(d) level and their charge delocalization paths were deduced based on magnitude of the computed [capital Delta][small delta](13)C values and the NPA-derived changes in charges. Relative aromaticity/antiaromaticity in various rings in the energetically favored mono- and dications was estimated via NICS and [capital Delta]NICS. Calculated NMR chemical shift data for and were compared with the available experimental NMR values. The available data on chemical and physical properties of DCPH and DCHP are extremely limited and biological activity data are non-existent. The present study provides the first glance into their carbocations and oxidation dications, while augmenting and reinforcing the previous stable ion data on the pyrenium cations.
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Affiliation(s)
- Takao Okazaki
- Department of Chemistry, Kent State University, Kent, OH 44242, USA
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