1
|
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.
Collapse
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
| |
Collapse
|
2
|
Sengupta S, Das P. Application of diazonium chemistry in purine modifications: A focused review. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saumitra Sengupta
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
| |
Collapse
|
3
|
Taniguchi Y, Sagara I, Nagata Y, Kikukawa Y, Sasaki S. Effects of the 2-Substituted Adenosine-1,3-diazaphenoxazine 5'-Triphosphate Derivatives on the Single Nucleotide Primer Extension Reaction by DNA Polymerase. Chem Pharm Bull (Tokyo) 2019; 67:1123-1130. [PMID: 31582632 DOI: 10.1248/cpb.c19-00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The adenosine triphosphate derivatives of 2-oxo-1,3-diazaphenoxazine (dAdapTP) showed a significant discrimination ability for the template strand including that between 8-oxo-2'-deoxyguanosine (8-oxodG) and 2'-deoxyguanosine (dG) by the single nucleotide primer extension reaction using the Klenow Fragment. In this study, we synthesized new dAdapTP derivatives, i.e., 2-amino-dAdapTP, 2-chloro-dAdapTP and 2-iodo-dAdapTP, to investigate the effect on the selectivity and efficiency of incorporation for the primer extension reaction using a variety of DNA polymerases. In contrast to the previously tested dAdapTP, the selectivity and efficiency of the 2-halo-dAdapTP incorporation were dramatically decreased using the Klenow Fragment. Moreover, the efficiency of the 2-amino-dAdapTP incorporation into the T-containing template was almost the same with that of dAdapTP. In the case of the Bsu DNA polymerase, the efficiency of all the dAdapTP derivatives decreased compared to that using the Klenow Fragment. However, the incorporation selectivity of dAdapTP had improved against the oxodG-containing template for all the template sequences including the T-containing template. Moreover, 2-amino-dAdapTP showed a better efficiency than dAdapTP using the Bsu DNA polymerase. The 2-amino group of the adenosine unit may interact with syn-oxodG at the active site of the Bsu DNA polymerase during the single primer extension reaction.
Collapse
Affiliation(s)
| | - Ikuko Sagara
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Yusuke Nagata
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | | | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
| |
Collapse
|
4
|
Satishkumar S, Vuram PK, Relangi SS, Gurram V, Zhou H, Kreitman RJ, Martínez Montemayor MM, Yang L, Kaliyaperumal M, Sharma S, Pottabathini N, Lakshman MK. Cladribine Analogues via O⁶-(Benzotriazolyl) Derivatives of Guanine Nucleosides. Molecules 2015; 20:18437-63. [PMID: 26473811 PMCID: PMC4841790 DOI: 10.3390/molecules201018437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/20/2015] [Accepted: 09/22/2015] [Indexed: 11/16/2022] Open
Abstract
Cladribine, 2-chloro-2'-deoxyadenosine, is a highly efficacious, clinically used nucleoside for the treatment of hairy cell leukemia. It is also being evaluated against other lymphoid malignancies and has been a molecule of interest for well over half a century. In continuation of our interest in the amide bond-activation in purine nucleosides via the use of (benzotriazol-1yl-oxy)tris(dimethylamino)phosphonium hexafluorophosphate, we have evaluated the use of O⁶-(benzotriazol-1-yl)-2'-deoxyguanosine as a potential precursor to cladribine and its analogues. These compounds, after appropriate deprotection, were assessed for their biological activities, and the data are presented herein. Against hairy cell leukemia (HCL), T-cell lymphoma (TCL) and chronic lymphocytic leukemia (CLL), cladribine was the most active against all. The bromo analogue of cladribine showed comparable activity to the ribose analogue of cladribine against HCL, but was more active against TCL and CLL. The bromo ribose analogue of cladribine showed activity, but was the least active among the C6-NH₂-containing compounds. Substitution with alkyl groups at the exocyclic amino group appears detrimental to activity, and only the C6 piperidinyl cladribine analogue demonstrated any activity. Against adenocarcinoma MDA-MB-231 cells, cladribine and its ribose analogue were most active.
Collapse
Affiliation(s)
- Sakilam Satishkumar
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Prasanna K Vuram
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Siva Subrahmanyam Relangi
- Discovery and Analytical Services, GVK Biosciences Pvt. Ltd., 28A IDA Nacharam, Hyderabad 500076, India.
| | - Venkateshwarlu Gurram
- Discovery and Analytical Services, GVK Biosciences Pvt. Ltd., 28A IDA Nacharam, Hyderabad 500076, India.
| | - Hong Zhou
- Clinical Immunotherapy Section, Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Robert J Kreitman
- Clinical Immunotherapy Section, Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | | | - Lijia Yang
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Muralidharan Kaliyaperumal
- Discovery and Analytical Services, GVK Biosciences Pvt. Ltd., 28A IDA Nacharam, Hyderabad 500076, India.
| | - Somesh Sharma
- Discovery and Analytical Services, GVK Biosciences Pvt. Ltd., 28A IDA Nacharam, Hyderabad 500076, India.
| | - Narender Pottabathini
- Discovery and Analytical Services, GVK Biosciences Pvt. Ltd., 28A IDA Nacharam, Hyderabad 500076, India.
| | - Mahesh K Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA.
| |
Collapse
|
5
|
Garlapati R, Pottabathini N, Gurram V, Chaudhary AB, Chunduri VR, Patro B. Pd-catalyzed amination of 6-halo-2-cyclopropyl-3-(pyridyl-3-ylmethyl) quinazolin-4(3H)-one. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.07.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Gurram V, Pottabathini N, Garlapati R, Chaudhary AB, Patro B, Lakshman MK. C-C cross-coupling reactions of O6-alkyl-2-haloinosine derivatives and a one-pot cross-coupling/O6-deprotection procedure. Chem Asian J 2012; 7:1853-61. [PMID: 22570232 PMCID: PMC3518038 DOI: 10.1002/asia.201200093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Indexed: 11/11/2022]
Abstract
Reaction conditions for the CC cross-coupling of O(6)-alkyl-2-bromo- and 2-chloroinosine derivatives with aryl-, hetaryl-, and alkylboronic acids were studied. Optimization experiments with silyl-protected 2-bromo-O(6)-methylinosine led to the identification of [PdCl(2)(dcpf)]/K(3)PO(4) in 1,4-dioxane as the best conditions for these reactions (dcpf=1,1'-bis(dicyclohexylphosphino)ferrocene). Attempted O(6)-demethylation, as well as the replacement of the C-6 methoxy group by amines, was unsuccessful, which led to the consideration of Pd-cleavable groups such that C-C cross-coupling and O(6)-deprotection could be accomplished in a single step. Thus, inosine 2-chloro-O(6)-allylinosine was chosen as the substrate and, after re-evaluation of the cross-coupling conditions with 2-chloro-O(6)-methylinosine as a model substrate, one-step C-C cross-coupling/deprotection reactions were performed with the O(6)-allyl analogue. These reactions are the first such examples of a one-pot procedure for the modification and deprotection of purine nucleosides under C-C cross-coupling conditions.
Collapse
Affiliation(s)
- Venkateshwarlu Gurram
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
- Jawaharlal Nehru Technological University, Kukatpally, Hyderabad 500085, Andhra Pradesh, India
| | - Narender Pottabathini
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Ramesh Garlapati
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Avinash B. Chaudhary
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Balaram Patro
- Medicinal and Analytical Chemistry Divisions, GVK Biosciences Pvt. Ltd., 28A, IDA Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - Mahesh K. Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
| |
Collapse
|
7
|
Lakshman MK, Kumar A, Balachandran R, Day BW, Andrei G, Snoeck R, Balzarini J. Synthesis and biological properties of C-2 triazolylinosine derivatives. J Org Chem 2012; 77:5870-83. [PMID: 22758929 DOI: 10.1021/jo300628y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O(6)-(Benzotriazol-1H-yl)guanosine and its 2'-deoxy analogue are readily converted to the O(6)-allyl derivatives that upon diazotization with t-BuONO and TMS-N(3) yield the C-2 azido derivatives. We have previously analyzed the solvent-dependent azide·tetrazole equilibrium of C-6 azidopurine nucleosides, and in contrast to these, the O(6)-allyl C-2 azido nucleosides appear to exist predominantly in the azido form, relatively independent of solvent polarity. In the presently described cases, the tetrazole appears to be very minor. Consistent with the presence of the azido functionality, each neat C-2 azide displayed a prominent IR band at 2126-2130 cm(-1). A screen of conditions for the ligation of the azido nucleosides with alkynes showed that CuCl in t-BuOH/H(2)O is optimal, yielding C-2 1,2,3-triazolyl nucleosides in 70-82% yields. Removal of the silyl groups with Et(3)N·3HF followed by deallylation with PhSO(2)Na/Pd(PPh(3))(4) gave the C-2 triazolylinosine nucleosides. In a continued demonstration of the versatility of O(6)-(benzotriazol-1H-yl)purine nucleosides, one C-2 triazolylinosine derivative was converted to two adenosine analogues via these intermediates, under mild conditions. Products were desilylated for biological assays. The two C-2 triazolyl adenosine analogues demonstrated pronounced antiproliferative activity in human ovarian and colorectal carcinoma cell cultures. When evaluated for antiviral activity against a broad spectrum of DNA and RNA viruses, some of the C-2 triazolylinosine derivatives showed modest inhibitory activity against cytomegalovirus.
Collapse
Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | | | | | | | | | | | | |
Collapse
|
8
|
Abstract
The reaction of O6-benzyl-3',5'-bis- O-( tert-butyldimethylsilyl)-2'-deoxyxanthosine with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) yielded the nucleoside C-2 tris(dimethylamino)phosphonium hexafluorophosphate salt as a stable, isolable species. This is in contrast to reactions of inosine nucleosides with BOP, where the in situ formed phosphonium salts undergo subsequent reaction to yield O6-(benzotriazol-1-yl)inosine derivatives. The phosphonium salt obtained from the 2'-deoxyxanthosine derivative can be effectively used to synthesize N2-modified 2'-deoxyguanosine analogues. Using this salt, a new synthesis of an acrolein-2'-deoxyguanosine adduct has also been accomplished.
Collapse
Affiliation(s)
- Suyeal Bae
- Department of Chemistry, The City College and The City University of New York, New York, New York 10031-9198, USA
| | | |
Collapse
|
9
|
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
| |
Collapse
|
10
|
|
11
|
Spitale RC, Heller MG, Pelly AJ, Wedekind JE. Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. J Org Chem 2007; 72:8551-4. [PMID: 17902696 PMCID: PMC2546599 DOI: 10.1021/jo7015778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Substitution of oxygen with a weak hydrogen bond acceptor such as fluorine provides a single-atom modification that can have grave effects on the chemical and medicinal properties of nucleoside analogues. To that end, we present a simple and high-yielding method for the novel synthesis of 5'-deoxy-5'-fluoroguanosine and 5'-deoxy-5'-fluoroinosine utilizing an intramolecular electron-withdrawing approach. The properties of the resulting modified nucleosides, as well as the halogenated intermediates, are notable for their similarity to nucleoside analogues used in the treatment of cancer, as well as enzyme inhibitors designed to target parasitic protozoa.
Collapse
Affiliation(s)
- Robert C. Spitale
- Department of Chemistry, Biological Chemistry Cluster, RC Box 270216, Rochester, NY 14627-0216
| | - Moriah G. Heller
- Department of Biochemistry & Biophysics, 601 Elmwood Avenue Box 712, Rochester New York 14642
| | - Amanda J. Pelly
- Department of Biochemistry & Biophysics, 601 Elmwood Avenue Box 712, Rochester New York 14642
| | - Joseph E. Wedekind
- Department of Biochemistry & Biophysics, 601 Elmwood Avenue Box 712, Rochester New York 14642
- Department of Chemistry, Biological Chemistry Cluster, RC Box 270216, Rochester, NY 14627-0216
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
| | | | - Mahesh K. Lakshman
- *Address correspondence to M.K.L. Tel: (212) 650-7835, fax: (212) 650-6107
| |
Collapse
|