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Wang Q, Mu J, Zeng J, Wan L, Zhong Y, Li Q, Li Y, Wang H, Chen F. Additive-controlled asymmetric iodocyclization enables enantioselective access to both α- and β-nucleosides. Nat Commun 2023; 14:138. [PMID: 36627283 PMCID: PMC9831021 DOI: 10.1038/s41467-022-35610-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
β-Nucleosides and their analogs are dominant clinically-used antiviral and antitumor drugs. α-Nucleosides, the anomers of β-nucleosides, exist in nature and have significant potential as drugs or drug carriers. Currently, the most widely used methods for synthesizing β- and α-nucleosides are via N-glycosylation and pentose aminooxazoline, respectively. However, the stereoselectivities of both methods highly depend on the assisting group at the C2' position. Herein, we report an additive-controlled stereodivergent iodocyclization method for the selective synthesis of α- or β-nucleosides. The stereoselectivity at the anomeric carbon is controlled by the additive (NaI for β-nucleosides; PPh3S for α-nucleosides). A series of β- and α-nucleosides are prepared in high yields (up to 95%) and stereoselectivities (β:α up to 66:1, α:β up to 70:1). Notably, the introduced iodine at the C2' position of the nucleoside is readily functionalized, leading to multiple structurally diverse nucleoside analogs, including stavudine, an FDA-approved anti-HIV agent, and molnupiravir, an FDA-approved anti-SARS-CoV-2 agent.
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Affiliation(s)
- Qi Wang
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jiayi Mu
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jie Zeng
- Pharmaceutical Research Institute, Wuhan Institute of Technology, 430205, Wuhan, China
| | - Linxi Wan
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yangyang Zhong
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Qiuhong Li
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yitong Li
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Huijing Wang
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Fener Chen
- Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China. .,Engineering Center of Catalysis and synthesis for Chiral Molecules, Department of chemistry, Fudan University, Shanghai, 200433, China. .,Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
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2
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He ZX, Zhao TQ, Gong YP, Zhang X, Ma LY, Liu HM. Pyrimidine: A promising scaffold for optimization to develop the inhibitors of ABC transporters. Eur J Med Chem 2020; 200:112458. [PMID: 32497962 DOI: 10.1016/j.ejmech.2020.112458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
The multidrug resistance (MDR) phenomenon in cancer cells is the major obstacle leading to failure of chemotherapy accompanied by the feature of intractable and recurrence of cancers. As significant contributors that cause MDR, ABC superfamily proteins can transport the chemotherapeutic drugs out of the tumor cells by the energy of adenosine triphosphate (ATP) hydrolysis, thereby reducing their intracellular accumulation. The ABC transports like ABCB1, ABCC1 and ABCG2 have been extensively studied to develop modulators for overcoming MDR. To date, no reversal agents have been successfully marketed for clinical application, and little information about the ABC proteins bound to specific inhibitors is known, which make the design of MDR inhibitors with potency, selectivity and low toxicity a major challenge. In recent years, it has been increasingly recognized that pyrimidine-based derivatives have the potential for reversing ABC-mediated MDR. In this review, we summarized the pyrimidine-based inhibitors of ABC transporters, and mainly focused on their structure optimizations, development strategies and structure-activity relationship studies in hope of providing a reference for medicinal chemists to develop new modulators of MDR with highly potency and fewer side effects.
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Affiliation(s)
- Zhang-Xu He
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Tao-Qian Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yun-Peng Gong
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xin Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Li-Ying Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
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3
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Bairagi KM, Venugopala KN, Mondal PK, Gleiser RM, Chopra D, García D, Odhav B, Nayak SK. Larvicidal study of tetrahydropyrimidine scaffolds against Anopheles arabiensis and structural insight by single crystal X-ray studies. Chem Biol Drug Des 2018; 92:1924-1932. [PMID: 29923688 DOI: 10.1111/cbdd.13351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 11/29/2022]
Abstract
A series of methyl or ethyl 4-(substitutedphenyl/pyridyl)-6-methyl-2-oxo/thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (HPM) analogues 4a-g were synthesized and evaluated for larvicidal activity against Anopheles arabiensis. These newly synthesized compounds were characterized by spectral studies such as FT-IR, NMR (1 H and 13 C), LC-MS, and elemental analysis. The conformational features and supramolecular assembly of molecules 4a, 4b, and 4e were further analyzed from single crystal X-ray study. The larvicidal activity of these tetrahydropyrimidine pharmacophore series was analyzed based on their relative substituents. Among the synthesized HPM analogous from the series, compounds 4d and 4e both having electron withdrawing chlorine group on phenyl ring at the fourth position of the tetrahydropyrimidine pharmacophore exhibited the most promising larvicidal activity.
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Affiliation(s)
- Keshab M Bairagi
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra, India
| | - Katharigatta N Venugopala
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Pradip Kumar Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Raquel M Gleiser
- CREAN-IMBIV (CONICET-UNC), Córdoba, Argentina.,FCEFyN, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
| | - Daniel García
- Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT-CONICET), Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Susanta K Nayak
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra, India
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4
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Phosphorus Pentachloride Promoted gem-Dichlorination of 2'- and 3'-Deoxynucleosides. Molecules 2018; 23:molecules23061457. [PMID: 29914115 PMCID: PMC6100136 DOI: 10.3390/molecules23061457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 11/16/2022] Open
Abstract
Halogen substitution at various positions of canonical nucleosides has generated a number of bioactive structural variants. Herein, the synthesis of two unique series of sugar modified nucleosides bearing a gem-dichloro group is presented. The synthetic plan entails the controlled addition of phosphorus pentachloride to suitably protected 2′- or 3′-ketodeoxynucleoside intermediates as the key step, facilitating the rapid construction of such functionalized molecules. Under the same reaction conditions, the highest chemoselectivity was observed for the formation of 2′,2′-dichloro-2′,3′-dideoxynucleosides, while a competing 2′,3′-elimination process occurred in the case of the 3′,3′-dichloro counterparts.
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5
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Hollecker L, Choo H, Chong Y, Chu CK, Lostia S, McBrayer TR, Stuyver LJ, Mason JC, Du J, Rachakonda S, Shi J, Schinazi RF, Watanabe KA. Synthesis of β-Enantiomers of N4-Hydroxy-3′-Deoxy-Pyrimidine Nucleosides and Their Evaluation against Bovine Viral Diarrhoea Virus and Hepatitis C Virus in Cell Culture. ACTA ACUST UNITED AC 2016; 15:43-55. [PMID: 15074714 DOI: 10.1177/095632020401500105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
N4-Hydroxycytidine (NHC) was recently reported to have anti-pestivirus and anti-hepacivirus activity. It is thought that this nucleoside acts as a weak alternative substrate for the hepatitis C virus (HCV) polymerase. In addition to NHC, 3′-deoxyuridine (3′-dU) was found to inhibit bovine diarrhoea virus (BVDV) production by 1 log10 at 37.2 μM. These initial findings prompted the synthesis of β-D and β-L analogues of (i) base-modified 3′-deoxy-NHC; (ii) 3′-deoxyuridine; and 3′-deoxycytidine. The antiviral activity of these 42 nucleosides was evaluated against BVDV and HCV bicistronic replicon in cell culture. Among the NHC analogues, the antiviral activity observed for the β-L-3′-deoxy-5-fluoro-derivative 1-(3-deoxy-β-L- erythro-pentofuranosyl)-5-fluoro-4-hydrox-yaminopyrimidin-2( 1H)-one and the β-D-3′-deoxy-5-iodo-derivative 1-(3-deoxy-β-D-erythro-pentofuranosyl)-5-iodocytosine in the replicon system (1 log10 reduction at 100 μM) was due to the concomitant toxicity towards intracellular ribosomal RNA levels (CC90 equal or lower than the EC90). In conclusion, none of the newly synthesized derivatives exhibited enhanced antiviral activity compared to the parent nucleoside NHC.
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6
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Jasmine NJ, Muthiah PT, Arunagiri C, Subashini A. Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N'-hydroxy-pyrimidine-2-carboximidamide by DFT approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 144:215-225. [PMID: 25756689 DOI: 10.1016/j.saa.2015.02.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/01/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
The FT-IR, FT-Raman, (1)H, (13)C NMR and UV-Visible spectral measurements of N'-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure.
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Affiliation(s)
- N Jeeva Jasmine
- School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, (TN), India
| | - P Thomas Muthiah
- School of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, (TN), India
| | - C Arunagiri
- PG & Research Department of Physics, Government Arts College, Ariyalur 621 713, (TN), India
| | - A Subashini
- PG & Research Department of Chemistry, Seethalakshmi Ramaswami College, Tiruchirappalli 620 002, (TN), India.
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7
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Kuranaga T, Sesoko Y, Inoue M. Cu-mediated enamide formation in the total synthesis of complex peptide natural products. Nat Prod Rep 2014; 31:514-32. [PMID: 24567066 DOI: 10.1039/c3np70103d] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cu-mediated C(sp(2))-N bond formation has received intense interest recently, and has been applied to the total synthesis of a wide variety of structurally complex natural products. This review covers the synthetic assembly of peptide natural products in which Cu-mediated enamide formation is the key transformation. The total syntheses of cyclopeptide alkaloids, pacidamycin D, and yaku'amide A exemplify the versatility of the Cu-catalyzed cross-coupling reaction in comparison to other synthetic methods.
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Affiliation(s)
- Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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8
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Okamoto K, Sakagami M, Feng F, Togame H, Takemoto H, Ichikawa S, Matsuda A. Total Synthesis and Biological Evaluation of Pacidamycin D and Its 3′-Hydroxy Analogue. J Org Chem 2012; 77:1367-77. [DOI: 10.1021/jo202159q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazuya Okamoto
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Japan
| | - Masahiro Sakagami
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Japan
| | - Fei Feng
- Faculty of Advanced Life Science, Hokkaido University, Kita-21, Nishi-11, Kita-ku, Sapporo,
001-0021, Japan
| | - Hiroko Togame
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Japan
| | - Hiroshi Takemoto
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11, Kita-ku, Sapporo 001-0021, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical
Sciences, Hokkaido University, Kita-12,
Nishi-6, Kita-ku, Sapporo
060-0812, Japan
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9
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Patil PR, Ravindranathan Kartha KP. Application of Ball Milling Technology to Carbohydrate Reactions: I. Regioselective Primary Hydroxyl Protection of Hexosides and Nucleoside by Planetary Ball Milling‡. J Carbohydr Chem 2008. [DOI: 10.1080/07328300802218713] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Zlatev I, Vasseur JJ, Morvan F. Deoxygenation of 5- O-benzoyl-1,2-isopropylidene-3- O-imidazolylthiocarbonyl-α-d-xylofuranose using dimethyl phosphite: an efficient alternate method towards a 3'-deoxynucleoside glycosyl donor. Tetrahedron Lett 2008; 49:3288-3290. [PMID: 32287438 PMCID: PMC7111737 DOI: 10.1016/j.tetlet.2008.03.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/04/2008] [Accepted: 03/17/2008] [Indexed: 11/13/2022]
Abstract
An efficient radical deoxygenation reaction of thiocarbonylimidazolyl activated glycoside analogue using dimethyl phosphite as hydrogen source and radical chain carrier was performed as a key step in a multi step synthesis towards a common 3-deoxy glycosyl donor for 3′-deoxynucleosides. This method has safety and cost advantages compared to the generally used radical reduction reagents.
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Affiliation(s)
- Ivan Zlatev
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1, Université Montpellier 2, Place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1, Université Montpellier 2, Place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1, Université Montpellier 2, Place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
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11
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Gagneron J, Gosselin G, Mathé C. Synthesis and Conformational Analysis of C-4′-Modified (2-Oxabicyclo[3.1.0]hexyl)pyrimidine Nucleosides. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Hocek M, Šilhár P, Pohl R. Cytostatic and Antiviral 6-Arylpurine Ribonucleosides VIII. Synthesis and Evaluation of 6-Substituted Purine 3'-Deoxyribonucleosides. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20061484] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A series of purine 3'-deoxyribonucleosides bearing diverse C-substituents (alkyl, aryl, hetaryl or hydroxymethyl) in the position 6 was prepared by Pd-catalyzed cross-coupling reactions of 6-iodo-9-[2,5-bis-O-(tert-butyldimethylsilyl)-3-deoxy-β-D-ribofuranosyl]purine with the corresponding organometallics followed by deprotection by (HF)3·Et3N. None of the title 3'-deoxyribonucleoside showed any cytostatic activity or anti-HCV effect in replicon assay.
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13
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Honcharenko D, Varghese OP, Plashkevych O, Barman J, Chattopadhyaya J. Synthesis and Structure of Novel Conformationally Constrained 1‘,2‘-Azetidine-Fused Bicyclic Pyrimidine Nucleosides: Their Incorporation into Oligo-DNAs and Thermal Stability of the Heteroduplexes. J Org Chem 2005; 71:299-314. [PMID: 16388649 DOI: 10.1021/jo052115x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
[structures: see text] The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, and 42) for automated solid-phase oligonucleotide synthesis is reported. The novel bicyclonucleoside "azetidine" monomers were synthesized by two different strategies starting from the known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-D-psicofuranose. Conformational analysis performed by molecular modeling (ab initio and MD simulations) and NMR showed that the azetidine-fused furanose sugar is locked in a North-East conformation with pseudorotational phase angle (P) in the range of 44.5-53.8 degrees and sugar puckering amplitude (phi(m)) of 29.3-32.6 degrees for the azetidine-modified T, U, C, and 5-Me-C nucleosides. Thermal denaturation studies of azetidine-modified oligo-DNA/RNA heteroduplexes show that the azetidine-fused nucleosides display improved binding affinities when compared to that of previously synthesized North-East sugar constrained oxetane fused analogues.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden
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Shim J, Larson G, Lai V, Naim S, Wu JZ. Canonical 3'-deoxyribonucleotides as a chain terminator for HCV NS5B RNA-dependent RNA polymerase. Antiviral Res 2003; 58:243-51. [PMID: 12767472 DOI: 10.1016/s0166-3542(03)00007-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nucleoside chain terminators represent one of the most promising classes of antiviral drug for DNA viruses and retroviral infection; however, they have not been fully explored against RNA viral polymerases. In this report, we investigate the notion of employing canonical 3'-deoxyribonucleoside triphosphates (3'-dNTPs) as a chain terminator for hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp). Using a HCV RNA transcript-dependent RNA elongating assay, we found that they inhibit NS5B RdRp with K(i) ranged from 0.7 to 23 microM. Additional structure-activity relationship studies showed that removal of 2'-hydroxyl group, elimination of ribose's 2',3'-carbon-carbon bond, or addition of 5-methyl group to a pyrimidine base is detrimental to 3'-dNTP's potency. Direct evidence was obtained that all four canonical 3'-dNTP are incorporated into elongating RNA chains and the incorporation terminates NS5B RdRp-catalyzed RNA synthesis. The K(i) values for each of 3'-dNTPs were determined in the single nucleotide incorporation experiments. The nucleoside form of 3'-dNTPs was further evaluated in a cell culture-based HCV subgenomic replicon assay. The discrepancy between the potent in vitro activity and the weak cellular activity of these chain terminators was discussed in the context of nucleoside metabolism. This proof of concept study demonstrates that canonical 3'-dNTPs can function as an effective chain terminator for HCV NS5B RdRp with cytidine as the preferred nucleoside scaffold. Our results further sheds light on the potential hurdles that need to be overcome for successful development of active nucleoside chain terminators in vivo for a viral RNA polymerase, especially the HCV NS5B RdRp.
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Affiliation(s)
- Jaehoon Shim
- Drug discovery, Ribapharm Corporation, 3300 Hyland Avenue, Costa Mesa, CA 92626, USA
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15
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Obika S, Morio KI, Nanbu D, Hari Y, Itoh H, Imanishi T. Synthesis and conformation of 3′,4′-BNA monomers, 3′-O,4′-C-methyleneribonucleosides. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00227-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Shigeta S, Mori S, Kira T, Takahashi K, Kodama E, Konno K, Nagata T, Kato H, Wakayama T, Koike N, Saneyoshi M. Anti-herpesvirus activities and cytotoxicities of 2-thiopyrimidine nucleoside analogues in vitro. Antivir Chem Chemother 1999; 10:195-209. [PMID: 10480738 DOI: 10.1177/095632029901000404] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Twenty 2-thiopyrimidine nucleoside analogues were synthesized and examined for inhibitory activity against herpes simplex virus (HSV) type 1 and 2, varicella-zoster virus (VZV), human cytomegalovirus (HCMV) and thymidine kinase-deficient HSV (HSV-TK-) replication in vitro. 2-thiouracil (thymine) arabinoside, 2'-deoxy-2-thiouridine (or 2-thiothymidine) and their 5-halogenated derivatives showed anti-HSV activity in both RPM18226 (human B-lymphoblastoid cells) and MRC-5 (human embryo lung cells). 2'-deoxy-5-halogenated-2-thiocytidines were also inhibitory against HSV, whereas 2-thiocytosine arabinoside and its derivatives were not inhibitory against HSV replication, except 5-bromo and 5-iodo congeners (TN-31, TN-32). Substitution of the halogen atom at the 5-position of the pyrimidine rings to an atom with a higher molecular weight increased anti-HSV and VZV activities, except for the anti-HSV activity of 2-thiouracil arabinosides. 2'-deoxy-5-methyl-, and 2'-deoxy-5-iodo-2-thiouridines (TN-17, TN-44) showed the most potent anti-HSV activity, and 2'-deoxy-5-chloro- and 2'-deoxy-5-bromo-2-thiocytidines were potent inhibitors of VZV replication. However, none of the compounds inhibited HCMV and HSV-TK- replication. TN-31 and TN-32 were shown to inhibited HCMV and HSV-TK- as well as HSV and VZV replication. The cytotoxicity of the 2-thio-pyrimidine nucleoside analogues was less than that of the 2-oxy-congeners of the compounds (5-iodo-2'-deoxyuridine, 5-iodo-2'-deoxycytidine, thymine arabinoside and cytosine arabinoside). The selectivity index of 2'-deoxy-5-iodo-2-thiouridine (TN-44) was higher than that of 5-iodo-deoxyuridine. TN-17 and TN-44 were not cytotoxic to resting or stimulated human peripheral blood mononuclear cells at 400 microM, although TN-32 was cytotoxic at a concentration of 20 microM.
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Affiliation(s)
- S Shigeta
- Department of Microbiology, School of Medicine, Fukushima Medical University, Japan.
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17
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Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3, -endo sugar puckering. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)10322-7] [Citation(s) in RCA: 444] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Hiebl J, Zbiral E. Synthesis of 2,2′-Anhydro Nucleosides with a Modified Sugar Side-Chain. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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el Kouni MH, Naguib FN, Panzica RP, Otter BA, Chu SH, Gosselin G, Chu CK, Schinazi RF, Shealy YF, Goudgaon N, Ozerov AA, Ueda T, Iltzsch MH. Effects of modifications in the pentose moiety and conformational changes on the binding of nucleoside ligands to uridine phosphorylase from Toxoplasma gondii. Biochem Pharmacol 1996; 51:1687-700. [PMID: 8687484 DOI: 10.1016/0006-2952(96)00213-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
One hundred and fifty analogues of uridine, with various modifications to the uracil and pentose moieties, have been tested and compared with uridine with respect to their potency to bind to uridine phosphorylase (UrdPase, EC 2.4.2.3) from Toxoplasma gondii. The effects of the alpha- and beta-anomers, the L- and D-enantiomers, as well as restricted syn and anti rotamers, on binding were examined. Pseudo-, lyxo-, 2,3'-anhydro-2'-deoxy-, 6,5'-cyclo-, 6,3'-methano-, O5',6-methano- and carbocyclic uridines did not bind to the enzyme. Ribosides bound better than the corresponding xylosides, which were better than the deoxyribosides. The binding of deoxyribosides was in the following manner: 2',3'-dideoxynucleosides > 2',5'-dideoxynucleosides > 2'-deoxyribosides > 3'- and 5'-deoxyribosides. alpha-2'-Deoxyribosides bound to the enzyme, albeit less tightly than the corresponding beta-anomers. The acyclo- and 2,2'-anhydrouridines bound strongly, with the 2,2'-anhydro-derivatives being the better ligands. 2,5'-Anhydrouridine bound to UrdPase less effectively than 2,2'-anhydrouridine and acyclouridine. Arabinosyluracil was at best a very poor ligand, but bound better if a benzyl group was present at the 5-position of the pyrimidine ring. This binding was enhanced further by adding a 5-benzyloxybenzyl group. A similar enhancement of the binding by increased hydrophobicity at the 5-position of the pyrimidine ring was observed with ribosides, alpha- and beta-anomers of the 2'-deoxyribosides, acyclonucleosides, and 2,2'-anhydronucleosides. Among all the compounds tested, 5-(benzyloxybenzyl)-2,2'-anhydrouridine was identified as the best ligand of T. gondii UrdPase with an apparent Ki value of 60 +/- 3 nM. It is concluded that the presence of an N-glycosyl bond is a prerequisite for a nucleoside ligand to bind to T. gondii UrdPase. On the other hand, the presence of a 2'-, 3'-, or 5'-hydroxyl group, or an N-glycosyl bond in the beta-configuration, enhanced but was not essential for binding. Furthermore, the potency of the binding of 2,2'-anhydrouridines (fixed high syn isomers) in contrast to the weaker binding of the 6,1'-anhydro- or 2,5'-anhydrouridines (fixed syn isomers), and the complete lack of binding of the 6,5'-cyclo, O5',6-methano- and 6,3'-methanouridines (fixed anti isomers) to T. gondii UrdPase indicate that the binding of ligands to this enzyme is in the syn/high syn conformation around the N-glycosyl bond. The results also indicate that the parasite but not the mammalian host UrdPase can participate in hydrogen bonding with N3 of the pyrimidine ring of nucleoside ligands. T. gondii UrdPase also has a larger hydrophobic pocket adjacent to the C5 of the pyrimidine moiety than the host enzyme, and can accommodate modifications in the pentose moiety which cannot be tolerated by the host enzyme. Most prominent among these modifications is the absence and/or lack of the ribo orientation of the 3'-hydroxyl group, which is a requirement for a ligand to bind to mammalian UrdPase. These differences between the parasite and host, enzymes can be useful in designing specific inhibitors or "subversive" substrates for T. gondii UrdPase.
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Affiliation(s)
- M H el Kouni
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham 35294, USA.
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20
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Modified dideoxynucleosides: Synthesis of 2′-N-alkyl-3′-hydroxyalkyl-1′,2′-isoxazolidinyl thymidine and 5-fluorouridine derivatives. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00437-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Wallis MP, Spiers ID, Schwalbe CH, Fraser W. Direct synthesis, substitution, and structure of 1-(2′-deoxyβ-D-erythro-pentofuranosyl)-4-pentafluorophenylpyrimidin-2H-one. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00587-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Schinazi RF. Competitive inhibitors of human immunodeficiency virus reverse transcriptase. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf02171660] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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