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Manna T, Maji S, Maity M, Debnath B, Panda S, Khan SA, Nath R, Akhtar MJ. Anticancer potential and structure activity studies of purine and pyrimidine derivatives: an updated review. Mol Divers 2024:10.1007/s11030-024-10870-4. [PMID: 38856835 DOI: 10.1007/s11030-024-10870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/02/2024] [Indexed: 06/11/2024]
Abstract
Cancer is the world's leading cause of death impacting millions of lives globally. The increasing research over the past several decades has focused on the development of new anticancer drugs, but still cancer continues to be a global health challenge. Thus, several new alternative therapeutic strategies have been tried for the drug design and discovery. Purine and pyrimidine heterocyclic compounds have received attention recently due to their potential in targeting various cancers. It is evident from the recently published data over the last decade that incorporation of the purine and pyrimidine rings in the synthesized derivatives resulted in the development of potent anticancer molecules. This review presents synthetic strategies encompassing several examples of recently developed purine and pyrimidine-containing compounds as anticancer agents. In addition, their structure-activity relationships are represented in the schemes indicating the fragment or groups that are essential for the enhanced anticancer activities. Purine and pyrimidines combined with other heterocyclic compounds have resulted in many novel anticancer molecules that address the challenges of drug resistance. The purine and pyrimidine derivatives showed significantly enhanced anticancer activities against targeted receptor proteins with numerous compounds with an IC50 value in the nanomolar range. The review will support medicinal chemists and contribute in progression and development of synthesis of more potent chemotherapeutic drug candidates to mitigate the burden of this dreadful disease.
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Affiliation(s)
- Tanushree Manna
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Sumit Maji
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Mousumi Maity
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Biplab Debnath
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Shambo Panda
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India
| | - Shah Alam Khan
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PC 130, Azaiba, Bousher, PO 620, Muscat, Sultanate of Oman
| | - Rajarshi Nath
- Department of Pharmacy, Bharat Technology, Uluberia, 711316, Howrah, West Bengal, India.
- JIS University, Agarpara Campus, Kolkata-81, Nilgunj Road, Agarpara, Kolkata, 700109, India.
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PC 130, Azaiba, Bousher, PO 620, Muscat, Sultanate of Oman.
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2
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Tang X, Zhou Y, Wang Y, Lin Y, Pan S, Che Q, Sang J, Gao Z, Zhang W, Wang Y, Li G, Gao L, Wang Z, Yang X, Liu A, Wang S, Yu B, Xu P, Wang Z, Zhang Z, Yang P, Xie W, Sun H, Li W. Direct Synthesis of α- and β-2'-Deoxynucleosides with Stereodirecting Phosphine Oxide via Remote Participation. J Am Chem Soc 2024; 146:8768-8779. [PMID: 38483318 DOI: 10.1021/jacs.4c01780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
2'-Deoxynucleosides and analogues play a vital role in drug development, but their preparation remains a significant challenge. Previous studies have focused on β-2'-deoxynucleosides with the natural β-configuration. In fact, their isomeric α-2'-deoxynucleosides also exhibit diverse bioactivities and even better metabolic stability. Herein, we report that both α- and β-2'-deoxynucleosides can be prepared with high yields and stereoselectivity using a remote directing diphenylphosphinoyl (DPP) group. It is particularly efficient to prepare α-2'-deoxynucleosides with an easily accessible 3,5-di-ODPP donor. Instead of acting as a H-bond acceptor on a 2-(diphenylphosphinoyl)acetyl (DPPA) group in our previous studies for syn-facial O-glycosylation, the phosphine oxide moiety here acts as a remote participating group to enable highly antifacial N-glycosylation. This proposed remote participation mechanism is supported by our first characterization of an important 1,5-briged P-heterobicyclic intermediate via variable-temperature NMR spectroscopy. Interestingly, antiproliferative assays led to a α-2'-deoxynucleoside with IC50 values in the low micromole range against central nervous system tumor cell lines SH-SY5Y and LN229, whereas its β-anomer exhibited no inhibition at 100 μM. Furthermore, the DPP group significantly enhanced the antitumor activities by 10 times.
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Affiliation(s)
- Xintong Tang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yueer Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yingjie Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yetong Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Shuheng Pan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Qianwei Che
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jinpeng Sang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Ziming Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Weiting Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yuanyuan Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Guolong Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Longwei Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhimei Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Xudong Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Ao Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Suyu Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Biao Yu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhe Wang
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhaolun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Peng Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Weijia Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
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Elsayed GA, Mahmoud NFH. Synthesis and Biological Assessment of New Nucleosides of Pyrido[2,3-d]pyrimidine Derivatives Bearing Ribose and 2-Deoxyribose Moieties. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2074476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Galal A. Elsayed
- Synthetic Carbohydrates Laboratory, Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, Cairo, Egypt
| | - Naglaa F. H. Mahmoud
- Synthetic Carbohydrates Laboratory, Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, Cairo, Egypt
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4
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El-Etrawy AAS, Sherbiny FF. Design, synthesis, biological evaluation and molecular modeling investigation of new N'-(2-Thiouracil-5-oyl) hydrazone derivatives as potential anti-breast cancer and anti-bacterial agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129993] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Design, synthesis, biological assessment and molecular docking studies of some new 2-Thioxo-2,3-dihydropyrimidin-4(1H)-ones as potential anticancer and antibacterial agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Abu-Zaied M, Mahmoud NM, Elgemeie GH. Toward Developing Therapies against Corona Virus: Synthesis and Anti-Avian Influenza Virus Activity of Novel Cytosine Thioglycoside Analogues. ACS OMEGA 2020; 5:20042-20050. [PMID: 32832758 PMCID: PMC7439276 DOI: 10.1021/acsomega.0c01537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
A series of pyrimidine and pyrimidine thioglycoside derivatives were newly synthesized using sodium 2-cyano-3-(arylamino)prop-1-ene-1,1-bis(thiolates) and urea to give the corresponding sodium 6-amino-5-aryl-2-oxo-1,2-dihydropyrimidine-4-thiolates. Stirring of the latter with peracetylated α-d-gluco- and galacto-pyranosyl bromides in DMF afforded the corresponding pyrimidine thioglycosides. On the other hand, treatment of 6-amino-5-aryl-2-oxo-1,2-dihydropyrimidine-4-thiolate salts with hydrochloric acid produced the corresponding pyrimidine-4-thioles, which on stirring with α-d-gluco- and galacto-pyranosyl bromides in sodium hydride and DMF gave the corresponding pyrimidine thioglycosides. Deacetylation of the protected pyrimidine thioglycosides gave the corresponding free pyrimidine thioglycosides. The synthesized compounds have been characterized by 13C NMR, 1H NMR, and IR spectroscopy. The pyrimidine thioglycosides and free pyrimidine thioglycosides were tested against avian influenza H5N1 virus strain and exhibited highest to moderate activity.
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Affiliation(s)
- Mamdouh
A. Abu-Zaied
- Green
Chemistry Department, National Research
Centre, 33 El Bohouth
Street, Dokki, Giza 12622, Egypt
| | - Nashwa M. Mahmoud
- Chemistry
Department, Faculty of Science, Suez University, Suez 43511, Egypt
| | - Galal H. Elgemeie
- Chemistry Department, Faculty of
Science, Helwan University, Helwan, Cairo 11731, Egypt
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7
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Mondal PK, Bhandary S, Javoor MG, Cleetus A, Mangalampalli SRNK, Ramamurty U, Chopra D. Probing the distinct nanomechanical behaviour of a new co-crystal and a known solvate of 5-fluoroisatin and identification of a new polymorph. CrystEngComm 2020. [DOI: 10.1039/c9ce01659g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystalline forms of 5-fluoroisatin have been characterized by thermal, structural, and mechanical methods. The hardness and elastic modulus of the DMSO solvate is significantly higher than those of the picolinic acid co-crystal of 5-fluoroisatin.
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Affiliation(s)
- Pradip Kumar Mondal
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Subhrajyoti Bhandary
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Manjunath G. Javoor
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Annie Cleetus
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - S. R. N. Kiran Mangalampalli
- Nanomechanics Laboratory
- Department of Physics and Nanotechnology
- SRM Institute of Science and Technology
- Kattankulathur-603203
- India
| | - Upadrasta Ramamurty
- School of Mechanical and Aerospace Engineering
- Nanyang Technological University (NTU)
- Singapore
| | - Deepak Chopra
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
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8
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Elgemeie GH, Alkhursani SA, Mohamed RA. New synthetic strategies for acyclic and cyclic pyrimidinethione nucleosides and their analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:12-87. [PMID: 30729891 DOI: 10.1080/15257770.2018.1498511] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pyrimidinethione nucleosides are effective compounds and have significant and pivotal effects in several fields. New synthetic strategies for many pyrimidinethione nucleosides including acyclic and cyclic derivatives have been reported.
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Affiliation(s)
- Galal H Elgemeie
- a Chemistry Department, Faculty of Science , Helwan University , Helwan , Cairo , Egypt
| | - Sheikha A Alkhursani
- b Chemistry Department, Girls College of Science , Immam Abdulrahman Bin Faisal University , Dammam , Kingdom of Saudi Arabia
| | - Reham A Mohamed
- c Chemistry of Natural and Microbial Products Department, National Research Center , Dokki , Cairo , Egypt
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9
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Ni G, Du Y, Tang F, Liu J, Zhao H, Chen Q. Review of α-nucleosides: from discovery, synthesis to properties and potential applications. RSC Adv 2019; 9:14302-14320. [PMID: 35519323 PMCID: PMC9064229 DOI: 10.1039/c9ra01399g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleic acids play an important role in the genetic process of organisms; nucleosides, the building block of nucleic acids, typically exist in nature in a β configuration. As an anomer of β-nucleoside, α-nucleoside is extremely rare in nature. Because of their unique and interesting properties such as high stability, specific parallel double-stranded structure and some other biochemical properties, α-nucleosides have attracted wide attention. Various methods including but not limited to the mercuri procedure, fusion reaction and Vorbrüggen glycosylation have been used to synthesize α-nucleosides and their derivatives. However, to the best of our knowledge, there is no review that has summarized these works. Therefore, we systematically review the discovery, synthesis, properties, and potential applications of α-nucleosides in this article and look to provide a reference for subsequent studies in the coming years. A systematic summary of the discovery, synthesis, properties and potential applications of α-nucleosides and their derivatives.![]()
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Affiliation(s)
- Guangcheng Ni
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Yuqi Du
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Fan Tang
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Jiang Liu
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Hang Zhao
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Qianming Chen
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
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10
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El-Naggar AM, Abou-El-Regal MM, El-Metwally SA, Sherbiny FF, Eissa IH. Synthesis, characterization and molecular docking studies of thiouracil derivatives as potent thymidylate synthase inhibitors and potential anticancer agents. Mol Divers 2017; 21:967-983. [DOI: 10.1007/s11030-017-9776-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/02/2017] [Indexed: 11/27/2022]
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11
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Prasanthkumar KP, Alvarez-Idaboy JR, Kumar PV, Singh BG, Priyadarsini KI. Contrasting reactions of hydrated electron and formate radical with 2-thio analogues of cytosine and uracil. Phys Chem Chem Phys 2016; 18:28781-28790. [DOI: 10.1039/c6cp04483b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-thiocytosine (TC) and 2-thiouracil (TU) were found to react with formate radical via reductive and oxidative pathways simultaneously.
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Affiliation(s)
| | - Juan R. Alvarez-Idaboy
- Departamento de Física y Química Teórica
- Facultad de Química
- Universidad Nacional Autónoma de México
- México D. F
- Mexico
| | - Pavitra V. Kumar
- Radiation and Photochemistry Division
- Chemistry Group
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - Beena G. Singh
- Radiation and Photochemistry Division
- Chemistry Group
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
| | - K. Indira Priyadarsini
- Radiation and Photochemistry Division
- Chemistry Group
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
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12
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Sochacka E, Szczepanowski RH, Cypryk M, Sobczak M, Janicka M, Kraszewska K, Bartos P, Chwialkowska A, Nawrot B. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. Nucleic Acids Res 2015; 43:2499-512. [PMID: 25690900 PMCID: PMC4357714 DOI: 10.1093/nar/gkv109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Ks. J. Trojdena 4, 02-109 Warsaw, Poland
| | - Marek Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Magdalena Janicka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Karina Kraszewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Anna Chwialkowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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13
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Yang W, Hu Y. Conformations of 2-thiouracil in the aqueous solution and its adsorption behavior on the gold substrates explored by DFT calculations and experimental methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:399-405. [PMID: 25025312 DOI: 10.1016/j.saa.2014.06.119] [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: 04/23/2014] [Revised: 06/16/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
2-Thiouracil, a thio-derivative of uracil, may appear in various tautomeric forms due to the different positions of protons. In this paper, the adsorption behavior and conformations of 2-thiouracil on the gold substrates are inspected by means of surface-enhanced Raman scattering (SERS) and density functional theory (DFT) calculations. The results indicate that all the enhanced bands are assigned to in-plane vibration modes. Besides, most of the bands related to N and S atoms are significantly enhanced and have obvious shifts in the SERS spectra. Furthermore, the CO stretching band at 1695 cm(-1) also appears in the SERS spectra. The theoretical SERS spectra of 2TU-Au₄ and 2TU2-Au₄ complexes agree well with the experimental SERS spectra of 2-thiouracil at 0.04 mM. Meanwhile, we calculate that the binding energies for 2TU2-Au₄ and 2TU-Au₄ are ca. 70 and 50 kcal/mol, respectively. Those results above imply that the 2TU and 2TU2 conformers can exist stably in the aqueous solution and both of them are vertically chemisorbed on the gold surfaces. For the 2TU, it is adsorbed on the gold surfaces through N1H position and the sulfur atom. While the 2TU2 adsorbed on the gold substrates through the N1 site and its deprotonated sulfur atom.
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Affiliation(s)
- Wenpeng Yang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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14
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Kong D, Li Q, Chen L, Chi Y, Chen G. Capillary electrophoresis coupled with electrochemiluminescence detection for the separation and determination of thyreostatic drugs in animal feed. J Sep Sci 2014; 37:1199-205. [DOI: 10.1002/jssc.201301254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/23/2014] [Accepted: 02/24/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Dexian Kong
- School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou Fujian China
- Key Laboratory of Analysis and Detection Technology for Food Safety (Ministry of Education and Fujian Province); College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Qinglu Li
- School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou Fujian China
| | - Lichan Chen
- Key Laboratory of Analysis and Detection Technology for Food Safety (Ministry of Education and Fujian Province); College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Yuwu Chi
- Key Laboratory of Analysis and Detection Technology for Food Safety (Ministry of Education and Fujian Province); College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Guonan Chen
- Key Laboratory of Analysis and Detection Technology for Food Safety (Ministry of Education and Fujian Province); College of Chemistry; Fuzhou University; Fuzhou Fujian China
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15
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Relaxation of the T1 excited state of 2-thiothymine, its riboside and deoxyriboside-enhanced nonradiative decay rate induced by sugar substituent. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2013.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Puzzarini C, Biczysko M, Barone V, Peña I, Cabezas C, Alonso JL. Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study. Phys Chem Chem Phys 2013; 15:16965-75. [PMID: 24002739 PMCID: PMC4596004 DOI: 10.1039/c3cp52347k] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
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Sharma RK, Singh S, Tiwari R, Mandal D, Olsen CE, Parmar VS, Parang K, Prasad AK. O-Aryl α,β-d-ribofuranosides: Synthesis & highly efficient biocatalytic separation of anomers and evaluation of their Src kinase inhibitory activity. Bioorg Med Chem 2012; 20:6821-30. [DOI: 10.1016/j.bmc.2012.09.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 01/20/2023]
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Prasanthkumar KP, Suresh CH, Aravindakumar CT. Oxidation reactions of 2-thiouracil: a theoretical and pulse radiolysis study. J Phys Chem A 2012; 116:10712-20. [PMID: 23061532 DOI: 10.1021/jp303808r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of hydroxyl radical ((•)OH) with the nucleic acid base analogue 2-thiouracil (1) has been studied by pulse radiolysis experiments and DFT. The generic intermediate radicals feasible for the (•)OH reactions with 1, namely, one electron oxidation product (1(•+)), (•)OH-adducts (3(•), 4(•), and 5(•)), and H-abstracted radicals (6(•) and 7(•)), were characterized by interpreting their electronic and structural properties along with calculated energetics and UV-vis spectra. Pulse radiolysis experiments showed that the transient formed in the reaction of (•)OH with 1 in water at pH 6.5 has λ(max) at 430 nm. A bimolecular rate constant, k(2) of 9.6 × 10(9) M(-1) s(-1), is determined for this reaction via competition kinetics with 2-propanol. The experiments suggested that the transient species could be a dimer radical cation 2(•+), formed by the reaction of 1 with the radical cation 1(•+). For this reaction, an equilibrium constant of 4.7 × 10(3) M(-1) was determined. The transient formed in the reaction of 1 with pulse radiolytically produced Br(2)(•-) at pH 6.5 as well as Cl(2)(•-) at pH 1 has also produced λ(max) at 430 nm and suggested the formation of 2(•+). The calculated UV-vis spectra of the transient species (1(•+), 3(•), 4(•), 5(•), 6(•), and 7(•)) showed no resemblance to the experimental spectra, while that of 2(•+) (λ(max) = 420 nm) agreed well with the experimental value and thus confirmed the formation of 2(•+). The 420 nm peak was due to σ → σ* electronic excitation centered on a 2-center-3-electron (2c-3e) sulfur-sulfur bond [-S∴S-]. 2(•+) is the first reported example of a dimer radical cation in a pyrimidine heterocyclic system. Further, 5-C and 6-C substituted (substituents are -F, -Cl, -NH(2), -N(CH(3))(2), -OCH(3), -CF(3), -CH(3), -CH(2)CH(3), n-propyl, phenyl, and benzyl) and 5,6-disubstituted 2-thiouracil systems have been characterized by DFT and found that the reaction (1 + 1(•+) → 2(•+)) is exergonic (1.12-13.63 kcal/mol) for many of them.
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Affiliation(s)
- K P Prasanthkumar
- School of Chemical Sciences, Mahatma Gandhi University, Kottayam 686560, India
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Kraszewska K, Kaczyńska I, Jankowski S, Karolak-Wojciechowska J, Sochacka E. Desulfurization of 2-thiouracil nucleosides: conformational studies of 4-pyrimidinone nucleosides. Bioorg Med Chem 2011; 19:2443-9. [PMID: 21396827 DOI: 10.1016/j.bmc.2011.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
4-Pyrimidinone ribofuranoside (H(2)o(4)U) and 4-pyrimidinone 2'-deoxyribofuranoside (dH(2)o(4)U) were synthesized by the oxidative desulfurization of parent 2-thiouracil nucleosides with m-chloroperbenzoic acid. The crystal structures of H(2)o(4)U and dH(2)o(4)U and their conformations in solution were determined and compared with corresponding 2-thiouracil and uracil nucleosides. The absence of a large 2-thiocarbonyl/2-carbonyl group in the nucleobase moiety results in C2'-endo puckering of the ribofuranose ring (S conformer) in the crystal structure of H(2)o(4)U, which is not typical of RNA nucleosides. Interestingly, the hydrogen bonding network in the crystals of dH(2)o(4)U stabilizes the sugar moiety conformation in the C3'-endo form (N conformer), rarely found in DNA nucleosides. In aqueous solution, dH(2)o(4)U reveals a similar population of the C2'-endo conformation (65%) to that of 2'-deoxy-2-thiouridine (62%), while the 62% population of the S conformer for H(2)o(4)U is significantly different from that of the parent 2-thiouridine, for which the N conformer is dominant (71%). Such a difference may be of biological importance, as the desulfurization process of natural tRNA 2-thiouridines may occur under conditions of oxidative stress in the cell and may influence the decoding process.
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Affiliation(s)
- Karina Kraszewska
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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Zhang X, Xu YZ. NMR and UV studies of 4-thio-2'-deoxyuridine and its derivatives. Molecules 2011; 16:5655-64. [PMID: 21725278 PMCID: PMC6264492 DOI: 10.3390/molecules16075655] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 06/10/2011] [Indexed: 11/16/2022] Open
Abstract
5-Substituted-4-thio-2'-deoxyuridine nucleosides have been chemically synthesized and studied by NMR and UV spectroscopy. The results have been analyzed and discussed in connection with the previous data. The imino proton signal and the carbon signal of the thiocarbonyl group in the 5-substituted-4-thio-2'-deoxyuridines were found to be at much lower field, offering a potential for monitoring these modified bases at the DNA level. All 4-thionucleosides have strong absorptions at around 340 nm and consequently would be useful as potential UVA-induced anticancer agents.
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Affiliation(s)
- Xiaohui Zhang
- College of Environment and Chemical Engineering, Dalian University, Dalian 116622, China.
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Gourdain S, Petermann C, Martinez A, Harakat D, Clivio P. Synthesis and Photochemical Behavior of the Tetrazolo Tautomer of 2-Azido-4-pyrimidinone-2′-deoxyriboside. J Org Chem 2011; 76:1906-9. [DOI: 10.1021/jo102316r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphanie Gourdain
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Christian Petermann
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Agathe Martinez
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Dominique Harakat
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Pascale Clivio
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
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Vetter C, Kaluđerović GN, Paschke R, Kluge R, Schmidt J, Steinborn D. Synthesis, characterization and in vitro cytotoxicity studies of platinum(IV) complexes with thiouracil ligands. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.03.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kong D, Chi Y, Chen L, Dong Y, Zhang L, Chen G. Determination of thyreostatics in animal feeds by CE with electrochemical detector. Electrophoresis 2009; 30:3489-95. [DOI: 10.1002/elps.200800649] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ziemkowski P, Felczak K, Poznański J, Kulikowski T, Zieliński Z, Cieśla J, Rode W. Interactions of 2'-fluoro-substituted dUMP analogues with thymidylate synthase. Biochem Biophys Res Commun 2007; 362:37-43. [PMID: 17692822 DOI: 10.1016/j.bbrc.2007.07.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 07/19/2007] [Indexed: 11/22/2022]
Abstract
A series of 2'-fluoro-substituted dUMP/FdUMP analogues were synthesized, their interaction with human recombinant thymidylate synthase investigated, and structural (1)H and (19)F NMR study of the corresponding nucleosides performed. While 2'-F-dUMP (fluorine in the "down" configuration), in striking contrast to 2'-F-ara-UMP (fluorine in the "up" configuration) and 2',2''-diF-dUMP, showed substrate activity, 2'-F-ara-UMP and 2',2''-diF-dUMP were classic inhibitors, and 2',5-diF-ara-UMP behaved as a strong slow-binding inhibitor, suggesting the 2'-F substituent in the "up" position to interfere with the active center cysteine thiol addition to the pyrimidine C(6) and the pyrimidine C(5)-F to prevent this interference. In support, the direct through space heteronuclear coupling J(HF) was observed for the fluorine "up" derivatives, 2'-F-ara-U and 2',5-diF-ara-U, causing the splitting of the H(6) resonance lines. The absence of such splitting in 2',2''-diF-dUrd, indicating an unusual orientation of the base in relation to the furanose, was associated with an exceptionally weak interaction with the enzyme.
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Affiliation(s)
- Przemysław Ziemkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Krzysztof Felczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Tadeusz Kulikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawińskiego Street, 02-106 Warszawa, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warszawa, Poland.
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García J, Díaz-Rodríguez A, Fernandez S, Sanghvi YS, Ferrero M, Gotor V. New Concept for the Separation of an Anomeric Mixture of α/β-d-Nucleosides through Regioselective Enzymatic Acylation or Hydrolysis Processes. J Org Chem 2006; 71:9765-71. [PMID: 17168595 DOI: 10.1021/jo062033o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An efficient and high yield protocol for the synthesis and separation of 3'- and/or 5'-protected alpha-2'-deoxynucleosides has been developed through regioselective acylation/deacylation processes catalyzed by enzymes. Pseudomonas cepacia lipase (PSL-C) was found to be highly chemo- and regioselective toward the 3'-position of the beta-2'-deoxynucleoside derivatives, whereas PSL-C displayed opposite selectivity toward the 5'-position for the corresponding alpha-anomer. The successful application of this protocol was demonstrated by a convenient separation of an alpha/beta-mixture of thymidine derivatives from an industrial waste stream. Furthermore, this technique was also applied for the separation of an anomeric mixture of 2'-deoxy-2'-fluoro-alpha/beta-arabinonucleosides that are useful building blocks for the antisense constructs.
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Affiliation(s)
- Javier García
- Departamento de Química OrgAnica e InorgAnica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
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Chi Y, Duan J, Lin S, Chen G. Flow Injection Analysis System Equipped with a Newly Designed Electrochemiluminescent Detector and Its Application for Detection of 2-Thiouracil. Anal Chem 2006; 78:1568-73. [PMID: 16503609 DOI: 10.1021/ac051508t] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new flow injection analysis (FIA) system equipped with an electrochemiluminescent (ECL) detector has been developed and applied for the ECL detection of 2-thiouracil. The FIA-ECL system used a specially designed flow-through ECL thin-layer cell to reduce the dead volume, the IR drop across the cell, and the probability of accumulation of gas bubbles in the cell. It was thus envisioned to improve the detection limit of the FIA-ECL method. After being established, the new FIA-ECL system was used to investigate the ECL response of 2-thiouracil in the presence of the ECL of Ru(bpy)3(2+). It was found that 2-thiouracil could enhance the ECL of Ru(bpy)3(2+) over a wide pH range (pH 4.0-12.0). A highly sensitive method for detection of 2-thiouracil in biological samples was developed by the new FIA-ECL system after optimizing several experimental conditions, such as the applied potential of the working electrode, the pH value of the aqueous solution, the flow rate of carrier solution, and the concentration of Ru(bpy)3(2+).
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Affiliation(s)
- Yuwu Chi
- MOE Key Laboratory of Analysis and Detection Technology for Food Safety, and Department of Chemistry, Fuzhou University, Fuzhou, Fujian, 350002, China
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Jarmuła A, Cieplak P, Leś A, Rode W. Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP. J Comput Aided Mol Des 2004; 17:699-710. [PMID: 15068368 DOI: 10.1023/b:jcam.0000017377.07094.2e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Free energy perturbation calculations have been applied to evaluate the relative free energies of binding of 2'-deoxyuridine-5'-monophosphate (dUMP) and its 2- and/or 4-thio and/or 5-fluoro analogues to the wild-type E. coli thymidylate synthase (ecTS). The results accurately reproduce experimentally measured differences in the free energy of binding of dUMP versus 5-fluoro-dUMP to thymidylate synthase. They indicate that preferred binding of dUMP compared to 5-fluoro-dUMP in the binary complex is equally related to (i) more favorable electrostatic interactions of the dUMP molecule in the enzyme active site, and (ii) its less favorable solvation in the aqueous solution. The relative free energies of binding in the binary complex show moderate and qualitatively indistinguishable discrimination among the studied fluorinated and non-fluorinated 2- and/or 4-thio analogues of dUMP. The binding free energies of monothio analogues of dUMP and 5-fluoro-dUMP correspond quite well with experimentally measured activities of these nucleotides in the thymidylate synthase reaction. On the other hand, the binding free energies of both dithio analogues, 2,4-dithio-dUMP and 2,4-dithio-FdUMP, show lack of such correlation. The latter suggests that very low activities of the dithio analogues of dUMP and 5-fluoro-dUMP may relate more to the covalent reaction of these nucleotides within the ternary complex with TS and 5,10-methylenetetrahydrofolate, than to their pre-covalent binding. We speculate that a lack of substrate activity of 2,4-dithio-dUMP is related to the high aromaticity of its pyrimidine ring that prevents the Michael addition of the active site cysteine thiol to the pyrimidine C6 atom. A stronger affinity of the fluorinated analogues of dUMP to thymidylate synthase, compared to the non-fluorinated congeners, results from the fluorine substituent producing a local strain in the C6 region in the pyrimidine ring, thus sensitizing C6 to the Michael addition of the cysteine thiol.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland.
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Palafox MA, Rastogi VK, Tanwar RP, Mittal L. Vibrational frequencies and structure of 2-thiouracil by Hartree-Fock, post-Hartree-Fock and density functional methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2003; 59:2473-2486. [PMID: 12963443 DOI: 10.1016/s1386-1425(02)00409-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Vibrational study of the biomolecule 2-thiouracil was carried out. Ab initio and density functional calculations were performed to assign the experimental spectra. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted frequencies of 2-thiouracil. Several scaling procedures were used. The geometry structure of the molecule was determined. The effect of sulfur substitution at C2 position in the uracil molecule, on the N1-H and N3-H frequencies and intensities reflects changes in proton donor abilities of these groups. Calculations with the 6-31 G** basis set with HF and DFT methods appear in general to be useful for interpretation of the general features of the IR and Raman spectra of the molecule. Using specific scale factors a very small error was obtained. The use of these specific scale factors resolve and correct some of the controversial assignments in the literature.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Quimica-Fisica (Espectroscopia), Facultad de Ciencias Quimicas, Universidad, Compultense, Madrid 28040, Spain
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Elgemeie GH, Ahmed MA. A new class of biheterocyclic thioglycosides from pyridine-2-(1H)-thiones. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:837-47. [PMID: 12537025 DOI: 10.1081/ncn-120016511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A reported method for preparation of a new class of biheterocyclic thioglycosides via reaction of pyridinethiones with 2,3,4,6-tetra-O-acetyl-alpha-D-gluco- and galactopyranosyl bromides has been studied.
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Affiliation(s)
- Galal H Elgemeie
- Chemistry Department, Faculty of Science, Helwan University, Ain-Helwan, Cairo, Egypt.
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Elgemeie GH, Kamal EA. Pyrimidinethione nucleosides and their deaza analogues. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:287-325. [PMID: 12182345 DOI: 10.1081/ncn-120006827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The methods of preparation, structure, chemical properties and synthetic potentiality of pyrimidinethione nucleosides and their deaza analogues are reported.
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Affiliation(s)
- Galal H Elgemeie
- Chemistry Department, Faculty of Science, Helwan University, Ain-Helwan, Cairo, Egypt.
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Chambert S, Décout JL. RECENT DEVELOPMENTS IN THE SYNTHESIS, CHEMICAL MODIFICATIONS AND BIOLOGICAL APPLICATIONS OF SULFUR MODIFIED NUCLEOSIDES, NUCLEOTIDES AND OLIGONUCLEOTIDES. ORG PREP PROCED INT 2002. [DOI: 10.1080/00304940209355745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gołos B, Dzik JM, Kazimierczuk Z, Cieśla J, Zieliński Z, Jankowska J, Kraszewski A, Stawiński J, Rode W, Shugar D. Interaction of thymidylate synthase with the 5'-thiophosphates, 5'-dithiophosphates, 5'-H-phosphonates and 5'-S-thiosulfates of 2'-deoxyuridine, thymidine and 5-fluoro-2'-deoxyuridine. Biol Chem 2001; 382:1439-45. [PMID: 11727827 DOI: 10.1515/bc.2001.177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
New analogs of dUMP, dTMP and 5-fluoro-dUMP, including the corresponding 5'-thiophosphates (dUMPS, dTMPS and FdUMPS), 5'-dithiophosphates (dUMPS2, dTMPS2 and FdUMPS2), 5'-H-phosphonates (dUMP-H, dTMP-H and FdUMP-H) and 5'-S-thiosulfates (dUSSO3, dTSSO3 and FdUSSO3), have been synthesized and their interactions studied with highly purified mammalian thymidylate synthase. dUMPS and dUMPS2 proved to be good substrates, and dTMPS and dTMPS2 classic competitive inhibitors, only slightly weaker than dTMP. Their 5-fluoro congeners behaved as potent, slow-binding inhibitors. By contrast, the corresponding 5'-H-phosphonates and 5'-S-thiosulfates displayed weak activities, only FdUMP-H and FdUSSO3 exhibiting significant interactions with the enzyme, as weak competitive slow-binding inhibitors versus dUMR The pH-dependence of enzyme time-independent inhibition by FdUMP and FdUMPS was found to correlate with the difference in pKa values of the phosphate and thiophosphate groups, the profile of FdUMPS being shifted (approximately 1 pH unit) toward lower pH values, so that binding of dUMP and its analogs is limited by the phosphate secondary hydroxyl ionization. Hence, together with the effects of 5'-H-phosphonate and 5'-S-thiosulfate substituents, the much weaker interactions of the nucleotide analogs (3-5 orders of magnitude lower than for the parent 5'-phosphates) with the enzyme is further evidence that the enzyme's active center prefers the dianionic phosphate group for optimum binding.
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Affiliation(s)
- B Gołos
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa
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Anderson AC, O'Neil RH, Surti TS, Stroud RM. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. ACTA ACUST UNITED AC 2001; 8:445-57. [PMID: 11358692 DOI: 10.1016/s1074-5521(01)00023-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Using fixed receptor sites derived from high-resolution crystal structures in structure-based drug design does not properly account for ligand-induced enzyme conformational change and imparts a bias into the discovery and design of novel ligands. We sought to facilitate the design of improved drug leads by defining residues most likely to change conformation, and then defining a minimal manifold of possible conformations of a target site for drug design based on a small number of identified flexible residues. RESULTS The crystal structure of thymidylate synthase from an important pathogenic target Pneumocystis carinii (PcTS) bound to its substrate and the inhibitor, BW1843U89, is reported here and reveals a new conformation with respect to the structure of PcTS bound to substrate and the more conventional antifolate inhibitor, CB3717. We developed an algorithm for determining which residues provide 'soft spots' in the protein, regions where conformational adaptation suggests possible modifications for a drug lead that may yield higher affinity. Remodeling the active site of thymidylate synthase with new conformations for only three residues that were identified with this algorithm yields scores for ligands that are compatible with experimental kinetic data. CONCLUSIONS Based on the examination of many protein/ligand complexes, we develop an algorithm (SOFTSPOTS) for identifying regions of a protein target that are more likely to accommodate plastically to regions of a drug molecule. Using these indicators we develop a second algorithm (PLASTIC) that provides a minimal manifold of possible conformations of a protein target for drug design, reducing the bias in structure-based drug design imparted by structures of enzymes co-crystallized with inhibitors.
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Affiliation(s)
- A C Anderson
- Department of Biochemistry and Biophysics, University of California at San Francisco, Box 0448, 94143-0448, USA.
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Poznański J, Felczak K, Bretner M, Kulikowski T, Remin M. 1H NMR Conformational Study of a Variety of α-Anomers of C5-Substituted 2′-Deoxyuridines: Comparison to Their Antiherpetic β Counterparts. Biochem Biophys Res Commun 2001; 283:1142-9. [PMID: 11355892 DOI: 10.1006/bbrc.2001.4921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although alpha-nucleosides are not found in nucleic acid, they do occur as constituents of smaller molecules in living cells, e.g., in vitamin B(12). There are now several examples of alpha-nucleosides exerting a biological activity in some instances equal to, or even exceeding, that of the corresponding beta-anomer. Examples include growth inhibitory properties against mouse leukemia cells and antitumor activity. From stereochemical point of view, alpha-anomers serve as references for studying of interaction of the base with the sugar moiety in beta-anomers and may help in better understanding of structure-activity relationships. One important problem preventing conformational analysis of alpha nucleosides is uncertainty in the determination of vicinal coupling constants from simulation of overlapping sugar proton resonances of strongly coupled spin systems. A successful resolution of near-isochronous H3' and H4' resonances made possible a full conformational analysis for a series of alpha-anomers C5-substituted 2'-deoxyuridines, including methyl, ethyl, isopropyl, fluor, vinyl, and bromovinyl, in comparison to their beta counterparts. Conformation of the sugar ring is determined from proton-proton coupling constants and described in terms of pseudorotation between two main puckering domains C2'endo (S) and C3'endo (N). A thorough analysis of chemical shifts as well as conformation of the sugar ring and C4'-C5' rotamers made possible determination of conformational preferences in equilibrium about the glycosidic bond between two regions, anti and syn. This work provides insights into the role of anomeric configuration of the base in conformational behavior of the sugar moiety, a link in the backbone of nucleic acids.
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Affiliation(s)
- J Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, Warsaw, 02-106, Poland
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37
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Naumov P, Anastasova F. Experimental and theoretical vibrational study of isatin, its 5-(NO2, F, Cl, Br, I, CH3) analogues and the isatinato anion. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:469-481. [PMID: 11300558 DOI: 10.1016/s1386-1425(00)00393-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Effects of 5-R substitution (R = NO2, F, Cl, Br, I, CH3) and N-deprotonation on the 4000-400 cm(-1) region of the low temperature FT IR spectrum and the molecular structure of solid isatin are investigated. Harmonic IR spectra and molecular geometries of the 5-R isatins (except for Br and I analogues) are calculated at the HF/6-31G(d, p) level and compared with the experimental solid-state data. In general, substitution has small effect on the molecular structure and the IR spectrum of isatin. The v(CO) triplet in the IR spectra of isatin and its 5-substituted analogues is resulted by vibrational splitting of the out-of-phase CO stretching, v(op)[(CO)2]. While the frequency of the v(op)[(CO)2] mode is relatively less affected by 5-substitution and mainly depends on the substituent mass, the frequency of the in-phase stretching, v(ip)[(CO)2], is strongly sensitive to both mass and electronic properties of the substituent. Substitution at C5 has relatively greater influence on the electron density and the force constant of the amide than on the ketone carbonyl group. Strong electron-donors shorten and stabilize the unusually long alpha-dicarbonyl CC bond, while electron-accepting groups tend to stretch this bond further. N-Deprotonation brings to elongation of the five membered-ring along the N-C(CO(ketone)) vector and expansion of the bonds within the alpha-dicarbonyl part. Theoretical v(CO) frequency of isatin is lowered for about 180 cm(-1) upon conversion into isatinato ion. Harmonic vibrational analysis reveals that only the highest-frequency v(CO) mode of the isolated isatinato anion can be considered good group vibration for empirical assignments in spectra of solid isatinates. Owing to the solid-state influences on the v[(CO)2] modes, no reliable spectra structure correlations could be established from the present experimental spectroscopic data.
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Affiliation(s)
- P Naumov
- Institute of Chemistry, Faculty of Sciences, Sv. Kiril i Metodij University, Skopje, Macedonia.
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38
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Kryachko E, Nguyen MT, Zeegers-Huyskens T. Thiouracils: Acidity, Basicity, and Interaction with Water. J Phys Chem A 2001. [DOI: 10.1021/jp003703b] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eugene Kryachko
- Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
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39
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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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40
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Jarmuła A, Anulewicz R, Leś A, Cyrański MK, Adamowicz L, Bretner M, Felczak K, Kulikowski T, Krygowski TM, Rode W. Crystal structures of 5-fluoro-dUrd and its 2 and/or 4-thio analogues: models of substituted dUMP pyrimidine ring interacting with thymidylate synthase. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1382:277-86. [PMID: 9540799 DOI: 10.1016/s0167-4838(97)00169-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In order to understand the influence on thymidylate synthase interactions with dUMP analogues of the pyrimidine ring 2- and/or 4-thio, and 5-fluoro substitutions, X-ray diffractions by crystals of 5-fluoro-dUrd and its 2- and 4-thio, and 2,4-dithio analogues were measured, the four structures solved and refined. The following conclusions were suggested by results of comparative analyses of structural parameters (bond lengths, valence angles), followed by theoretical considerations based on calculated resonance structure distributions and aromaticity indices of the uracil, thiouracil, fluorouracil and fluorothiouracil rings. The effect of 4-thio substitution of FdUMP, altering specificity of inactivation of thymidylate synthases from various sources, is probably due to weaker proton acceptor power of the 4-thio substituent and increasing acidity (enhanced proton-donor power) of the N(3)-H moiety, resulting in an impaired fitness into the network of hydrogen bonds in the enzyme active center cleft. 2,4-Dithio substitution results in (i) impaired pyrimidine ring recognition by the enzyme active center, due to the 4-thio substituent (ii) increased pyrimidine ring aromaticity in dUMP, leading to resistance of C(6) to nucleophilic attack by the enzyme active center cysteine and (iii) altered planarity of the pyrimidine ring and deflections, with respect to the ring plane, of substituents at C(2), C(4) and C(5). 5-Fluoro substitution apparently activates the pyrimidine ring towards the interaction with thymidylate synthase by producing local strain, which results in an increased reactivity as predicted by the Walsh-Bent rule.
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Affiliation(s)
- A Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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41
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Abstract
Thymidylate synthase (TS) is a very interesting target in antiproliferative diseases. Its inhibition causes thimineless death of the cells and compounds inhibiting TS are widely used in anticancer therapy. The classical antifolate TS inhibitors are structural analogs of the folate cofactor; they often share the same metabolic pathways and this causes the development of resistance inside the cells. A detailed analysis of the available x-ray crystal structures of the complexes of the enzyme with different substrates and inhibitors support the finding of a structural basis of their biological activity. TS inhibitors nonstructural analog of folate, non-analog antifolate inhibitors (NAAI), are welcome as a new interesting research topic. Among the most recent and interesting ones, compounds from Agouron related to the indole structure, are independent on the folate metabolism, highly active and specific for human TS. Other compounds, phthalein derivatives, can inhibit TS enzymes from various sources and show an interesting biological activity profile: they inhibit better bacterial and fungal TS than human TS. The x-ray crystal structures of some of these inhibitors with TS show that they bind in a different binding site from that of the classical folate TS inhibitors. This indicates a potential allosteric binding site useful for future drug discovery studies.
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Affiliation(s)
- M P Costi
- Dipartimento di Scienze Farmaceutiche, Universitá di Modena, Italy
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42
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Bretner M, Felczak K, Dzik JM, Golos B, Rode W, Drabikowska A, Poznanski J, Krawiec K, Piasek A, Shugar D, Kulikowski T. Thiated Pyrimidine Deoxynucleoside Analogues, Potential Chemotherapeutic Agents, and Substrates/Inhibitors in Various Enzyme Systems. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006174] [Citation(s) in RCA: 4] [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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43
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Dzik JM, Bretner M, Kulikowski T, Gołos B, Jarmuła A, Poznański J, Rode W, Shugar D. Synthesis and interactions with thymidylate synthase of 2,4-dithio analogues of dUMP and 5-fluoro-dUMP. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1293:1-8. [PMID: 8652614 DOI: 10.1016/0167-4838(95)00219-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The 2,4-dithio analogues of 2'-deoxyuridine and 2'-deoxy-5-fluorouridine have been synthesized by thiation of the previously described 2-thio analogues, and then phosphorylated enzymatically or chemically to yield 2,4-dithio-dUMP and 2,4-dithio-5-fluoro-dUMP. In striking contrast to the 2-thio and 4-thio analogues of dUMP, which are good substrates of thymidylate synthase, 2,4-dithio-dUMP is not a substrate. But, surprisingly, it is a competitive inhibitor, relative to dUMP, of the purified enzymes from both parental and FdUrd-resistant L1210 cells, with K(i) values of 32 microM and 55 microM, respectively. Although 2,4-dithio-5-fluoro-dUMP behaved as a typical slow-binding inhibitor of the enzyme, its K(i) value was 10(3)-10(4)-fold higher than those for the corresponding 2-thio and 4-thio congeners. Similarly, 2,4-dithio-FdUrd was a much weaker inhibitor of tumour cell growth (IC50 approximately 10(-5)M) than FdUrd (IC50 approximately 10(-9)M), 2-thio-FdUrd(IC50 approximately 10(-7)M) or 4-thio-FdUrd (IC50 approximately 5x10(-8)M), while with 2,4-dithio-dUrd no influence on cell growth could be observed. Theoretical considerations, based on calculated aromaticities of the uracil and thiouracil rings, suggest that lack of substrate activity of 2,4-dithio-dUMP may result from increased pyrimidine ring aromaticity of the latter, leading to resistance of C(6) to nucleophilic attack by the enzyme active center cysteine.
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Affiliation(s)
- J M Dzik
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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44
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Stout TJ, Stroud RM. The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition. Structure 1996; 4:67-77. [PMID: 8805515 DOI: 10.1016/s0969-2126(96)00010-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Thymidylate synthase (TS) is critical to DNA synthesis as it catalyzes the rate limiting step in the only biosynthetic pathway for deoxythymidine monophosphate (dTMP) production. TS is therefore an important target for anti-proliferative and anti-cancer drug design. The TS enzymatic mechanism involves the reductive methylation of the substrate, deoxyuridine monophosphate (dUMP), by transfer of a methylene group from the co-factor, methylenetetrahydrofolate (CH2H4folate), resulting in the production of deoxythymidine monophosphate (dTMP) and dihydrofolate (H2folate). Previous drug design efforts based on co-factor analogues have produced good inhibitors of TS, but poor bioavailability and toxicity have limited their usefulness. BW1843U89, a folate analogue, is a recently developed compound which is an exceptionally strong inhibitor (Ki = 0.09 nM), has good bioavailability and in clinical trials thus far has not demonstrated significant toxicity. RESULTS We report the crystal structure of E. coli TS in ternary complex with dUMP and BW1843U89 at 2.0 A resolution. Although the benzoquinazoline ring system of the inhibitor binds to TS in much the same manner as previously determined for H2folate and CB3717, the larger size of the ligand is accommodated by the enzyme through a local distortion of the active site, that is not strictly conserved in both monomers in the asymmetric unit. Several conserved waters that had been previously implicated in mechanistic roles have been displaced. CONCLUSIONS BW1843U89 forms a ternary complex with dUMP and completes with CH2H4 folate at the active site. Inhibition of TS by BW1843U89 shows four unique aspects in its mechanism of action. BW1843U89 prevents the Michael addition of dUMP to Cys146, in contrast to the mechanisms implicated from crystallography of other quinazoline based inhibitors; displaces a catalytic water from the active site; reorders a peptide loop (Leu72-Trp83) in the active site; and is unique amongst the antifolates in inactivating TS at a stoichiometric ratio of one molecule per TS dimer. Thus, it exploits the principles of negative cooperativity that are increasingly being recognized in the catalytic mechanism of the enzyme per se. The structure suggests that this 'half-the-sites' effect is catalytic and not related to ligand binding. Therefore BW1843U89 is both a competitive inhibitor (at the binding site) and a non-competitive inhibitor at the other site.
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Affiliation(s)
- T J Stout
- Department of Biochemistry and Biophysics, School of Medicine, University of California at San Francisco 94143-0448, USA
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45
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Cieśla J, Gołos B, Dzik JM, Pawełczak K, Kempny M, Makowski M, Bretner M, Kulikowski T, Machnicka B, Rzeszotarska B. Thymidylate synthases from Hymenolepis diminuta and regenerating rat liver: purification, properties, and inhibition by substrate and cofactor analogues. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1249:127-36. [PMID: 7599165 DOI: 10.1016/0167-4838(95)00032-p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Comparative studies of thymidylate synthases, isolated from the tapeworm, Hymenolepis diminuta, and regenerating liver of its host, rat, aimed at a possibility of specific inhibition of the helminthic enzyme, are presented. While similar in structure (dimers with monomer molecular masses of 33.7 kDa and 34.9 kDa, respectively) and parameters describing interactions with substrates and products, the tapeworm and rat enzymes differed in the dependences of reaction velocity on temperature (Arrhenius plots biphasic and linear, respectively). The tapeworm, compared with the host, enzyme was less sensitive to the competitive slow-binding inhibition by 5-fluoro-dUMP and its 2-thio congener, but equally sensitive to inhibition by 4-thio-5-fluoro-dUMP, N4-hydroxy-dCMP and N4-hydroxy-5-fluoro-dCMP, the latter being more potent inhibitor of the parasite enzyme than 5-fluoro-dUMP. alpha-Anomer of 5-fluoro-dUMP behaved as a very weak competitive slow-binding inhibitor of both enzymes. Both enzymes differed markedly in sensitivity to inhibition by 10-propargyl-5,8-dideazafolate and its di- and triglutamates (pddPteGlu1-3), with pddPteGlu1 being stronger inhibitor of the mammalian enzyme, but pddPteGlu3 showing opposite specificity. Sulfonamidobenzoylglutamate analogue of pddPteGlu (pddPteSO2Glu) and 2-desamino-2-methyl derivative of this analogue (CH3pddPteSO2Glu) were weaker inhibitors of both enzymes than the parent compound. Substitution of the glutamyl residue in CH3pddPteSO2Glu with either norvaline or alanine increased inhibition potency, whereas similar substitutions with glycine, valine or phenylglycine were without a distinct effect with the host enzyme but weakened inhibition of the tapeworm enzyme.
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Affiliation(s)
- J Cieśla
- Nencki Institute of Experimental Biology, Warsaw, Poland
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