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Li XY, Luo YT, Wang YH, Yang ZX, Shang YZ, Guan QX. Anti-inflammatory effect and antihepatoma mechanism of carrimycin. World J Gastroenterol 2023; 29:2134-2152. [PMID: 37122599 PMCID: PMC10130968 DOI: 10.3748/wjg.v29.i14.2134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND New drugs are urgently needed for the treatment of liver cancer, a feat that could be feasibly accomplished by finding new therapeutic purposes for marketed drugs to save time and costs. As a new class of national anti-infective drugs, carrimycin (CAM) has strong activity against gram-positive bacteria and no cross resistance with similar drugs. Studies have shown that the components of CAM have anticancer effects.
AIM To obtain a deeper understanding of CAM, its distribution, metabolism and anti-inflammatory effects were assessed in the organs of mice, and its mechanism of action against liver cancer was predicted by a network pharmacology method.
METHODS In this paper, the content of isovaleryl spiramycin III was used as an index to assess the distribution and metabolism of CAM and its effect on inflammatory factors in various mouse tissues and organs. Reverse molecular docking technology was utilized to determine the target of CAM, identify each target protein based on disease type, and establish a target protein-disease type network to ascertain the effect of CAM in liver cancer. Then, the key action targets of CAM in liver cancer were screened by a network pharmacology method, and the core targets were verified by molecular docking and visual analyses.
RESULTS The maximum CAM concentration was reached in the liver, kidney, lung and spleen 2.5 h after intragastric administration. In the intestine, the maximum drug concentration was reached 0.5 h after administration. In addition, CAM significantly reduced the interleukin-4 (IL-4) levels in the lung and kidney and especially the liver and spleen; moreover, CAM significantly reduced the IL-1β levels in the spleen, liver, and kidney and particularly the small intestine and lung. CAM is predicted to regulate related pathways by acting on many targets, such as albumin, estrogen receptor 1, epidermal growth factor receptor and caspase 3, to treat cancer, inflammation and other diseases.
CONCLUSION We determined that CAM inhibited inflammation. We also predicted the complex multitargeted effects of CAM that involve multiple pathways and the diversity of these effects in the treatment of liver cancer, which provides a basis and direction for further clinical research.
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Affiliation(s)
- Xiu-Yan Li
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yu-Ting Luo
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yan-Hong Wang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Zhi-Xin Yang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Yu-Zhou Shang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
| | - Qing-Xia Guan
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
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Ibrahim MH, El Menofy NG, El Kiki SM, Sherbiny FF, Ismail MMF. Development of fluorinated nicotinonitriles and fused candidates as antimicrobial, antibiofilm, and enzyme inhibitors. Arch Pharm (Weinheim) 2022; 355:e2200040. [PMID: 35411641 DOI: 10.1002/ardp.202200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/09/2022]
Abstract
The antimicrobial assessments of two new series of nicotinonitriles and pyrido[2,3-d]pyrimidines were performed using amoxicillin and nystatin as reference standards. Outstanding antifungal activities were achieved by some target compounds; for instance, compounds 7 and 9 displayed a minimal inhibitory concentration (MIC) value of 1.95 µg/ml toward Candida albicans, compound 11 showed a potent anti-Rhizopus effect (MIC 1.95 µg/ml) and compound 14 elicited remarkable antifungal effects against both Aspergillis niger and C. albicans (MIC 1.95 µg/ml). However, pyrido[2,3-d]pyrimidines 12, 14, and 16 showed moderate antibacterial activities against some gram-negative bacteria. The antibiofilm results of these compounds against resistant strains of Proteus mirabilis were better than those of Pseudomonas aeruginosa. Docking studies of these hits at the DNA gyrase active site revealed affinity and docking scores comparable to that of the reference standards. Gyrase-inhibitory activities revealed that 14 (IC50 = 0.31 µM) is the most potent hit as DNA gyrase A inhibitor; it exhibited 1.66-fold the activity of ciprofloxacin (IC50 = 0.50 µM) and it was a 44.3 times more potent gyrase B inhibitor (IC50 = 0.04 µM) than novobiocin (IC50 = 1.77 µM). Regarding its antifungal activity, it displayed 0.78% of the fluconazole activity as a 14α-demethylase inhibitor. The cytotoxicity of 12, 14, and 16 on human diploid lung fibroblasts (WI38 cells) ensured their safety. Moreover, they are orally bioavailable with no permeation of the blood-brain barrier.
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Affiliation(s)
- Mona H Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Nagwan G El Menofy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Shereen M El Kiki
- Department of Health Radiation Research, National Centre for Radiation Research and Technology, Atomic Energy Authority, Cairo, Egypt
| | - Farag F Sherbiny
- Department of Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Magda M F Ismail
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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3
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Bhilare NV, Auti PB, Marulkar VS, Pise VJ. Diverse Thiophenes as Scaffolds in Anti-cancer Drug Development: A Concise Review. Mini Rev Med Chem 2021; 21:217-232. [PMID: 33267760 DOI: 10.2174/1389557520666201202113333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/14/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Thiophenes are one of the abundantly found heterocyclic ring systems in many biologically active compounds. Moreover, various substituted thiophenes exert numerous pharmacological actions on account of their isosteric resemblance with compounds of natural origin, thus rendering them with diverse actions like antibacterial, antifungal, antiviral, anti-inflammatory, analgesic, antiallergic, hypotensives, etc. In this review, we specifically explore the chemotherapeutic potential of a variety of structures consisting of thiophene scaffolds as prospective anticancer agents.
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Affiliation(s)
- Neha V Bhilare
- Department of Pharmaceutical Chemistry, Arvind Gavali College of Pharmacy, Satara-415004, Maharashtra, India
| | - Pratibha B Auti
- Department of Pharmaceutical Chemistry, Sinhagad Institute of Pharmacy, Narhe, Pune-411041, Maharashtra, India
| | - Vinayak S Marulkar
- Department of Pharmaceutical Chemistry, Arvind Gavali College of Pharmacy, Satara-415004, Maharashtra, India
| | - Vilas J Pise
- Department of Pharmaceutical Chemistry, Arvind Gavali College of Pharmacy, Satara-415004, Maharashtra, India
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4
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Yang C, Pohl R, Tichý M, Gurská S, Pavliš P, Džubák P, Hajdúch M, Hocek M. Synthesis, Photophysical Properties, and Biological Profiling of Benzothieno-Fused 7-Deazapurine Ribonucleosides. J Org Chem 2020; 85:8085-8101. [PMID: 32432875 DOI: 10.1021/acs.joc.0c00927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Two isomeric series of benzothieno-fused 7-deazapurine (benzo[4',5']thieno[3',2':4,5]- and benzo[4',5']thieno[2',3':4,5]pyrrolo[2,3-d]pyrimidine) ribonucleosides were designed and synthesized. Key steps of the synthesis included the Negishi coupling of zincated dichloropyrimidine with 2- or 3-iodobenzothiophene followed by azidation, thermal or photochemical cyclization, glycosylation, and final functionalization at position 6 through cross-couplings or nucleophilic substitutions. Deprotection gave the final nucleosides, some of which showed moderate cytotoxic and antiviral activity. Most of the free nucleosides showed moderate to strong fluorescence with emission maxima of 362-554 nm. 2'-Deoxyribonucleoside and its 5'-O-triphosphate were also prepared from benzothieno-fused 7-deazaadenine derivative, and the triphosphate was a good substrate for KOD XL DNA polymerase in primer extension synthesis of modified DNA which exerted a weak fluorescence which was slightly enhanced in double-stranded DNA as compared to single-stranded oligonucleotides.
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Affiliation(s)
- Chao Yang
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská 5, CZ-77515 Olomouc, Czech Republic
| | - Petr Pavliš
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská 5, CZ-77515 Olomouc, Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská 5, CZ-77515 Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital in Olomouc, Faculty of Medicine and Dentistry, Hněvotínská 5, CZ-77515 Olomouc, Czech Republic
| | - Michal Hocek
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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5
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Vichier-Guerre S, Ku TC, Pochet S, Seley-Radtke KL. An Expedient Synthesis of Flexible Nucleosides through Enzymatic Glycosylation of Proximal and Distal Fleximer Bases. Chembiochem 2020; 21:1412-1417. [PMID: 31899839 PMCID: PMC7228337 DOI: 10.1002/cbic.201900714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 01/24/2023]
Abstract
The structurally unique “fleximer” nucleosides were originally designed to investigate how flexibility in a nucleobase could potentially affect receptor–ligand recognition and function. Recently they have been shown to have low‐to‐sub‐micromolar levels of activity against a number of viruses, including coronaviruses, filoviruses, and flaviviruses. However, the synthesis of distal fleximers in particular has thus far been quite tedious and low yielding. As a potential solution to this issue, a series of proximal fleximer bases (flex‐bases) has been successfully coupled to both ribose and 2′‐deoxyribose sugars by using the N‐deoxyribosyltransferase II of Lactobacillus leichmannii (LlNDT) and Escherichia coli purine nucleoside phosphorylase (PNP). To explore the range of this facile approach, transglycosylation experiments on a thieno‐expanded tricyclic heterocyclic base, as well as several distal and proximal flex‐bases were performed to determine whether the corresponding fleximer nucleosides could be obtained in this fashion, thus potentially significantly shortening the route to these biologically significant compounds. The results of those studies are reported herein.
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Affiliation(s)
- Sophie Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 28, rue du Dr Roux, 75015, Paris, France
| | - Therese C Ku
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS UMR3523, 28, rue du Dr Roux, 75015, Paris, France
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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6
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Design and synthesis of novel heterofused pyrimidine analogues as effective antimicrobial agents. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.105] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Shah R, Verma PK. Therapeutic importance of synthetic thiophene. Chem Cent J 2018; 12:137. [PMID: 30564984 PMCID: PMC6768136 DOI: 10.1186/s13065-018-0511-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 12/04/2018] [Indexed: 11/12/2022] Open
Abstract
Thiophene and its substituted derivatives are very important class of heterocyclic compounds which shows interesting applications in the field of medicinal chemistry. It has made an indispensable anchor for medicinal chemists to produce combinatorial library and carry out exhaustive efforts in the search of lead molecules. It has been reported to possess a wide range of therapeutic properties with diverse applications in medicinal chemistry and material science, attracting great interest in industry as well as academia. It has been proven to be effectual drugs in present respective disease scenario. They are remarkably effective compounds both with respect to their biological and physiological functions such as anti-inflammatory, anti-psychotic, anti-arrhythmic, anti-anxiety, anti-fungal, antioxidant, estrogen receptor modulating, anti-mitotic, anti-microbial, kinases inhibiting and anti-cancer. Thus the synthesis and characterization of novel thiophene moieties with wider therapeutic activity is a topic of interest for the medicinal chemist to synthesize and investigate new structural prototypes with more effective pharmacological activity. However, several commercially available drugs such as Tipepidine, Tiquizium Bromides, Timepidium Bromide, Dorzolamide, Tioconazole, Citizolam, Sertaconazole Nitrate and Benocyclidine also contain thiophene nucleus. Therefore, it seems to be a requirement to collect recent information in order to understand the current status of the thiophene nucleus in medicinal chemistry research.
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Affiliation(s)
- Rashmi Shah
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Prabhakar Kumar Verma
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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8
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Seley-Radtke KL, Yates MK. The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold. Antiviral Res 2018; 154:66-86. [PMID: 29649496 PMCID: PMC6396324 DOI: 10.1016/j.antiviral.2018.04.004] [Citation(s) in RCA: 307] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023]
Abstract
This is the first of two invited articles reviewing the development of nucleoside-analogue antiviral drugs, written for a target audience of virologists and other non-chemists, as well as chemists who may not be familiar with the field. Rather than providing a simple chronological account, we have examined and attempted to explain the thought processes, advances in synthetic chemistry and lessons learned from antiviral testing that led to a few molecules being moved forward to eventual approval for human therapies, while others were discarded. The present paper focuses on early, relatively simplistic changes made to the nucleoside scaffold, beginning with modifications of the nucleoside sugars of Ara-C and other arabinose-derived nucleoside analogues in the 1960's. A future paper will review more recent developments, focusing especially on more complex modifications, particularly those involving multiple changes to the nucleoside scaffold. We hope that these articles will help virologists and others outside the field of medicinal chemistry to understand why certain drugs were successfully developed, while the majority of candidate compounds encountered barriers due to low-yielding synthetic routes, toxicity or other problems that led to their abandonment.
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Affiliation(s)
- Katherine L Seley-Radtke
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Mary K Yates
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
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9
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A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA. J Mol Graph Model 2017; 77:339-349. [DOI: 10.1016/j.jmgm.2017.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022]
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10
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Chen Z, Ku TC, Seley-Radtke KL. Thiophene-expanded guanosine analogues of Gemcitabine. Bioorg Med Chem Lett 2015; 25:4274-6. [PMID: 26316465 PMCID: PMC4579529 DOI: 10.1016/j.bmcl.2015.07.086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022]
Abstract
The chemotherapeutic drug Gemcitabine, 2',2'-difluoro-2'-deoxycytidine, has long been the standard of care for a number of cancers. Gemcitabine's chemotherapeutic properties stem from its 2',2'-difluoro-2'-deoxyribose sugar, which mimics the natural nucleoside, but also disrupts nucleic acid synthesis, leading to cell death. As a result, numerous analogues have been prepared to further explore the biological implications for this structural modification. In that regard, a thieno-expanded guanosine analogue was of interest due to biological activity previously observed for the tricyclic heterobase scaffold. Several analogues were prepared, including the McGuigan ProTide, however the parent nucleoside exhibited the best chemotherapeutic activity, specifically against breast cancer cell lines (89.53% growth inhibition).
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Affiliation(s)
- Zhe Chen
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Therese C Ku
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Katherine L Seley-Radtke
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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11
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Chen Z, Jochmans D, Ku T, Paeshuyse J, Neyts J, Seley-Radtke KL. Bicyclic and Tricyclic "Expanded" Nucleobase Analogues of Sofosbuvir: New Scaffolds for Hepatitis C Therapies. ACS Infect Dis 2015; 1:357-66. [PMID: 27624884 DOI: 10.1021/acsinfecdis.5b00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Given the impressive success of Gilead's Sofosbuvir, many laboratories, including ours, have explored the unique 2'-sugar modification (2'-Me, 2'-F) of nucleoside analogues in the hopes of exploiting the biological activity that this unique modification has imparted to the nucleoside scaffold. In that regard, we have combined our tricyclic "expanded" purine base motif with the 2'-Me, 2'-F sugar modification. Although the synthesis of these complex molecules proved to be nontrivial, with the best results coming from a linear approach, the overall strategy resulted in highly promising biological results for several of the target compounds, including their corresponding McGuigan ProTides. Modest activity against HCV was observed with inhibitory concentrations of as low as 20 μM.
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Affiliation(s)
- Zhe Chen
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Dirk Jochmans
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Therese Ku
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Jan Paeshuyse
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johan Neyts
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Katherine L. Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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12
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Antiproliferative activities of halogenated pyrrolo[3,2-d]pyrimidines. Bioorg Med Chem 2015; 23:4354-4363. [PMID: 26122770 DOI: 10.1016/j.bmc.2015.06.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 06/04/2015] [Accepted: 06/10/2015] [Indexed: 11/20/2022]
Abstract
In vitro evaluation of the halogenated pyrrolo[3,2-d]pyrimidines identified antiproliferative activities in compounds 1 and 2 against four different cancer cell lines. Upon screening of a series of pyrrolo[3,2-d]pyrimidines, the 2,4-Cl compound 1 was found to exhibit antiproliferative activity at low micromolar concentrations. Introduction of iodine at C7 resulted in significant enhancement of potency by reducing the IC50 into sub-micromolar levels, thereby suggesting the importance of a halogen at C7. This finding was further supported by an increased antiproliferative effect for 4 as compared to 3. Cell-cycle and apoptosis studies conducted on the two potent compounds 1 and 2 showed differences in their cytotoxic mechanisms in triple negative breast cancer MDA-MB-231 cells, wherein compound 1 induced cells to accumulate at the G2/M stage with little evidence of apoptotic death. In contrast, compound 2 robustly induced apoptosis with concomitant G2/M cell cycle arrest in this cell model.
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Zhang L, Zhang Z, Ren T, Tian J, Wang M. New size-expanded RNA nucleobase analogs: a detailed theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 140:407-415. [PMID: 25617981 DOI: 10.1016/j.saa.2015.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/20/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson-Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO-LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462 nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.
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Affiliation(s)
- Laibin Zhang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Zhenwei Zhang
- Linyi Academy of Technology Cooperation and Application, Linyi 276001, PR China
| | - Tingqi Ren
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Jianxiang Tian
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Mei Wang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
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14
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Temburnikar KW, Zimmermann SC, Kim NT, Ross CR, Gelbmann C, Salomon CE, Wilson GM, Balzarini J, Seley-Radtke KL. Antiproliferative activities of halogenated thieno[3,2-d]pyrimidines. Bioorg Med Chem 2014; 22:2113-22. [PMID: 24631358 PMCID: PMC4565497 DOI: 10.1016/j.bmc.2014.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/10/2014] [Accepted: 02/18/2014] [Indexed: 12/17/2022]
Abstract
The in vitro evaluation of thieno[3,2-d]pyrimidines identified halogenated compounds 1 and 2 with antiproliferative activity against three different cancer cell lines. A structure activity relationship study indicated the necessity of the chlorine at the C4-position for biological activity. The two most active compounds 1 and 2 were found to induce apoptosis in the leukemia L1210 cell line. Additionally, the compounds were screened against a variety of other microbial targets and as a result, selective activity against several fungi was also observed. The synthesis and preliminary biological results are reported herein.
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Affiliation(s)
- Kartik W Temburnikar
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Sarah C Zimmermann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Nathaniel T Kim
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Christina R Ross
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Christopher Gelbmann
- Center for Drug Design, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Christine E Salomon
- Center for Drug Design, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Katherine L Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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15
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Zhang L, Zhou L, Tian J, Li X. Hetero-ring-expansion design for purine analogs: A theoretical study on the structural, electronic, and excited-state properties. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Zhang L, Zhou L, Tian J, Li X. Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study. Phys Chem Chem Phys 2014; 16:4338-49. [DOI: 10.1039/c3cp54505a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Zhang L, Ren T, Zhou L, Tian J, Li X. DFT investigation of the intermolecular interactions of a thieno-separated tricyclic guanine analog with gold nanoclusters. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Temburnikar K, Brace K, Seley-Radtke KL. Synthesis of 2'-deoxy-9-deaza nucleosides using Heck methodology. J Org Chem 2013; 78:7305-11. [PMID: 23806030 DOI: 10.1021/jo400913k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During the synthesis of a series of 2'-deoxy-9-deaza nucleosides using Heck methodology, the necessity for a pyrrole protecting group was discovered. The results of this brief study revealed that the benzyloxymethyl (BOM) group proved optimal, and Heck coupling using Jeffery conditions increased the coupling yield significantly. The results are reported herein.
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Affiliation(s)
- Kartik Temburnikar
- University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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19
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Sharma P, Lait LA, Wetmore SD. yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar-base orientation, hydrogen-bonding interactions and stacking abilities. Phys Chem Chem Phys 2013; 15:2435-48. [PMID: 23303174 DOI: 10.1039/c2cp43910g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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20
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21
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Synthesis and biological evaluation of a series of thieno-expanded tricyclic purine 2'-deoxy nucleoside analogues. Bioorg Med Chem 2012; 20:3009-15. [PMID: 22464686 DOI: 10.1016/j.bmc.2012.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/23/2012] [Accepted: 03/01/2012] [Indexed: 11/22/2022]
Abstract
Introducing structural diversity into the nucleoside scaffold for use as potential chemotherapeutics has long been considered an important approach to drug design. In that regard, we have designed and synthesized a number of innovative 2'-deoxy expanded nucleosides where a heteroaromatic thiophene spacer ring has been inserted in between the imidazole and pyrimidine ring systems of the natural purine scaffold. The synthetic efforts towards realizing the expanded 2'-deoxy-guanosine and -adenosine tricyclic analogues as well as the preliminary biological results are presented herein.
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22
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Synthetic strategies toward carbocyclic purine-pyrimidine hybrid nucleosides. Bioorg Med Chem 2009; 17:5520-5. [PMID: 19592260 DOI: 10.1016/j.bmc.2009.06.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 06/13/2009] [Accepted: 06/16/2009] [Indexed: 11/20/2022]
Abstract
The blending of key structural features from the purine and pyrimidine nucleobase scaffolds gives rise to a new class of hybrid nucleosides. The purine-pyrimidine hybrid nucleosides can be viewed as either N-3 ribosylated purines or 5,6-disubstituted pyrimidines, thus recognition by both purine- and pyrimidine-metabolizing enzymes is possible. Given the increasing reports of the development of resistance in many enzymatic systems, a drug that could be recognized by more than one enzyme could prove highly advantageous in overcoming resistance mechanisms related to binding site mutations. In that regard, the design, synthesis and results of preliminary biological activity for a series of carbocyclic uracil derivatives with either a fused imidazole or thiazole ring are presented herein.
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23
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Zhang Z, Wauchope OR, Seley-Radtke KL. Mechanistic studies in the synthesis of a series of thieno-expanded xanthosine and guanosine nucleosides. Tetrahedron 2008; 64:10791-10797. [PMID: 19946353 PMCID: PMC2629406 DOI: 10.1016/j.tet.2008.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
During the synthetic pursuit of guanosine (triG) and xanthosine (triX) tricyclic nucleosides analogues, an interesting side product was discovered. In an effort to uncover the mechanistic factors leading to this result, a series of reaction conditions were investigated. It was found that by varying the conditions, the appearance of the side product could be controlled. In addition, the yield of the desired products could be manipulated to afford either a 50:50 mix of both triG and triX, or a majority of one or the other. To demonstrate the broad utility of the method, it was also adapted to the synthesis of guanosine and xanthosine from 5-amino-1-beta-D-ribofuranosyl-4-imidazolecarboxyamide (AICAR). The mechanistic details surrounding the synthetic efforts are reported herein.
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Affiliation(s)
- Zhibo Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
| | - Orrette R. Wauchope
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
| | - Katherine L. Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
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25
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Lait LA, Rutledge LR, Millen AL, Wetmore SD. yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location. J Phys Chem B 2008; 112:12526-36. [DOI: 10.1021/jp805547p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda A. Lait
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
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26
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Seley-Radtke KL, Zhang Z, Wauchope OR, Zimmermann SC, Ivanov A, Korba B. Hetero-expanded purine nucleosides. Design, synthesis and preliminary biological activity. NUCLEIC ACIDS SYMPOSIUM SERIES (2004) 2008; 52:635-6. [PMID: 18776540 PMCID: PMC2785017 DOI: 10.1093/nass/nrn321] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Several thieno-expanded purine nucleoside analogues were synthesized for use as tools in ongoing investigations into nucleic acid structure and function in our laboratories. The inclusion of the thiophene ring system in the nucleoside endows the purine scaffold with advantages not previously available in other reported expanded purines. The synthesis and preliminary biological studies are reported herein.
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27
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Lee AHF, Kool ET. Exploring the limits of DNA size: naphtho-homologated DNA bases and pairs. J Am Chem Soc 2007; 128:9219-30. [PMID: 16834396 PMCID: PMC2505348 DOI: 10.1021/ja0619004] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new design for DNA bases and base pairs is described in which the pyrimidine bases are widened by naphtho-homologation. Two naphtho-homologated deoxyribosides, dyyT (1) and dyyC (2), were synthesized and could be incorporated into oligonucleotides as suitably protected phosphoramidite derivatives. The deoxyribosides were found to be fluorescent, with emission maxima at 446 and 433 nm, respectively. Studies with single substitutions of 1 and 2 in the natural DNA context revealed exceptionally strong base stacking propensity for both. Sequences containing multiple substitutions of 1 and 2 paired opposite adenine and guanine were subsequently mixed and studied by several analytical methods. Data from UV mixing experiments, FRET measurements, fluorescence quenching experiments, and hybridizations on beads suggest that complementary "doublewide DNA" (yyDNA) strands may self-assemble into helical complexes with 1:1 stoichiometry. Data from thermal denaturation plots and CD spectra were less conclusive. Control experiments in one sequence context gave evidence that yyDNA helices, if formed, are preferentially antiparallel and are sequence selective. Hypothesized base pairing schemes are analogous to Watson-Crick pairing, but with glycosidic C1'-C1' distances widened by over 45%, to ca. 15.2 A. The possible self-assembly of the double-wide DNA helix establishes a new limit for the size of information-encoding, DNA-like molecules, and the fluorescence of yyDNA bases suggests uses as reporters in monomeric and oligomeric forms.
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28
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Zhang J, Cukier RI, Bu Y. Rational Design of Hetero-ring-Expanded Guanine Analogs with Enhanced Properties for Modified DNA Building Blocks. J Phys Chem B 2007; 111:8335-41. [PMID: 17580864 DOI: 10.1021/jp073592h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The properties and modes of recognition of physiological DNAs associated with the four natural nucleobases might be extended, in principle, by the design of non-natural nucleobase derivatives. The goal is an expansion of the genetic alphabet, with the possible outcome of producing new DNAs with improved physical or biological properties. In this work, a new series of hetero-ring-expanded guanine analogs are proposed, and their relevant structural characteristics and electronic properties are determined by density functional theory. The stabilities of the decamer DNA duplexes (dn.dC)10 (where n represents the corresponding expanded guanine analog designed here) are also examined, using molecular dynamics. The simulations show that the designed motifs can form stable DNA-like structures. We determined the pairing energies for the Watson-Crick (WC) hydrogen-bonded dimers between the expanded G-analogs and the natural C, and found that the pairing energies are close to those of the natural GC pair. The calculated adiabatic ionization potentials (IPs) of the size-expanded guanine analogs and their base pairs, and the corresponding vertical ionization potentials, show that some are distinctly smaller than the corresponding natural versions. The HOMO-LUMO energy gaps for most of the size-expanded guanine analogs and their WC base pairs are considerably lower than those of the corresponding natural base and base pairs. Thus, the expanded G bases may be considered as DNA genetic motifs, and they may serve as building blocks for potential biological applications and the development of molecular electronic devices.
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Affiliation(s)
- Jinmei Zhang
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China
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29
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McConnell TL, Wetmore SD. How Do Size-Expanded DNA Nucleobases Enhance Duplex Stability? Computational Analysis of the Hydrogen-Bonding and Stacking Ability of xDNA Bases. J Phys Chem B 2007; 111:2999-3009. [PMID: 17388411 DOI: 10.1021/jp0670079] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Computational chemistry (B3LYP, MP2) is used to study the properties of size-expanded DNA nucleobases generated by inserting a benzene spacer into the natural nucleobases. Although the addition of the spacer does not significantly affect the hydrogen-bonding properties of natural nucleobases, the orientation of the base about the glycosidic bond necessary for Watson-Crick binding is destabilized, which could have implications for the selectivity of expanded bases, as well as the stability of expanded duplexes. Consideration of the (stacked) binding energies in the preferred relative orientation of natural and expanded nucleobases aligned according to their centers of mass reveals that the stacking within natural dimers can be increased by up to 50% upon expansion of one nucleobase and up to 90% upon expansion of two nucleobases. The implications of these findings to the stability of expanded duplexes were revealed by considering simplified models of natural and mixed duplexes composed of four nucleobases. Although intra- and interstrand interactions within double helices are typically less than those predicted when nucleobases are stacked according to their centers of mass, some nucleobases utilize their full stacking potential within double helices, where both intra- and interstrand interactions can be significant. Most importantly, increasing the size of nucleobases within the duplex significantly increases both intra- and interstrand stacking interactions. Specifically, some interactions are double the magnitude of the corresponding intrastrand interactions in natural helices, and even greater increases in interstrand interactions are sometimes found. Thus, our work suggests that mixed duplexes composed of natural bases hydrogen bound to expanded bases may exploit the increase in the inherent stacking ability of the expanded bases in more than one way and thereby afford duplexes with greater stability than natural DNA.
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Affiliation(s)
- Tom L McConnell
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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30
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Krueger AT, Lu H, Lee AHF, Kool ET. Synthesis and properties of size-expanded DNAs: toward designed, functional genetic systems. Acc Chem Res 2007; 40:141-50. [PMID: 17309194 PMCID: PMC2539066 DOI: 10.1021/ar068200o] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA ("expanded DNA") and yDNA ("wide DNA"). The large component bases are fluorescent, and they display high stacking affinity. When singly substituted into natural DNA, they are destabilizing because the benzo-expanded base pair size is too large for the natural helix. However, when all base pairs are expanded, xDNA and yDNA form highly stable, sequence-selective double helices. The size-expanded DNAs are candidates for components of new, functioning genetic systems. In addition, the fluorescence of expanded DNA bases makes them potentially useful in probing nucleic acids.
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31
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32
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Torregrosa R, Pastor IM, Yus M. Isoprene-catalysed lithiation: deprotection and functionalisation of imidazole derivatives. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.11.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Abstract
We report on the synthesis, stacking, and pairing properties of a new structural class of size-expanded pyrimidine nucleosides, abbreviated dyT and dyC. Their bases are benzo-homologated variants of thymine and cytosine and have a design that is distinct from a previously described class of size-expanded (xDNA) pyrimidines, with a different vector of expansion relative to the sugar. We term this new base geometry "yDNA" (a mnemonic for "wide DNA"). Both C-glycosides were prepared using Pd-mediated coupling of iodinated base derivatives with a deoxyribose precursor. As free deoxynucleosides, both dyT and dyC displayed robust fluorescence, with emission maxima at 375 and 390 nm, respectively. Both widened pyrimidines could be incorporated readily as protected phosphoramidite derivatives into synthetic oligonucleotides. Experiments in "dangling end" DNA contexts revealed that both yT and yC stack more favorably than their natural counterparts. When opposite natural bases in the context of Watson-Crick DNA were paired, the yT nucleotide formed a pair with A that was equally stable as a T-A pair, despite the mismatch in size with the neighboring natural pairs. The yC nucleotide (paired opposite G) was destabilizing by a small amount in the same context. Despite the large size of the pairs, both yT and yC were selective for their Watson-Crick complementary partners A and G, respectively. The pairing properties and fluorescence of yDNA nucleotides may lead to useful applications in the study of steric effects in DNA-protein interactions. In addition, the compounds may serve as building blocks for a large-sized artificial genetic system.
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Affiliation(s)
- Alex H F Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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34
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Wallace LJM, Candlish D, Hagos A, Seley KL, de Koning HP. Selective transport of a new class of purine antimetabolites by the protozoan parasite Trypanosoma brucei. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1441-4. [PMID: 15571273 DOI: 10.1081/ncn-200027660] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Purine antimetabolites have been very successful therapeutic agents against a host of infectious diseases and malignancies. Success of the treatment relies as much on the efficient accumulation by the target cell or organism as it does on selective action on a vital biochemical pathway of the target cell. Here we compare the ability of a new class of tricyclic purine antimetabolites to interact with transporters from human erythrocytes or Trypanosoma brucei. We show that these compounds display a remarkable selectivity for the parasite's transporters. The adenine analogue showed greater trypanocidal activity than the hypoxanthine or guanine analogues in vitro.
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Affiliation(s)
- L J M Wallace
- Institute of Biomedical and Life Sciences, Division of Infection and Immunity, University of Glasgow, Glasgow, UK
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35
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Wardakhan WW, Gaber HM, Ouf SA, Sherif SM. Studies on 2-Aminothiophenes: Synthesis, Transformations, and Biological Evaluation of Functionally-Substituted Thiophenes and Their Fused Derivatives. PHOSPHORUS SULFUR 2005. [DOI: 10.1080/104265090517406] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Gaber HM, Elgemeie GEH, Ouf SA, Sherif SM. Heterocyclic synthesis with 4-hydrazinopyridothienopyrimidines: Synthesis of pyridothienotriazolopyrimidines and heterocyclylpyridothienopyrimidines with biological interest. HETEROATOM CHEMISTRY 2005. [DOI: 10.1002/hc.20126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Abstract
Density functional theory was used to study the potential energy surface for rotation about the carbon-carbon bonds in a variety of guanosine, adenosine, and inosine fleximers, which are modified purines with the imidazole and pyrimidine rings separated by a single carbon-carbon bond. Various connectivities between C4 or C5 of the imidazole ring and C5' or C6' of the pyrimidine ring were considered. Calculations on fleximer nucleobases in the absence of the ribose moiety suggest that a planar relative arrangement of the imidazole and pyrimidine rings is favored, and that all fleximers are indeed very flexible with regards to rotation about the carbon-carbon bond, where calculated barriers are generally less than 40 kJ mol(-1). Furthermore, calculated binding energies of fleximer-pyrimidine pairs indicate that the hydrogen-bonding properties of these modified nucleobases mimic those of the corresponding natural purine. Inclusion of the sugar moiety often leads to a favored nonplanar orientation of the two rings, and either a reduction in the rotational barrier height or small changes in the rotational surface depending on the connectivity and nucleobase considered. It is concluded that several connectivities may have favorable properties for biochemical applications where flexible nucleobases would be beneficial.
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Affiliation(s)
- Alma B Bardon
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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38
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Sharma P, Sharma S, Rane N. Synthesis and in vitro antimicrobial activities of 2-hydroxy-6-methyl-7-(arylamino)-1,7-dihydropurin-8-ones. Bioorg Med Chem 2004; 12:3135-9. [PMID: 15158781 DOI: 10.1016/j.bmc.2004.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Revised: 04/07/2004] [Accepted: 04/08/2004] [Indexed: 10/26/2022]
Abstract
A number of 2-hydroxy-6-methyl-7-(arylamino)-1,7-dihydropurin-8-ones have been synthesized. 3-Oxo-2-(arylhydrazono)butyric acid ethyl ester were acetylated and treated with triethyl amine and formamide in presence of 1,4-dioxane to yield N-(5-acetyl-4-ethoxy-2-oxo-2,5-dihydro-imidazol-1-yl)-N-arylacetamide, which on refluxation with urea and freshly prepared sodium ethoxide yielded the title compound. All the newly synthesized compounds have been characterized by spectroscopic and elemental analysis data. The synthesized compounds were screened against a representative panel of susceptible and resistant Gram-positive and Gram-negative bacteria using a standard antibiotic drug purinthol as control. Quantitative structure-activity relationship has also been interpreted in terms of correlation of biological activity with molecular refractive index parameters (M(R)) and Hammett substituent constant (sigma).
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Affiliation(s)
- Pratibha Sharma
- School of Chemical Sciences, D.A. University, Indore 452 017, India.
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39
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Liu H, Gao J, Maynard L, Saito YD, Kool ET. Toward a new genetic system with expanded dimensions: size-expanded analogues of deoxyadenosine and thymidine. J Am Chem Soc 2004; 126:1102-9. [PMID: 14746479 DOI: 10.1021/ja038384r] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the design, preparation, and properties of two key building blocks of a size-expanded genetic system. Nucleoside analogues of the natural nucleosides dA and dT are reported in which the fusion of a benzo ring increases their size by ca. 2.4 A. The expanded dA analogue (dxA), having a tricyclic base, was first reported by Leonard nearly three decades ago. We describe a shortened and more efficient approach to this compound. The expanded dT analogue (dxT), a methylquinazolinedione C-glycoside, was previously unknown; we describe its preparation in eight steps from 5-methylanthranilic acid. The key glycoside bond formation employed Pd-mediated coupling of an aryl iodide precursor with a dihydrofuran derivative of deoxyribose. Both nucleosides are shown to be efficient fluorophores, emitting light in the blue-violet range. The base-protected phosphoramidite derivatives were prepared, and short oligonucleotides containing them were characterized. The two size-expanded nucleosides are key components of a new four-base genetic system designed to form helical paired structures having a diameter greater than that of natural DNA. Elements of the design of this expanded genetic molecule, termed xDNA, are discussed, including the possibility of up to eight base pairs of information storage capability.
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Affiliation(s)
- Haibo Liu
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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40
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Carvalho MA, Zaki MEA, Alvares Y, Proença MF, Booth BL. Synthesis of novel 6-enaminopurines. Org Biomol Chem 2004; 2:2340-5. [PMID: 15305216 DOI: 10.1039/b406806h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two different approaches have been used for the synthesis of 6-enaminopurines 6 from 5-amino-4-cyanoformimidoyl imidazoles. In the first approach imidazoles 1 were reacted with ethoxymethylenemalononitrile or ethoxymethylenecyanoacetate under mild experimental conditions and this led to 9-substituted-6-(1-amino-2,2-dicyanovinyl) purines 6a-f or 9-substituted-6-(1-amino-2-cyano-2-methoxycarbonylvinyl) purines 6g-k. These reactions are postulated to occur through an imidazo-pyrrolidine intermediate 7, which rapidly rearranges to the 6-enaminopurine 6. In the second approach 6-methoxyformimidoyl purines 3, prepared in two efficient steps from 5-amino-4-cyanoformimidoyl imidazoles 1, were reacted with malononitrile and methylcyanoacetate with a mild acid catalysis (ammonium acetate or piperidinium acetate) to give 6-enaminopurines 6a, 6d, 6f, 6g and 6k in very good yields. Only low yields were obtained for the 6-enaminopurine 6j, as competing nucleophilic attack on C-8 of either 3d or 6jcauses ring opening with formation of pyrimido-pyrimidines 11 and 10a respectively.
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Affiliation(s)
- M Alice Carvalho
- Departamento de Química, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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41
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Seley KL, Zhang L, Hagos A, Quirk S. "Fleximers". Design and synthesis of a new class of novel shape-modified nucleosides(1). J Org Chem 2002; 67:3365-73. [PMID: 12003548 DOI: 10.1021/jo0255476] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new class of shape-modified nucleosides is introduced. These novel "fleximers" feature the purine ring systems of adenosine, inosine, and guanosine split into their individual imidazole and pyrimidine components (as in 1-3). This structural modification serves to introduce flexibility into the nucleoside while still retaining the elements essential for recognition. As a consequence, these novel fleximers should find use as bioprobes for investigating enzyme-coenzyme binding sites as well as nucleic acid and protein interactions. Their design and synthesis are described.
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Affiliation(s)
- Katherine L Seley
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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42
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Abstract
[structure: see text] A new class of shape-modified nucleosides is introduced. The purine heterobases of adenosine and guanosine have been split into their imidazole and pyrimidine components, thereby introducing flexibility while retaining the elements necessary for recognition. As a consequence, these novel "fleximers" should find use as bioprobes for investigating enzyme-coenzyme binding sites as well as nucleic acid and protein interactions. Their design and synthesis is described.
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Affiliation(s)
- K L Seley
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
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