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Soroudi S, Jaafari MR, Arabi L. Lipid nanoparticle (LNP) mediated mRNA delivery in cardiovascular diseases: Advances in genome editing and CAR T cell therapy. J Control Release 2024; 372:113-140. [PMID: 38876358 DOI: 10.1016/j.jconrel.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/05/2024] [Accepted: 06/09/2024] [Indexed: 06/16/2024]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of global mortality among non-communicable diseases. Current cardiac regeneration treatments have limitations and may lead to adverse reactions. Hence, innovative technologies are needed to address these shortcomings. Messenger RNA (mRNA) emerges as a promising therapeutic agent due to its versatility in encoding therapeutic proteins and targeting "undruggable" conditions. It offers low toxicity, high transfection efficiency, and controlled protein production without genome insertion or mutagenesis risk. However, mRNA faces challenges such as immunogenicity, instability, and difficulty in cellular entry and endosomal escape, hindering its clinical application. To overcome these hurdles, lipid nanoparticles (LNPs), notably used in COVID-19 vaccines, have a great potential to deliver mRNA therapeutics for CVDs. This review highlights recent progress in mRNA-LNP therapies for CVDs, including Myocardial Infarction (MI), Heart Failure (HF), and hypercholesterolemia. In addition, LNP-mediated mRNA delivery for CAR T-cell therapy and CRISPR/Cas genome editing in CVDs and the related clinical trials are explored. To enhance the efficiency, safety, and clinical translation of mRNA-LNPs, advanced technologies like artificial intelligence (AGILE platform) in RNA structure design, and optimization of LNP formulation could be integrated. We conclude that the strategies to facilitate the extra-hepatic delivery and targeted organ tropism of mRNA-LNPs (SORT, ASSET, SMRT, and barcoded LNPs) hold great prospects to accelerate the development and translation of mRNA-LNPs in CVD treatment.
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Affiliation(s)
- Setareh Soroudi
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Leila Arabi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Hou X, Wang R, Zhang C, Xu Y, Zhu S, Zhang Y, Liu X, Che Y. Rogersonins C-F, 9 H-Imidazo[2,1- i]purine-Incorporating Adenine-Polyketide Hybrids from an Ophiocordyceps-Associated Clonostachys rogersoniana. JOURNAL OF NATURAL PRODUCTS 2024; 87:1618-1627. [PMID: 38887968 DOI: 10.1021/acs.jnatprod.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Rogersonins C-F (1-4), four unprecedented adenine-polyketide hybrids featuring a rare 9H-imidazo[2,1-i]purine (1,N6-ethenoadenine) moiety, were isolated from an Ophiocordyceps-associated fungus, Clonostachys rogersoniana. Their structures were elucidated primarily by NMR experiments. The absolute configurations of 1-4 were assigned by a combination of the modified Mosher method, chemical degradation, electronic circular dichroism (ECD) calculations, and X-ray crystallography using Cu Kα radiation. Compound 3 downregulated the expression of PD-L1 protein in MDA-MB-231 and A549 cells, but did not show detectable effect on mRNA transcription of the PD-L1-encoding gene CD274.
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Affiliation(s)
- Xintong Hou
- State Key Laboratory of Bioactive Substance & Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Ruikun Wang
- State Key Laboratory of Bioactive Substance & Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Chunyan Zhang
- State Key Laboratory of Bioactive Substance & Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yang Xu
- State Key Laboratory of Bioactive Substance & Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shuaiming Zhu
- State Key Laboratory of Toxicology & Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, People's Republic of China
| | - Yang Zhang
- State Key Laboratory of Toxicology & Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, People's Republic of China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongsheng Che
- State Key Laboratory of Bioactive Substance & Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
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3
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Liu YM, Wang S, Dickenson A, Mao J, Bai X, Liao X. An on-line SPE-LC-MS/MS method for quantification of nucleobases and nucleosides present in biological fluids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2505-2512. [PMID: 38584507 PMCID: PMC11151739 DOI: 10.1039/d4ay00100a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Solid phase extraction (SPE) and liquid chromatographic (LC) separation of nucleobases and nucleosides are challenging due to the high hydrophilicity of these compounds. Herein we report a novel on-line SPE-LC-MS/MS method for their quantification after pre-column derivatization with chloroacetaldehyde (CAA). The method proposed is selective and sensitive with limits of detection at the nano-molar level. Analysis of urine and saliva samples by using this method is demonstrated. Adenine, guanine, cytosine, adenosine, guanosine, and cytidine were found in the range from 0.19 (guanosine) to 1.83 μM (cytidine) in urine and from 0.015 (guanosine) to 0.79 μM (adenine) in saliva. Interestingly, methylation of cytidine was found to be significantly different in urine from that in saliva. While 5-hydroxymethylcytidine was detected at a very low level (<0.05 μM) in saliva, it was found to be the most prominent methylated cytidine in urine at a high level of 3.33 μM. Since on-line SPE is deployed, the proposed LC-MS/MS quantitative assay is convenient to carry out and offers good assay accuracy and repeatability.
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Affiliation(s)
- Yi-Ming Liu
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Shuguan Wang
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Amani Dickenson
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Jinghe Mao
- Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA
| | - Xiaolin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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4
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Nascimento SMRD, Ferry A, Gallier F, Lubin-Germain N, Uziel J, Gonzales S, Miranda LSDME. Developments in the chemistry and biology of 1,2,3-triazolyl-C-nucleosides. Arch Pharm (Weinheim) 2024; 357:e2300580. [PMID: 38150650 DOI: 10.1002/ardp.202300580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/29/2023]
Abstract
In the last 50 years, nucleoside analogs have been introduced to drug therapy as antivirals for different types of cancer due to their interference in cellular proliferation. Among the first line of nucleoside treatment drugs, ribavirin (RBV) is a synthetic N-nucleoside with a 1,2,4-triazole moiety that acts as a broad-spectrum antiviral. It is on the World Health Organization (WHO) list of essential medicines. However, this important drug therapy causes several side effects due to its nonspecific mechanism of action. There is thus a need for a continuous study of its scaffold. A particular approach consists of connecting d-ribose to the nitrogen-containing base with a C-C bond. It provides more stability against enzymatic action and a better pharmacologic profile. The coronavirus disease (COVID) pandemic has increased the need for more solutions for the treatment of viral infections. Among these solutions, remdesivir, the first C-nucleoside, has been approved by the Food and Drug Administration (FDA) for clinical use against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It drew attention to the study of the C-nucleoside scaffold. Different C-nucleoside patterns have been synthesized over the years. They show many important activities against viruses and cancer cell lines. 1,2,3-Triazolyl-C-nucleoside derivatives are a prolific and efficient subclass of RBV analogs close to the already-known RBV with a C-C bond modification. These compounds are often prepared by alkynylation of the d-ribose ring followed by azide-alkyne cycloaddition. They are reported to be active against the Crimean-Congo hemorrhagic fever virus and several tumoral cell lines, showing promising biological potential. In this review, we explore such approaches to 1,2,3-triazolyl-C-nucleosides and their evolution over the years.
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Affiliation(s)
| | - Angélique Ferry
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Florian Gallier
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Nadège Lubin-Germain
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Jacques Uziel
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Simon Gonzales
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
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Liao X, Bai X, Wang S, Liggins C, Pan L, Wang M, Tchounwou P, Mao J, Liu YM. A novel one-pot fluorescence tagging and depyrimidination strategy for quantification of global DNA methylation. Anal Chim Acta 2023; 1239:340636. [PMID: 36628742 PMCID: PMC9834644 DOI: 10.1016/j.aca.2022.340636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
DNA methylation is intensively studied in medical science. Current HPLC methods for quantification of global DNA methylation involve digestion of a DNA sample and HPLC determination of both cytosine (C) and 5-methylcytosine (5mC) so that percentage of 5mC in total cytosine can be calculated as DNA methylation level. Herein we report a novel HPLC method based on a one-pot fluorescence tagging and depyrimidination reaction between DNA and chloroacetaldehyde (CAA) for highly sensitive quantification of global DNA methylation. In the one-pot reaction, C and 5mC residues in a DNA sequence react with CAA, forming fluorescent etheno-adducts that are then released from the sequence through depyrimidination. Interestingly, etheno-5mC (ε-5mC) is ∼20 times more fluorescent than ε-C and other ε-nucleobases resulting from the reaction, which greatly facilitates the quantification. Further, due to the tagging-induced increase in structural aromaticity, ε-nucleobases are far more separable by HPLC than intact nucleobases. The proposed HPLC method with fluorescence detection (HPLC-FD) is quick (i.e., < 1h per assay) and highly sensitive with a detection limit of 0.80 nM (or 250 fg on column) for 5mC. Using the method, DNA samples isolated from yeast, HCT-116 cells, and tissues were analyzed. Global DNA methylation was measured to be in the range from 0.35% to 2.23% in the samples analyzed. This sensitive method allowed accurate analyses of minute DNA samples (∼100 ng) isolated from milligrams of tissues.
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Affiliation(s)
- Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaolin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shuguan Wang
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Christany Liggins
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Li Pan
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Meiyuan Wang
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Paul Tchounwou
- Department of Biology, Jackson State University, Jackson, MS, 39217, USA
| | - Jinghe Mao
- Department of Biology, Tougaloo College, Tugaloo, MS, 39174, USA
| | - Yi-Ming Liu
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA.
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Pagliano P, Sellitto C, Ascione T, Scarpati G, Folliero V, Piazza O, Franci G, Filippelli A, Conti V. The preclinical discovery and development of molnupiravir for the treatment of SARS-CoV-2 (COVID-19). Expert Opin Drug Discov 2022; 17:1299-1311. [PMID: 36508255 DOI: 10.1080/17460441.2022.2153828] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Molnupiravir (MOV) is a broad-spectrum oral antiviral agent approved for the treatment of COVID-19. The results from in vitro and in vivo studies suggested MOV activity against many RNA viruses such as influenza virus and some alphaviruses agents of epidemic encephalitis. MOV is a prodrug metabolized into the ribonucleoside analog β-D-N4-hydroxycytidine. It is incorporated into the viral RNA chain causing mutations impairing coding activity of the virus, thereby inhibiting viral replication. AREAS COVERED This review analyzes the in vitro and in vivo studies that have highlighted the efficacy of MOV and the main pre-authorization randomized controlled trials evaluating its safety, tolerability, and pharmacokinetics, as well as its antiviral efficacy against SARS-COV-2 infection. EXPERT OPINION MOV is an antiviral agent with an excellent tolerability profile with few drug-drug interactions. Treatment of mild-to-moderate COVID-19 can benefit from MOV administration in the precocious phases of the disease, prior to the trigger of an aberrant immune response responsible for the parenchymal damage to pulmonary and extrapulmonary tissues. However, its suspected mutagenic effect can be a factor limiting its use at least in selected populations and studies on its teratogen effects should be planned before it is authorized for use in the pediatric population or in pregnant women.
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Affiliation(s)
- Pasquale Pagliano
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Infectious Diseases, University of Salerno, Baronissi, Italy
| | - Carmine Sellitto
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Tiziana Ascione
- Department of Medicine, Service of Infectious Diseases, Cardarelli Hospital, Naples, Italy
| | - Giuliana Scarpati
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ornella Piazza
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Anesthesiology, University of Salerno, Baronissi, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," Unit of Microbiology, University of Salerno, Baronissi, Italy
| | - Amelia Filippelli
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
| | - Valeria Conti
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana," Unit of Pharmacology, University of Salerno, Baronissi, Italy
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7
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Baranowski D, Boryski J, Ostrowski T. 7-(β-d-Ribofuranosyl)-3-methylguanine: Synthesis from guanine and comparative multinuclear NMR studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kumar S, Maity J, Kumar B, Kumar S, Prasad AK. Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues. Beilstein J Org Chem 2022; 18:95-101. [PMID: 35096178 PMCID: PMC8767562 DOI: 10.3762/bjoc.18.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022] Open
Abstract
Conformationally restricted diastereomeric homoarabinofuranosylpyrimidines (AZT analogue), i.e., (5′R)-3′-azido-3′-deoxy-2′-O,5′-C-bridged-β-ᴅ-homoarabinofuranosylthymine and -uracil had been synthesized starting from diacetone ᴅ-glucofuranose following chemoenzymatic and chemical routes in 34–35% and 24–25% overall yields, respectively. The quantitative and diastereoselective acetylation of primary hydroxy over two secondary hydroxy groups present in the key nucleoside precursor was mediated with Lipozyme® TL IM in 2-methyltetrahydrofuran following a chemoenzymatic pathway. Whereas, the protection of the primary hydroxy over the lone secondary hydroxy group in the key azido sugar precursor was achieved using bulky tert-butyldiphenylsilyl chloride (TBDPS-Cl) in pyridine in 92% yield following a chemical synthetic pathway. The chemoenzymatic method was found to be superior over the chemical method in respect of the number of synthetic steps and overall yield of the final product.
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Affiliation(s)
- Sandeep Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi- 110 007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen’s College, University of Delhi, Delhi- 110 007, India
| | - Banty Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi- 110 007, India
- Department of Chemistry, Rajdhani College, University of Delhi, Delhi- 110 015, India
| | - Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi- 110 007, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi- 110 007, India
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9
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Panda S, Poudel TN, Hegde P, Aldrich CC. Innovative Strategies for the Construction of Diverse 1'-Modified C-Nucleoside Derivatives. J Org Chem 2021; 86:16625-16640. [PMID: 34756029 DOI: 10.1021/acs.joc.1c01920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modified C-nucleosides have proven to be enormously successful as chemical probes to understand fundamental biological processes and as small-molecule drugs for cancer and infectious diseases. Historically, the modification of the glycosyl unit has focused on the 2'-, 3'-, and 4'-positions as well as the ribofuranosyl ring oxygen. By contrast, the 1'-position has rarely been studied due to the labile nature of the anomeric position. However, the improved chemical stability of C-nucleosides allows the modification of the 1'-position with substituents not found in conventional N-nucleosides. Herein, we disclose new chemistry for the installation of diverse substituents at the 1'-position of C-nucleosides, including alkyl, alkenyl, difluoromethyl, and fluoromethyl substituents, using the 4-amino-7-(1'-hydroxy-d-ribofuranosyl)pyrrolo[2,1-f][1,2,4]triazine scaffold as a representative purine nucleoside mimetic.
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Affiliation(s)
- Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tej Narayan Poudel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Verma V, Maity J, Maikhuri VK, Sharma R, Ganguly HK, Prasad AK. Double-headed nucleosides: Synthesis and applications. Beilstein J Org Chem 2021; 17:1392-1439. [PMID: 34194579 PMCID: PMC8204177 DOI: 10.3762/bjoc.17.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Double-headed nucleoside monomers have immense applications for studying secondary nucleic acid structures. They are also well-known as antimicrobial agents. This review article accounts for the synthetic methodologies and the biological applications of double-headed nucleosides.
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Affiliation(s)
- Vineet Verma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen’s College, University of Delhi, Delhi-110 007, India
| | - Vipin K Maikhuri
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Ritika Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata-700 054, India
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110 007, India
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11
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Ghodke PP, Mali JR, Patra A, Rizzo CJ, Guengerich FP, Egli M. Enzymatic bypass and the structural basis of miscoding opposite the DNA adduct 1,N 2-ethenodeoxyguanosine by human DNA translesion polymerase η. J Biol Chem 2021; 296:100642. [PMID: 33839151 PMCID: PMC8121704 DOI: 10.1016/j.jbc.2021.100642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022] Open
Abstract
Etheno (ε)-adducts, e.g., 1,N2-ε−guanine (1,N2-ε-G) and 1,N6-ε−adenine (1,N6-ε-A), are formed through the reaction of DNA with metabolites of vinyl compounds or with lipid peroxidation products. These lesions are known to be mutagenic, but it is unknown how they lead to errors in DNA replication that are bypassed by DNA polymerases. Here we report the structural basis of misincorporation frequencies across from 1,N2-ε-G by human DNA polymerase (hpol) η. In single-nucleotide insertions opposite the adduct 1,N2-ε-G, hpol η preferentially inserted dGTP, followed by dATP, dTTP, and dCTP. This preference for purines was also seen in the first extension step. Analysis of full-length extension products by LC-MS/MS revealed that G accounted for 85% of nucleotides inserted opposite 1,N2-ε-G in single base insertion, and 63% of bases inserted in the first extension step. Extension from the correct nucleotide pair (C) was not observed, but the primer with A paired opposite 1,N2-ε-G was readily extended. Crystal structures of ternary hpol η insertion-stage complexes with nonhydrolyzable nucleotides dAMPnPP or dCMPnPP showed a syn orientation of the adduct, with the incoming A staggered between adducted base and the 5’-adjacent T, while the incoming C and adducted base were roughly coplanar. The formation of a bifurcated H-bond between incoming dAMPnPP and 1,N2-ε-G and T, compared with the single H-bond formed between incoming dCMPnPP and 1,N2-ε-G, may account for the observed facilitated insertion of dGTP and dATP. Thus, preferential insertion of purines by hpol η across from etheno adducts contributes to distinct outcomes in error-prone DNA replication.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Jyotirling R Mali
- Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Amritraj Patra
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Carmelo J Rizzo
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA.
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12
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Urbonavičius J, Tauraitė D. Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea. Biomolecules 2020; 10:E1627. [PMID: 33276555 PMCID: PMC7761594 DOI: 10.3390/biom10121627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023] Open
Abstract
Tricyclic wyosine derivatives are present at position 37 in tRNAPhe of both eukaryotes and archaea. In eukaryotes, five different enzymes are needed to form a final product, wybutosine (yW). In archaea, 4-demethylwyosine (imG-14) is an intermediate for the formation of three different wyosine derivatives, yW-72, imG, and mimG. In this review, current knowledge regarding the archaeal enzymes involved in this process and their reaction mechanisms are summarized. The experiments aimed to elucidate missing steps in biosynthesis pathways leading to the formation of wyosine derivatives are suggested. In addition, the chemical synthesis pathways of archaeal wyosine nucleosides are discussed, and the scheme for the formation of yW-86 and yW-72 is proposed. Recent data demonstrating that wyosine derivatives are present in the other tRNA species than those specific for phenylalanine are discussed.
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Affiliation(s)
- Jaunius Urbonavičius
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, 10223 Vilnius, Lithuania;
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Pan L, Zhang H, Zhao J, Ogungbe IV, Zhao S, Liu Y. A New One‐Pot Fluorescence Derivatization Strategy for Highly Sensitive MicroRNA Analysis. Chemistry 2020; 26:5639-5647. [DOI: 10.1002/chem.201905639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Li Pan
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Huaisheng Zhang
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Jingjin Zhao
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal ResourcesGuangxi Normal University Guilin 541004 China
| | - Ifedayo Victor Ogungbe
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal ResourcesGuangxi Normal University Guilin 541004 China
| | - Yi‐Ming Liu
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
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14
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Pan L, Zhang H, Zhao J, Li X, Xu R, Mo Y, Tchounwou PB, Liu YM. A highly sensitive and selective signal-on strategy for microRNA quantification. Anal Chim Acta 2020; 1100:258-266. [PMID: 31987149 DOI: 10.1016/j.aca.2019.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/26/2019] [Accepted: 12/01/2019] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are associated with physiological and pathological processes. They are recognized as biomarkers for diseases diagnosis and treatment evaluation. Herein we propose a simple and cost-effective HPLC method for quantitative assay of target miRNAs with femtomolar sensitivity, single-base discrimination selectivity and low background. The assay is based on an innovative signal-on strategy. In this strategy, polyadenylation of poly(A) polymerase extends an all 'A' sequence at the end of target miRNA, and the substantially increased number of adenine bases are labeled with 2-Chloroacetaldehyde (CAA) to open a signal-on mode and realize a signal amplification. The linearly amplified fluorescence signal is separated from other inference signals and quantified by high performance liquid chromatography with fluorescence detection (HPLC-FD). Combining with affinity magnetic solid phase extraction (MSPE), the method is well suited for analysis of complex biological samples such as serum and cell lysate with nearly zero background fluorescence. Taking miRNA-21 as the model analyte, this absolute quantification method has a limit of detection of 200 fM and a linear calibration curve (R2 = 0.999) in the range from 2.00 pM to 1.00 nM. Using locked nucleic acid (LNA) modified probes rather than ssDNA probes, the assay selectivity is improved. Moreover, analysis of bovine serum and cell lysate samples by using the method is demonstrated. Intracellular content of miRNA-21 is found to be 0.0150 amol/cell in MCF-7 cells with an assay repeatability of 4.0% (RSD, n = 3). The present HPLC quantification of miRNA offers an accurate, reliable, and cost-effective means for quantitative assay of miRNAs occurring in biological samples. Also importantly, it eliminates the need for total RNA isolation for the analysis. It may be useful for more effective diagnosis of diseases and therapeutic evaluation.
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Affiliation(s)
- Li Pan
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Huaisheng Zhang
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Jingjin Zhao
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Xiangtang Li
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Rui Xu
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Yinyuan Mo
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 N. State St, Jackson, MS, 39250, USA
| | - Paul B Tchounwou
- Department of Biology, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA
| | - Yi-Ming Liu
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St, Jackson, MS, 39217, USA.
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15
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Stachelska-Wierzchowska A, Wierzchowski J, Górka M, Bzowska A, Stolarski R, Wielgus-Kutrowska B. Tricyclic Nucleobase Analogs and Their Ribosides as Substrates and Inhibitors of Purine-Nucleoside Phosphorylases III. Aminopurine Derivatives. Molecules 2020; 25:E681. [PMID: 32033464 PMCID: PMC7037862 DOI: 10.3390/molecules25030681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
Etheno-derivatives of 2-aminopurine, 2-aminopurine riboside, and 7-deazaadenosine (tubercidine) were prepared and purified using standard methods. 2-Aminopurine reacted with aqueous chloroacetaldehyde to give two products, both exhibiting substrate activity towards bacterial (E. coli) purine-nucleoside phosphorylase (PNP) in the reverse (synthetic) pathway. The major product of the chemical synthesis, identified as 1,N2-etheno-2-aminopurine, reacted slowly, while the second, minor, but highly fluorescent product, reacted rapidly. NMR analysis allowed identification of the minor product as N2,3-etheno-2-aminopurine, and its ribosylation product as N2,3-etheno-2-aminopurine-N2--D-riboside. Ribosylation of 1,N2-etheno-2-aminopurine led to analogous N2--d-riboside of this base. Both enzymatically produced ribosides were readily phosphorolysed by bacterial PNP to the respective bases. The reaction of 2-aminopurine-N9- -D-riboside with chloroacetaldehyde gave one major product, clearly distinct from that obtained from the enzymatic synthesis, which was not a substrate for PNP. A tri-cyclic 7-deazaadenosine (tubercidine) derivative was prepared in an analogous way and shown to be an effective inhibitor of the E. coli, but not of the mammalian enzyme. Fluorescent complexes of amino-purine analogs with E. coli PNP were observed.
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Affiliation(s)
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Michał Górka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
- Biological and Chemical Research Centre, University of Warsaw, 101 Zwirki i Wigury St., 02-089 Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
| | - Ryszard Stolarski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 5 Pasteura St., 02-093 Warsaw, Poland; (M.G.); (A.B.); (R.S.)
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16
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Stachelska-Wierzchowska A, Wierzchowski J, Górka M, Bzowska A, Wielgus-Kutrowska B. Tri-Cyclic Nucleobase Analogs and their Ribosides as Substrates of Purine-Nucleoside Phosphorylases. II Guanine and Isoguanine Derivatives. Molecules 2019; 24:E1493. [PMID: 30995785 PMCID: PMC6514686 DOI: 10.3390/molecules24081493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/27/2019] [Accepted: 04/09/2019] [Indexed: 11/17/2022] Open
Abstract
Etheno-derivatives of guanine, O6-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N2-etheno-guanine and 1,N6-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from E. coli, while O6-methyl-N2,3-etheno-guanine exhibited moderate activity vs. this enzyme. The latter two compounds displayed intense fluorescence in neutral aqueous medium, and so did the corresponding ribosylation products. By contrast, PNP from calf spleens exhibited only modest activity towards 1,N6-etheno-isoguanine; the remaining compounds were not ribosylated by this enzyme. The enzymatic ribosylation of 1,N6-etheno-isoguanine using two forms of calf PNP (wild type and N243D) and E. coli PNP (wild type and D204N) gave three different products, which were identified on the basis of NMR analysis and comparison with the product of the isoguanosine reaction with chloroacetic aldehyde, which gave an essentially single compound, identified unequivocally as N9-riboside. With the wild-type E. coli enzyme as a catalyst, N9--d- and N7--d-ribosides are obtained in proportion ~1:3, while calf PNP produced another riboside, tentatively identified as N6--d-riboside. The potential application of various forms of PNP for synthesis of the tri-cyclic nucleoside analogs is discussed.
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Affiliation(s)
- Alicja Stachelska-Wierzchowska
- Department of Physics and Biophysics, University of Varmia & Masuria in Olsztyn, 4 Oczapowskiego St., 10-719 Olsztyn, Poland.
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Varmia & Masuria in Olsztyn, 4 Oczapowskiego St., 10-719 Olsztyn, Poland.
| | - Michał Górka
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
- Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
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Yang R, Deng S, Dong XY, Song X, Cai H, Bai J, Xiao Q. Metal-free synthesis of 1, N6-ethenoadenines from N6-propargyl-adenines via NIS mediated radical cascade reaction. RSC Adv 2019; 9:38897-38901. [PMID: 35540232 PMCID: PMC9075968 DOI: 10.1039/c9ra09198j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
In the present paper, an efficient approach for the construction of 1,N6-ethenoadenines from conveniently prepared N6-propargyl-adenines is developed. This reaction merges N-iodosuccinimide radical initiation and aerobic aminooxygenation in dioxane. This mild, 5-exo-dig, and metal-free cascade reaction could be applied to a wide substrate scope to provide 1,N6-ethenoadenines in moderate to good yields. The reaction mechanism was proposed and tested using radical inhibitor (butylated hydroxytoluene) and isotopic labelling (18O2) experiments. An efficient approach for the construction of 1,N6-ethenoadenines is developed through the metal-free mediated radical cascade cyclization of conveniently prepared N6-propargyl-adenines.![]()
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Affiliation(s)
- Ruchun Yang
- Institute of Chemistry
- Nanchang University
- Nanchang 330031
- China
- Institute of Organic Chemistry
| | - Si Deng
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Xiang-you Dong
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Xianrong Song
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Hu Cai
- Institute of Chemistry
- Nanchang University
- Nanchang 330031
- China
| | - Jiang Bai
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Qiang Xiao
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
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18
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Stachelska-Wierzchowska A, Wierzchowski J, Bzowska A, Wielgus-Kutrowska B. Tricyclic nitrogen base 1,N 6-ethenoadenine and its ribosides as substrates for purine-nucleoside phosphorylases: Spectroscopic and kinetic studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:89-101. [PMID: 29376769 DOI: 10.1080/15257770.2017.1419255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The title compound is an excellent substrate for E. coli PNP, as well as for its D204N mutant. The main product of the synthetic reaction is N9-riboside, but some amount of N7-riboside is also present. Surprisingly, 1,N6-ethenoadenine is also ribosylated by both wild-type and mutated (N243D) forms of calf PNP, which catalyze the synthesis of a different riboside, tentatively identified as N6-β-D-ribosyl-1,N6-ethenoadenine. All ribosides are susceptible to phosphorolysis by the E. coli PNP (wild type). All the ribosides are fluorescent and can be utilized as analytical probes.
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Affiliation(s)
| | - Jacek Wierzchowski
- a Department of Biophysics , University of Varmia & Masuria in Olsztyn , 4 Oczapowskiego St, Olsztyn , Poland
| | - Agnieszka Bzowska
- b Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , 5 Pasteura St., Warsaw , Poland
| | - Beata Wielgus-Kutrowska
- b Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , 5 Pasteura St., Warsaw , Poland
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19
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Valdés FZ, Luna VZ, Arévalo BR, Brown NV, Gutiérrez MC. Adenosine: Synthetic Methods of Its Derivatives and Antitumor Activity. Mini Rev Med Chem 2018; 18:1684-1701. [PMID: 29769005 PMCID: PMC6327119 DOI: 10.2174/1389557518666180516163539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/23/2017] [Accepted: 11/27/2017] [Indexed: 01/13/2023]
Abstract
Since 1929, several researchers have conducted studies in relation to the nucleoside of adenosine (1) mainly distribution identifying, characterizing their biological importance and synthetic chemistry to which this type of molecule has been subjected to obtain multiple of its derivatives. The receptors that interact with adenosine and its derivatives, called purinergic receptors, are classified as A1, A2A, A2B and A3. In the presence of agonists and antagonists, these receptors are involved in various physiological processes and diseases. This review describes and compares some of the synthetic methods that have been developed over the last 30 years for obtaining some adenosine derivatives, classified according to substitution processes, complexation, mating and conjugation. Finally, we mention that although the concentrations of these nucleosides are low in normal tissues, they can increase rapidly in pathophysiological conditions such as hypoxia, ischemia, inflammation, trauma and cancer. In particular, the evaluation of adenosine derivatives as adjunctive therapy promises to have a significant impact on the treatment of certain cancers, although the transfer of these results to clinical practice requires a deeper understanding of how adenosine regulates the process of tumorigenesis.
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Affiliation(s)
- Francisco Z. Valdés
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
| | - Víctor Z. Luna
- Center for Bioinformatics and Molecular Simulation, University of Talca, Talca, Chile
| | - Bárbara R. Arévalo
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
| | - Nelson V. Brown
- Center for Medical Research, University of Talca School of Medicine, Talca, Chile
- Programa de Investigación Asociativa en cáncer gástrico (PIA-CG)
| | - Margarita C. Gutiérrez
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
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20
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Lu M, Lu QB, Honek JF. Squarate-based carbocyclic nucleosides: Syntheses, computational analyses and anticancer/antiviral evaluation. Bioorg Med Chem Lett 2017; 27:282-287. [DOI: 10.1016/j.bmcl.2016.11.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 12/31/2022]
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