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Chen Y, Li Y, Gao J, Yu Q, Zhang Y, Zhang J. Perspectives and challenges in developing small molecules targeting purine nucleoside phosphorylase. Eur J Med Chem 2024; 271:116437. [PMID: 38701712 DOI: 10.1016/j.ejmech.2024.116437] [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: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]
Abstract
As a cytosolic enzyme involved in the purine salvage pathway metabolism, purine nucleoside phosphorylase (PNP) plays an important role in a variety of cellular functions but also in immune system, including cell growth, apoptosis and cancer development and progression. Based on its T-cell targeting profile, PNP is a potential target for the treatment of some malignant T-cell proliferative cancers including lymphoma and leukemia, and some specific immunological diseases. Numerous small-molecule PNP inhibitors have been developed so far. However, only Peldesine, Forodesine and Ulodesine have entered clinical trials and exhibited some potential for the treatment of T-cell leukemia and gout. The most recent direction in PNP inhibitor development has been focused on PNP small-molecule inhibitors with better potency, selectivity, and pharmacokinetic property. In this perspective, considering the structure, biological functions, and disease relevance of PNP, we highlight the recent research progress in PNP small-molecule inhibitor development and discuss prospective strategies for designing additional PNP therapeutic agents.
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Affiliation(s)
- Yangyang Chen
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Li
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jing Gao
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Quanwei Yu
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yiwen Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Fan Q, Dong X, Wang Z, Yue Y, Yuan Y, Wang Z, Yue T. TMT-Based Quantitative Proteomics and Non-targeted Metabolomic Analyses Reveal the Antibacterial Mechanism of Hexanal against Vibrio parahaemolyticus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12105-12115. [PMID: 37498004 DOI: 10.1021/acs.jafc.3c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Hexanal is a phytochemical with antimicrobial activity. However, its antibacterial effect and mechanism against Vibrio parahaemolyticus (V. parahaemolyticus) remain unclear. The study aims to elucidate the associated mechanism using tandem mass tag quantitative proteomics and non-targeted metabolomics. Hexanal treatment reduced intracellular ATP concentration, increased membrane permeability, and destroyed the morphology and ultrastructure of V. parahaemolyticus cells. Proteomics and metabolomics data indicated that 572 differentially expressed proteins (DEPs) and 241 differential metabolites (DMs) were identified in hexanal-treated V. parahaemolyticus. These DEPs and DMs were involved in multiple biological pathways including amino acid metabolism, purine and pyrimidine biosynthesis, etc. Bioinformatics analysis revealed that hexanal damaged the structure and function of cell membranes, inhibited nucleotide metabolism, and disturbed carbohydrate metabolism and tricarboxylic acid cycle (TCA) cycle, which ultimately resulted in growth inhibition and bacterial death. The study is conducive to better understand the mode of action of hexanal against V. parahaemolyticus and offers experimental foundation for the application of hexanal as the antibacterial agent in the seafood-associated industry.
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Affiliation(s)
- Qiuxia Fan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinru Dong
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zewei Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Yue
- Xi'an Gaoxin No.1 High School, Xian 710000, People's Republic of China
| | - Yahong Yuan
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
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Ximenes IAT, Albino M, Sangregorio C, Cass QB, de Moraes MC. On-flow magnetic particle activity assay for the screening of human purine nucleoside phosphorylase inhibitors. J Chromatogr A 2021; 1663:462740. [PMID: 34942489 DOI: 10.1016/j.chroma.2021.462740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022]
Abstract
Human purine nucleoside phosphorylase (HsPNP) catalyzes reversible phosphorolysis of nucleosides and deoxynucleosides in the purine cascade. HsPNP has been a target on behalf of the development of new leads for the treatment of a variety of T-cell mediated disorders. Several studies on the HsPNP are focused on the identification of effective, safe, and selective inhibitors. Therefore, this study describes the development of direct, simple, reliable, and inexpensive enzymatic assays to screen HsPNP inhibitors. Initially, HsPNP was covalently immobilized on the surface of magnetic particles (MPs). Due to the versatility of the MPs as solid support for enzyme immobilization, two different methods to monitor the enzyme activity are presented. Firstly, the activity of HsPNP-MPs was assessed offline by HPLC-DAD quantifying the formed hypoxanthine. Then, HsPNP-MPs were trapped in a peek tube, furnishing a microreactor which was inserted on-flow in an HPLC-DAD system to monitor the enzyme activity by the hypoxanthine quantification. Kinetic assays provided KMapp values for the inosine substrate of 488.2 ± 49.1 and 1084 ± 111 µM for the offline and on-flow assays, respectively. For the first time, kinetic studies for Pi as substrate using the HsPNP-MPs exhibits a Michaelis-Menten kinetic, yielding KMapp values for offline and on-flow of 521.2 ± 62.9 µM and 601 ± 66.5 µM, respectively. Inhibition studies conducted with a fourth generation immucillin derivative (DI4G) were employed as proof of concept to validate the use of the HsPNP-MPs assays for screening purposes. Additionally, a small library containing 11 compounds was used to assess the selectivity of the developed assays. The results showed that both presented assays can be applied to selectively recognizing and characterizing HsPNP inhibitors. Particularly, the on-flow method exhibited a high throughput and performance because of its automation and represents an easy and practical approach to reuse the HsPNP-MPs. Besides, this novel enzyme activity assay model can be further applied to other biological targets.
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Affiliation(s)
- I A T Ximenes
- Instituto de Química, Universidade Federal Fluminense. Niterói, Rio de Janeiro, 24020-141, Brazil
| | - M Albino
- INSTM and Dept. of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - C Sangregorio
- INSTM and Dept. of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; ICCOM-CNR, via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Q B Cass
- SEPARARE - Núcleo de Pesquisa em Cromatografia, Department of Chemistry, Federal University of São Carlos, Rod. Washington Luiz, Km 235, São Carlos, SP, Brazil
| | - M C de Moraes
- Instituto de Química, Universidade Federal Fluminense. Niterói, Rio de Janeiro, 24020-141, Brazil.
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Huang YT, Yeh PC, Lan SC, Liu PF. Metabolites modulate the functional state of human uridine phosphorylase I. Protein Sci 2020; 29:2189-2200. [PMID: 32864839 DOI: 10.1002/pro.3939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/23/2022]
Abstract
Metabolic pathways in cancer cells typically become reprogrammed to support unconstrained proliferation. These abnormal metabolic states are often accompanied by accumulation of high concentrations of ATP in the cytosol, a phenomenon known as the Warburg Effect. However, how high concentrations of ATP relate to the functional state of proteins is poorly understood. Here, we comprehensively studied the influence of ATP levels on the functional state of the human enzyme, uridine phosphorylase I (hUP1), which is responsible for activating the chemotherapeutic pro-drug, 5-fluorouracil. We found that elevated levels of ATP decrease the stability of hUP1, leading to the loss of its proper folding and function. We further showed that the concentration of hUP1 exerts a critical influence on this ATP-induced destabilizing effect. In addition, we found that ATP interacts with hUP1 through a partially unfolded state and accelerates the rate of hUP1 unfolding. Interestingly, some structurally similar metabolites showed similar destabilization effects on hUP1. Our findings suggest that metabolites can alter the folding and function of a human protein, hUP1, through protein destabilization. This phenomenon may be relevant in studying the functions of proteins that exist in the specific metabolic environment of a cancer cell.
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Affiliation(s)
- Yu-Ting Huang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Pei-Chin Yeh
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Shih-Chun Lan
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung City, Taiwan, Republic of China
| | - Pei-Fen Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung City, Taiwan, Republic of China
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Hamon N, Slusarczyk M, Serpi M, Balzarini J, McGuigan C. Synthesis and biological evaluation of phosphoramidate prodrugs of two analogues of 2-deoxy-d-ribose-1-phosphate directed to the discovery of two carbasugars as new potential anti-HIV leads. Bioorg Med Chem 2014; 23:829-38. [PMID: 25616343 PMCID: PMC7127161 DOI: 10.1016/j.bmc.2014.12.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 11/22/2022]
Abstract
2-Deoxy-α-d-ribose-1-phosphate is of great interest as it is involved in the biosynthesis and/or catabolic degradation of several nucleoside analogues of biological and therapeutic relevance. However due to the lack of a stabilising group at its 2-position, it is difficult to synthesize stable prodrugs of this compound. In order to overcome this lack of stability, the synthesis of carbasugar analogues of 2-deoxyribose-1-phosphate was envisioned. Herein the preparation of a series of prodrugs of two carbocyclic analogues of 2-deoxyribose-1-phosphate using the phosphoramidate ProTide technology, along with their biological evaluation against HIV and cancer cell proliferation, is reported.
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Affiliation(s)
- Nadège Hamon
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Magdalena Slusarczyk
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Christopher McGuigan
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, King Edward VII Avenue, Cardiff CF10 3NB, UK.
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Quintiliani M, Balzarini J, McGuigan C. Design, synthesis, and biological evaluation of C1–phosphonamidate analogues of 2-deoxy-d-ribose-1-phosphate. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.08.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hamon N, Quintiliani M, Balzarini J, McGuigan C. Synthesis and biological evaluation of prodrugs of 2-fluoro-2-deoxyribose-1-phosphate and 2,2-difluoro-2-deoxyribose-1-phosphate. Bioorg Med Chem Lett 2013; 23:2555-9. [PMID: 23541671 PMCID: PMC7127338 DOI: 10.1016/j.bmcl.2013.02.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/26/2013] [Accepted: 02/28/2013] [Indexed: 12/24/2022]
Abstract
We report in this Letter the synthesis of prodrugs of 2-fluoro-2-deoxyarabinose-1-phosphate and 2,2-difluoro-2-deoxyribose-1-phosphate. We demonstrate the difficulty of realising a phosphorylation step on the anomeric position of 2-deoxyribose, and we discover that introduction of fluorine atoms on the 2 position of 2-deoxyribose enables the phosphorylation step: in fact, the stability of the prodrugs increases with the degree of 2-fluorination. Stability studies of produgs of 2-fluoro-2-deoxyribose-1-phosphate and 2,2-difluoro-2-deoxyribose-1-phosphate in acidic and neutral conditions were conducted to confirm our observation. Biological evaluation of prodrugs of 2,2-difluoro-2-deoxyribose-1-phosphate for antiviral and cytotoxic activity is reported.
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Affiliation(s)
- Nadege Hamon
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
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