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Al-Wahaibi LH, Alagappan K, Gomila RM, Blacque O, Frontera A, Percino MJ, El-Emam AA, Thamotharan S. A combined crystallographic and theoretical investigation of noncovalent interactions in 1,3,4-oxadiazole-2-thione- N-Mannich derivatives: in vitro bioactivity and molecular docking. RSC Adv 2023; 13:34064-34077. [PMID: 38019986 PMCID: PMC10660235 DOI: 10.1039/d3ra07169c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Two 1,3,4-oxadiazole-2-thione-N-Mannich derivatives, specifically 5-(4-chlorophenyl)-3-[(2-trifluoromethylphenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (1) and 5-(4-chlorophenyl)-3-[(2,5-difluorophenylamino)methyl]-1,3,4-oxadiazole-2(3H)-thione (2), were synthesized and then characterized by elemental analysis and NMR (1H and 13C) spectroscopy and the single crystal X-ray diffraction method. The formed weak intermolecular interactions in the solid-state structures of these derivatives were thoroughly investigated utilizing a variety of theoretical tools such as Hirshfeld surface analysis and quantum theory of atoms in molecules (QTAIM). Furthermore, the CLP-PIXEL and density functional theory calculations were used to study the energetics of molecular dimers. Numerous weak intermolecular interactions such as C-H⋯S/Cl/F/π interactions, a directional C-Cl⋯Cl halogen bond, π-stacking, type C-F⋯F-C contact and a short F⋯O interaction, help to stabilize the crystal structure of 1. Crystal structure 2 also stabilizes with several weak intermolecular contacts, including N-H⋯S, C-H⋯N//Cl/F interactions, a highly directional C1-Cl1⋯C(π) halogen bond and C(π)⋯C(π) interaction. In vitro antimicrobial potency of compounds 1 and 2 was assessed against various Gram-positive and Gram-negative bacterial strains and the pathogenic yeast-like Candida albicans. Both compounds showed marked activity against all tested Gram-positive bacteria and weak activity against Escherichia coli and lacked inhibitory activity against Pseudomonas aeruginosa. In addition, compounds 1 and 2 displayed good in vitro anti-proliferative activity against hepatocellular carcinoma (HepG-2) and mammary gland breast cancer (MCF-7) cancer cell lines. Molecular docking studies revealed the binding modes of title compounds at the active sites of prospective therapeutic targets.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University Riyadh 11671 Saudi Arabia
| | - Kowsalya Alagappan
- Biomolecular Crystallography Laboratory and DBT-Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur 613 401 India
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears Ctra. de Valldemossa km 7.5, Baleares 07122 Palma de Mallorca Spain
| | - Olivier Blacque
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears Ctra. de Valldemossa km 7.5, Baleares 07122 Palma de Mallorca Spain
| | - M Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo Independencia O2 Sur 50, San Pedro Zacachimalpa Puebla 72960 CP México
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory and DBT-Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed University Thanjavur 613 401 India
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2
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Du J, Zhang C, Liu F, Liu X, Wang D, Zhao D, Shui G, Zhao Y, Yan C. Distinctive metabolic remodeling in TYMP deficiency beyond mitochondrial dysfunction. J Mol Med (Berl) 2023; 101:1237-1253. [PMID: 37603049 DOI: 10.1007/s00109-023-02358-9] [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: 01/02/2023] [Revised: 07/09/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in the TYMP gene, which encodes thymidine phosphorylase (TP). As a cytosolic metabolic enzyme, TP defects affect biological processes that are thought to not be limited to the abnormal replication of mitochondrial DNA. This study aimed to elucidate the characteristic metabolic alterations and associated homeostatic regulation caused by TYMP deficiency. The pathogenicity of novel TYMP variants was evaluated in terms of clinical features, genetic analysis, and structural instability. We analyzed plasma samples from three patients with MNGIE; three patients with m.3243A > G mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS); and four healthy controls (HC) using both targeted and untargeted metabolomics techniques. Transcriptomics analysis and bioenergetic studies were performed on skin fibroblasts from participants in these three groups. A TYMP overexpression experiment was conducted to rescue the observed changes. Compared with controls, specific alterations in nucleosides, bile acids, and steroid metabolites were identified in the plasma of MNGIE patients. Comparable mitochondrial dysfunction was present in fibroblasts from patients with TYMP deficiency and in those from patients with the m.3243A > G mutation. Distinctively decreased sterol regulatory element binding protein (SREBP) regulated cholesterol metabolism and fatty acid (FA) biosynthesis as well as reduced FA degradation were revealed in fibroblasts with TYMP deficiency. The restoration of thymidine phosphorylase activity rescued the observed changes in MNGIE fibroblasts. Our findings indicated that more widespread metabolic disturbance may be caused by TYMP deficiency in addition to mitochondrial dysfunction, which expands our knowledge of the biochemical outcome of TYMP deficiency. KEY MESSAGES: Distinct metabolic profiles in patients with TYMP deficiency compared to those with m.3243A > G mutation. TYMP deficiency leads to a global disruption of nucleoside metabolism. Cholesterol and fatty acid metabolism are inhibited in individuals with MNGIE. TYMP is functionally related to SREBP-regulated pathways. Potential metabolite biomarkers that could be valuable clinical tools to improve the diagnosis of MNGIE.
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Affiliation(s)
- Jixiang Du
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chao Zhang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Fuchen Liu
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xihan Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dongdong Wang
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dandan Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuying Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chuanzhu Yan
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Qingdao, 266103, China.
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Ammar M, Safi W, Tlili A, Alila-Fersi O, Frikha F, Chouchen J, Mnif F, Kharrat M, Maalej M, Felhi R, Abid M, Mnif-Feki M, Kacem FH, Fakhfakh F, Mkaouar-Rebai E. A novel TYMP mutation in a family with MNGIE syndrome: Molecular docking, dynamic simulation and computational investigations. Int J Dev Neurosci 2022; 82:626-638. [PMID: 35841120 DOI: 10.1002/jdn.10215] [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: 04/04/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/11/2022] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE; OMIM 603041) is a rare inherited metabolic disorder mostly caused by mutations in TYMP gene encoding thymidine phosphorylase (TP) protein that affects the mitochondrial nucleotide metabolism. TP, functionally active as a homodimer, is involved in the salvage pathway of pyrimidine nucleosides. MNGIE-like syndrome having an overlapping phenotype of MNGIE was also described and has been associated with mutations in POLG and RRM2B genes. In the present study, we report the molecular investigation of a consanguineous family including two patients with clinical features suggestive of MNGIE syndrome. Bioinformatics analyses were carried out in addition to mtDNA deletion screening and copy number quantification in the blood of the two patients. Whole exome sequencing and Sanger sequencing analyses revealed the segregation in the affected family a novel mutation c.1205T>A (p.L402Q) within the exon 9 of the TYMP gene. In addition, mtDNA analysis revealed the absence of mtDNA deletions and a decrease of the copy number in the blood of the two patients of the studied family. The p.Leu402Gln mutation was located in a conserved amino acid within the α/β domain of the TP protein and several software supported its pathogenicity. In addition, and based on docking and molecular dynamic simulation analyses, results revealed that L402Q caused a conformational change in TP mutated structure and could therefore alter its flexibility and stability. These changes prevent also the formation of stable homodimer leading to non-functional protein with partial or complete loss of its catalytic activity.
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Affiliation(s)
- Marwa Ammar
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Wajdi Safi
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Olfa Alila-Fersi
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Fakher Frikha
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Jihen Chouchen
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Fatma Mnif
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Marwa Kharrat
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Marwa Maalej
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Rahma Felhi
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Mohamed Abid
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Mouna Mnif-Feki
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Faten Hadj Kacem
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
| | - Emna Mkaouar-Rebai
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences. University of Sfax, Tunisia
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Stary D, Kukułowicz J, Góral I, Baltrukevich H, Barbasevich M, Godyń J, Bajda M. Multilevel virtual screening approach for discovery of thymidine phosphorylase inhibitors as potential anticancer agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Warfield BM, Reigan P. Multifunctional role of thymidine phosphorylase in cancer. Trends Cancer 2022; 8:482-493. [DOI: 10.1016/j.trecan.2022.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
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Aknin K, Bontemps A, Farce A, Merlet E, Belmont P, Helissey P, Chavatte P, Sari MA, Giorgi-Renault S, Desbène-Finck S. Polycyclic nitrogen heterocycles as potential thymidine phosphorylase inhibitors: synthesis, biological evaluation, and molecular docking study. J Enzyme Inhib Med Chem 2021; 37:252-268. [PMID: 34933639 PMCID: PMC8725971 DOI: 10.1080/14756366.2021.2001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
New polycyclic heterocycles were synthesised and evaluated as potential inhibitors of thymidine phosphorylase (TP). Inspired by the pharmacophoric pyrimidinedione core of the natural substrate, four series have been designed in order to interact with large empty pockets of the active site: pyrimidoquinoline-2,4-diones (series A), pyrimidinedione linked to a pyrroloquinoline-1,3-diones (series B and C), the polycyclic heterocycle has been replaced by a pyrimidopyridopyrrolidinetetraone (series D). In each series, the tricyclic nitrogen heterocyclic moiety has been synthesised by a one-pot multicomponent reaction. Compared to 7-DX used as control, 2d, 2l, 2p (series A), 28a (series D), and the open intermediate 30 showed modest to good activities. A kinetic study confirmed that the most active compounds 2d, 2p are competitive inhibitors. Molecular docking analysis confirmed the interaction of these new compounds at the active binding site of TP and highlighted a plausible specific interaction in a pocket that had not yet been explored.
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Affiliation(s)
- Karen Aknin
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Alexis Bontemps
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Amaury Farce
- Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Université de Lille, Lille, France
| | - Eric Merlet
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Philippe Belmont
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Philippe Helissey
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Philippe Chavatte
- Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Université de Lille, Lille, France
| | - Marie-Agnès Sari
- Faculté des Sciences, CNRS, UMR 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université de Paris, Paris, France
| | - Sylviane Giorgi-Renault
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
| | - Stéphanie Desbène-Finck
- Faculté de Santé, Faculté de Pharmacie de Paris, Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), CNRS UMR8038, Université de Paris, Paris, France
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Karamitros CS, Somody CM, Agnello G, Rowlinson S. Engineering of the Recombinant Expression and PEGylation Efficiency of the Therapeutic Enzyme Human Thymidine Phosphorylase. Front Bioeng Biotechnol 2021; 9:793985. [PMID: 34976980 PMCID: PMC8718881 DOI: 10.3389/fbioe.2021.793985] [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: 10/12/2021] [Accepted: 11/12/2021] [Indexed: 12/01/2022] Open
Abstract
Human thymidine phosphorylase (HsTP) is an enzyme with important implications in the field of rare metabolic diseases. Defective mutations of HsTP lead to mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), a disease with a high unmet medical need that is associated with severe neurological and gastrointestinal complications. Current efforts focus on the development of an enzyme replacement therapy (ERT) using the Escherichia coli ortholog (EcTP). However, bacterial enzymes are counter-indicated for human therapeutic applications because they are recognized as foreign by the human immune system, thereby eliciting adverse immune responses and raising significant safety and efficacy risks. Thus, it is critical to utilize the HsTP enzyme as starting scaffold for pre-clinical drug development, thus de-risking the safety concerns associated with the use of bacterial enzymes. However, HsTP expresses very poorly in E. coli, whereas its PEGylation, a crucial chemical modification for achieving long serum persistence of therapeutic enzymes, is highly inefficient and negatively affects its catalytic activity. Here we focused on the engineering of the recombinant expression profile of HsTP in E. coli cells, as well as on the optimization of its PEGylation efficiency aiming at the development of an alternative therapeutic approach for MNGIE. We show that phylogenetic and structural analysis of proteins can provide important insights for the rational design of N’-terminus-truncation constructs which exhibit significantly improved recombinant expression levels. In addition, we developed and implemented a criteria-driven rational surface engineering strategy for the substitution of arginine-to-lysine and lysine-to-arginine residues to achieve more efficient, homogeneous and reproducible PEGylation without negatively affecting the enzymatic catalytic activity upon PEGylation. Collectively, our proposed strategies provide an effective way to optimize enzyme PEGylation and E. coli recombinant expression and are likely applicable for other proteins and enzymes.
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Timofeev VI, Zhukhlistova NE, Kuranova IP. Molecular Dynamics Study of Escherichia coli Thymidine Phosphorylase in a Complex with 3'-Azidothymidine Inhibitor and Phosphate. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract—
Using a molecular dynamics method, the state of the dimeric thymidine phosphorylase molecule from Escherichia coli in a complex with noncompetitive enzyme inhibitor 3'-azidothymidine and phosphate ion was studied on a trajectory of 50 ns. Previously obtained atomic coordinates of a complex of thymidine phosphorylase with azidothymidine and sulfate at a resolution of 1.52 Å were used as a starting model. It was demonstrated that both subunits of a dimeric enzyme molecule function asynchronously in a given time interval; moreover, each subunit maintains an open conformation. It was found that the nature of ligand at the nucleoside center affects the binding strength of phosphate in the phosphate center. In a complex with an inhibitor, both ligands over the entire time interval remain bound to the enzyme, while the release of phosphate from the active center is observed when simulating the behavior of thymidine phosphorylase in the presence of phosphate and thymidine substrate. The stabilizing effect of azidothymidine on phosphate binding is consistent with the behavior of azidothymidine as a noncompetitive inhibitor of thymidine phosphorylase.
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Warfield BM, Matheson CJ, McArthur DG, Backos DS, Reigan P. Evaluation of Thymidine Phosphorylase Inhibitors in Glioblastoma and Their Capacity for Temozolomide Potentiation. ACS Chem Neurosci 2021; 12:3477-3486. [PMID: 34472849 DOI: 10.1021/acschemneuro.1c00494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A number of studies have shown high levels of thymidine phosphorylase (TP) expression in glioblastoma (GBM), with trace or undetectable TP levels in normal developed brain tissue. TP catalyzes the reversible phosphorolysis of thymidine to thymine and 2-deoxyribose-1-phosphate, maintaining nucleoside homeostasis for efficient DNA replication and cell division. The TP-mediated catabolism of thymidine is responsible for multiple protumor processes and can support angiogenesis, glycation of proteins, and alternative metabolism. In this study, we examined the effect of TP inhibition in GBM using the known nanomolar TP inhibitors 5-chloro-6-[1-(2'-iminopyrrolidin-1'-yl)methyl]uracil (TPI) and the analogous 6-[(2'-aminoimidazol-1'-yl)methyl]uracils. Although these TP inhibitors did not demonstrate any appreciable cytotoxicity in GBM cell lines as single agents, they did enhance the cytotoxicity of temozolomide (TMZ). This pontetiated action of TMZ by TP inhibition may be due to limiting the availability of thymine for DNA repair and replication. These studies support that TP inhibitors could be used as chemosensitizing agents in GBM to improve the efficacy of TMZ.
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Affiliation(s)
- Becka M. Warfield
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States
| | - Christopher J. Matheson
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States
| | - Debbie G. McArthur
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States
| | - Donald S. Backos
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States
| | - Philip Reigan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States
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Zagórska A, Czopek A, Jaromin A, Mielczarek-Puta M, Struga M, Stary D, Bajda M. Design, Synthesis, and In Vitro Antiproliferative Activity of Hydantoin and Purine Derivatives with the 4-Acetylphenylpiperazinylalkyl Moiety. MATERIALS 2021; 14:ma14154156. [PMID: 34361351 PMCID: PMC8347464 DOI: 10.3390/ma14154156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022]
Abstract
Cancer represents one of the most serious health problems and the second leading cause of death around the world. Heterocycles, due to their prevalence in nature as well as their structural and chemical diversity, play an immensely important role in anti-cancer drug discovery. In this paper, a series of hydantoin and purine derivatives containing a 4-acetylphenylpiperazinylalkyl moiety were designed, synthesized, and biologically evaluated for their anticancer activity on selected cancer cell lines (PC3, SW480, SW620). Compound 4, a derivative of 3′,4′-dihydro-2′H-spiro[imidazolidine-4,1′-naphthalene]-2,5-dione, was the most effective against SW480, SW620, and PC3 cancer cell lines. Moreover, 4 has high tumor-targeting selectivity. Based on docking studies, it was concluded that R isomers of 3′,4′-dihydro-2′H-spiro[imidazolidine-4,1′-naphthalene]-2,5-dione could be further studied as promising scaffolds for the development of thymidine phosphorylase inhibitors.
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Affiliation(s)
- Agnieszka Zagórska
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland;
- Correspondence: (A.Z.); (A.J.); Tel.: +48-12-62-05-450 (A.Z.); +48-71-37-56-203 (A.J.)
| | - Anna Czopek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland;
| | - Anna Jaromin
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
- Correspondence: (A.Z.); (A.J.); Tel.: +48-12-62-05-450 (A.Z.); +48-71-37-56-203 (A.J.)
| | - Magdalena Mielczarek-Puta
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (M.M.-P.); (M.S.)
| | - Marta Struga
- Chair and Department of Biochemistry, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland; (M.M.-P.); (M.S.)
| | - Dorota Stary
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland; (D.S.); (M.B.)
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland; (D.S.); (M.B.)
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Bajaj S, Kumar MS, Tinwala H, Yc M. Design, synthesis, modelling studies and biological evaluation of 1,3,4-oxadiazole derivatives as potent anticancer agents targeting thymidine phosphorylase enzyme. Bioorg Chem 2021; 111:104873. [PMID: 33845381 DOI: 10.1016/j.bioorg.2021.104873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
A series of novel 1,3,4-oxadiazole derivatives with substituted phenyl ring were designed and synthesized with an objective of discovering newer anti-cancer agents targeting thymidine phosphorylase enzyme (TP). The 1,3,4-oxadiazole derivatives were synthesized by simple and convenient methods in the lab. Chemical structure of the all the synthesized compounds were characterized by IR, 1H NMR and mass spectral methods and evaluated for cytotoxicity by MTT method against two breast cancer cell lines (MCF-7 and MDA-MB-231). Further, results of TP assay identified that 1,3,4-oxadiazole molecules displayed anti-cancer activity partially by inhibition of phosphorylation of thymidine. The TP assay identified SB8 and SB9 as potential inhibitors with anti-cancer activity against both the cell lines. The molecular docking studies recognized the orientation and binding interaction of molecule at the active site amino acid residues of TP (PDB: 1UOU). Acute toxicity studies of compound SB8 at the dose of 5000 mg/kg has identified no signs of clinical toxicity was observed. The SARs study of synthesized derivatives revealed that the substitution of phenyl ring with electron withdrawing group at ortho position showed significant TP inhibitory activity compared to para substitution. The experimental data suggests that 1,3,4-oxadiazole with substituted phenyl can be taken as a lead for the design of efficient TP inhibitors and active compounds which can be taken up for further studies.
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Affiliation(s)
- Shalini Bajaj
- Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India
| | - Maushmi S Kumar
- Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India
| | - Hussain Tinwala
- Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India
| | - Mayur Yc
- Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India.
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12
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Belcher A, Zulfiker AHM, Li OQ, Yue H, Gupta AS, Li W. Targeting Thymidine Phosphorylase With Tipiracil Hydrochloride Attenuates Thrombosis Without Increasing Risk of Bleeding in Mice. Arterioscler Thromb Vasc Biol 2021; 41:668-682. [PMID: 33297751 PMCID: PMC8105268 DOI: 10.1161/atvbaha.120.315109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Current antiplatelet medications increase the risk of bleeding, which leads to a clear clinical need in developing novel mechanism-based antiplatelet drugs. TYMP (Thymidine phosphorylase), a cytoplasm protein that is highly expressed in platelets, facilitates multiple agonist-induced platelet activation, and enhances thrombosis. Tipiracil hydrochloride (TPI), a selective TYMP inhibitor, has been approved by the Food and Drug Administration for clinical use. We tested the hypothesis that TPI is a safe antithrombotic medication. Approach and Results: By coexpression of TYMP and Lyn, GST (glutathione S-transferase) tagged Lyn-SH3 domain or Lyn-SH2 domain, we showed the direct evidence that TYMP binds to Lyn through both SH3 and SH2 domains, and TPI diminished the binding. TYMP deficiency significantly inhibits thrombosis in vivo in both sexes. Pretreatment of platelets with TPI rapidly inhibited collagen- and ADP-induced platelet aggregation. Under either normal or hyperlipidemic conditions, treating wild-type mice with TPI via intraperitoneal injection, intravenous injection, or gavage feeding dramatically inhibited thrombosis without inducing significant bleeding. Even at high doses, TPI has a lower bleeding side effect compared with aspirin and clopidogrel. Intravenous delivery of TPI alone or combined with tissue plasminogen activator dramatically inhibited thrombosis. Dual administration of a very low dose of aspirin and TPI, which had no antithrombotic effects when used alone, significantly inhibited thrombosis without disturbing hemostasis. CONCLUSIONS This study demonstrated that inhibition of TYMP, a cytoplasmic protein, attenuated multiple signaling pathways that mediate platelet activation, aggregation, and thrombosis. TPI can be used as a novel antithrombotic medication without the increase in risk of bleeding.
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Affiliation(s)
- Adam Belcher
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Abu Hasanat Md Zulfiker
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Oliver Qiyue Li
- Marshall Institute for Interdisciplinary Research; Huntington, WV, 25701, USA
| | - Hong Yue
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Anirban Sen Gupta
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland OH 44106, USA
| | - Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
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13
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Meinders M, Shoemark D, Dobbe JGG, Streekstra GJ, Frayne J, Toye AM. Expression and Retention of Thymidine Phosphorylase in Cultured Reticulocytes as a Novel Treatment for MNGIE. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:822-830. [PMID: 32368563 PMCID: PMC7191122 DOI: 10.1016/j.omtm.2020.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 11/04/2022]
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare autosomal metabolic disorder caused by thymidine phosphorylase (TP) deficiency. Successful therapeutic interventions for this disease rely on a means for efficient and long-lasting circulation of the TP enzyme. In this study we exploit lentiviral transduction of hematopoietic stem cells and an erythroid cell line (BEL-A) to generate reticulocytes that contain active TP. Significant loss of overexpressed TP during erythroid differentiation can be reduced by addition of the ubiquitination inhibitor MG132. However, the ubiquitination sites are located in the substrate binding site in human TP, and their removal abolished enzyme activity. Examination of the TP structure and mechanism suggested that these sites are only exposed in the absence of substrate. We show that supplementation of culture media with thymidine during differentiation reduces enzyme degradation, doubling the amount of TP retained in reticulocytes. This study provides proof of principle that therapeutic reticulocytes expressing TP can be generated in vitro and that ubiquitin-mediated degradation can be subverted through masking ubiquitination sites to ensure retention of human TP in reticulocytes following erythroid differentiation.
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Affiliation(s)
- Marjolein Meinders
- Bristol Synthetic Biology Centre (BrisSynBio), University of Bristol, Bristol BS8 1TD, UK.,School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK.,NIHR Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol BS8 1TD, UK
| | - Debbie Shoemark
- Bristol Synthetic Biology Centre (BrisSynBio), University of Bristol, Bristol BS8 1TD, UK.,School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Johannes G G Dobbe
- Department of Biomedical Engineering and Physics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Geert J Streekstra
- Department of Biomedical Engineering and Physics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Jan Frayne
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Filton, Bristol BS34 7QH, UK
| | - Ashley M Toye
- Bristol Synthetic Biology Centre (BrisSynBio), University of Bristol, Bristol BS8 1TD, UK.,School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK.,NIHR Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol BS8 1TD, UK.,Bristol Institute for Transfusion Sciences, National Health Service Blood and Transplant (NHSBT), Filton, Bristol BS34 7QH, UK
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14
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Javaid S, Saad SM, Zafar H, Malik R, Khan KM, Choudhary MI, Rahman AU. Thymidine phosphorylase and prostrate cancer cell proliferation inhibitory activities of synthetic 4-hydroxybenzohydrazides: In vitro, kinetic, and in silico studies. PLoS One 2020; 15:e0227549. [PMID: 31986186 PMCID: PMC6984732 DOI: 10.1371/journal.pone.0227549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/11/2019] [Indexed: 02/02/2023] Open
Abstract
Over-expression of thymidine phosphorylase (TP) plays a key role in many pathological complications, including angiogenesis which leads to cancer cells proliferation. Thus in search of new anticancer agents, a series of 4-hydroxybenzohydrazides (1–29) was synthesized, and evaluated for in vitro thymidine phosphorylase inhibitory activity. Twenty compounds 1–3, 6–14, 16, 19, 22–24, and 27–29 showed potent to weak TP inhibitory activities with IC50 values in the range of 6.8 to 229.5 μM, in comparison to the standards i.e. tipiracil (IC50 = 0.014 ± 0.002 μM) and 7-deazaxanthine (IC50 = 41.0 ± 1.63 μM). Kinetic studies on selected inhibitors 3, 9, 14, 22, 27, and 29 revealed uncompetitive and non-competitive modes of inhibition. Molecular docking studies of these inhibitors indicated that they were able to interact with the amino acid residues present in allosteric site of TP, including Asp391, Arg388, and Leu389. Antiproliferative (cytotoxic) activities of active compounds were also evaluated against mouse fibroblast (3T3) and prostate cancer (PC3) cell lines. Compounds 1, 2, 19, and 22–24 exhibited anti-proliferative activities against PC3 cells with IC50 values between 6.5 to 10.5 μM, while they were largely non-cytotoxic to 3T3 (mouse fibroblast) cells proliferation. Present study thus identifies a new class of dual inhibitors of TP and cancer cell proliferation, which deserves to be further investigated for anti-cancer drug development.
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Affiliation(s)
- Sumaira Javaid
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- * E-mail: (SJ); (KMK)
| | - Syed Muhammad Saad
- H. E. J., Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Humaira Zafar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Rizwana Malik
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Khalid Mohammed Khan
- H. E. J., Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- * E-mail: (SJ); (KMK)
| | - M. Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- H. E. J., Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Atta-ur Rahman
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- H. E. J., Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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15
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Tozer T, Heale K, Manto Chagas C, de Barros ALB, Alisaraie L. Interdomain twists of human thymidine phosphorylase and its active-inactive conformations: Binding of 5-FU and its analogues to human thymidine phosphorylase versus dihydropyrimidine dehydrogenase. Chem Biol Drug Des 2019; 94:1956-1972. [PMID: 31356728 DOI: 10.1111/cbdd.13596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/02/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022]
Abstract
5-fluorouracil (5-FU) is an anticancer drug, which inhibits human thymidine phosphorylase (hTP) and plays a key role in maintaining the process of DNA replication and repair. It is involved in regulating pyrimidine nucleotide production, by which it inhibits the mechanism of cell proliferation and cancerous tumor growth. However, up to 80% of the administered drug is metabolized by dihydropyrimidine dehydrogenase (DPD). This work compares binding of 5-FU and its analogues to hTP and DPD, and suggests strategies to reduce drug binding to DPD to decrease the required dose of 5-FU. An important feature between the proteins studied here was the difference of charge distribution in their binding sites, which can be exploited for designing drugs to selectively bind to the hTP. The 5-FU presence was thought to be required for a closed conformation. Comparison of the calculation results pertaining to unliganded and liganded protein showed that hTP could still undergo open-closed conformations in the absence of the ligand; however, the presence of a positively charged ligand better stabilizes the closed conformation and rigidifies the core region of the protein more than unliganded or neutral liganded system. The study has also shown that one of the three hinge segments linking the two major α and α/β domains of the hTP is an important contributing factor to the enzyme's open-close conformational twist during its inactivation-activation process. In addition, the angle between the α/β-domain and the α-domain has shown to undergo wide rotations over the course of MD simulation in the absence of a phosphate, suggesting that it contributes to the stabilization of the closed conformation of the hTP.
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Affiliation(s)
- Tiffany Tozer
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Kali Heale
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Caroline Manto Chagas
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Andre Luis Branco de Barros
- Department of Clinical and Toxicological Analysis, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Laleh Alisaraie
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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16
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Zhang B, Shu M, Xu C, An C, Wang R, Lin Z. Virtual Screening, Docking, Synthesis and Bioactivity Evaluation of Thiazolidinediones as Potential PPARγ Partial Agonists for Preparation of Antidiabetic Agents. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180827123512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background:Peroxisome proliferator-activated receptor gamma (PPARγ) is one of the key targets of insulin resistance research, in addition to being ligand-activated transcription factors of the nuclear hormone receptor superfamily with a leading role in adiposeness activation and insulin sensitivity. They regulate cholesterol and carbohydrate metabolism through direct actions on gene expression. Despite their therapeutic importance, there are dose limiting side effects associated with PPARγ drug treatments, thus a new generation of safer PPARγ drugs are being actively sought after treatment.Methods:In this study, we used computer aided drug design to screen new series of PPARγ ligands, and synthesized a series of potential thiazolidinedione derivatives such as 5,7- dibenzyloxybenzyl-3-hydroxymethyl-4H-coumarin-4-ketone, using 4-steps to synthesize the target compounds and built streptozotocin (STZ) induced insulin resistance rat model to measure their antidiabetic activity.Results:We found that 10 mg/kg concentration of compound 0701C could significantly decrease blood glucose and serum PPARγ, serum insulin levels in insulin resistance model rat.Conclusion:We would conclude that compound 0701C might serve as a potential PPARγ partial agonist.
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Affiliation(s)
- Beina Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Chunmei Xu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Chunhong An
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Rui Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Zhihua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
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17
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de Moura Sperotto ND, Deves Roth C, Rodrigues-Junior VS, Ev Neves C, Reisdorfer Paula F, da Silva Dadda A, Bergo P, Freitas de Freitas T, Souza Macchi F, Moura S, Duarte de Souza AP, Campos MM, Valim Bizarro C, Santos DS, Basso LA, Machado P. Design of Novel Inhibitors of Human Thymidine Phosphorylase: Synthesis, Enzyme Inhibition, in Vitro Toxicity, and Impact on Human Glioblastoma Cancer. J Med Chem 2019; 62:1231-1245. [DOI: 10.1021/acs.jmedchem.8b01305] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Fávero Reisdorfer Paula
- Laboratório de Desenvolvimento e Controle de Qualidade em Medicamentos, Universidade Federal do Pampa, 97508-000 Uruguaiana, RS, Brazil
| | | | | | | | | | - Sidnei Moura
- Laboratório de Produtos Naturais e Sintéticos, Instituto de Biotecnologia, Universidade de Caxias do Sul, 95070-560 Caxias do Sul, RS, Brazil
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18
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Sidorov-Biryukov DD, Podshivalov DD, Timofeev VI, Zhukhlistova NE, Kuranova IP. Molecular Dynamics Study of Thymidine Phosphorylase from E. coli in the Apo Form and in Complexes with Substrates. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774518060287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Pacitti D, Levene M, Garone C, Nirmalananthan N, Bax BE. Mitochondrial Neurogastrointestinal Encephalomyopathy: Into the Fourth Decade, What We Have Learned So Far. Front Genet 2018; 9:669. [PMID: 30627136 PMCID: PMC6309918 DOI: 10.3389/fgene.2018.00669] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/04/2018] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare metabolic autosomal recessive disease, caused by mutations in the nuclear gene TYMP which encodes the enzyme thymidine phosphorylase. The resulting enzyme deficiency leads to a systemic accumulation of the deoxyribonucleosides thymidine and deoxyuridine, and ultimately mitochondrial failure due to a progressive acquisition of secondary mitochondrial DNA (mtDNA) mutations and mtDNA depletion. Clinically, MNGIE is characterized by gastrointestinal and neurological manifestations, including cachexia, gastrointestinal dysmotility, peripheral neuropathy, leukoencephalopathy, ophthalmoplegia and ptosis. The disease is progressively degenerative and leads to death at an average age of 37.6 years. As with the vast majority of rare diseases, patients with MNGIE face a number of unmet needs related to diagnostic delays, a lack of approved therapies, and non-specific clinical management. We provide here a comprehensive collation of the available knowledge of MNGIE since the disease was first described 42 years ago. This review includes symptomatology, diagnostic procedures and hurdles, in vitro and in vivo disease models that have enhanced our understanding of the disease pathology, and finally experimental therapeutic approaches under development. The ultimate aim of this review is to increase clinical awareness of MNGIE, thereby reducing diagnostic delay and improving patient access to putative treatments under investigation.
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Affiliation(s)
- Dario Pacitti
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
| | - Michelle Levene
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
| | - Caterina Garone
- MRC Mitochondrial Biology Unit, Cambridge Biomedical, Cambridge, United Kingdom
| | | | - Bridget E. Bax
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
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20
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Bajaj S, Roy PP, Singh J. Synthesis, thymidine phosphorylase inhibitory and computational study of novel 1,3,4-oxadiazole-2-thione derivatives as potential anticancer agents. Comput Biol Chem 2018; 76:151-160. [DOI: 10.1016/j.compbiolchem.2018.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 11/25/2022]
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21
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Taha M, Rashid U, Imran S, Ali M. Rational design of bis-indolylmethane-oxadiazole hybrids as inhibitors of thymidine phosphorylase. Bioorg Med Chem 2018; 26:3654-3663. [DOI: 10.1016/j.bmc.2018.05.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/29/2018] [Accepted: 05/26/2018] [Indexed: 10/16/2022]
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22
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Iftikhar F, Yaqoob F, Tabassum N, Jan MS, Sadiq A, Tahir S, Batool T, Niaz B, Ansari FL, Choudhary MI, Rashid U. Design, synthesis, in-vitro thymidine phosphorylase inhibition, in-vivo antiangiogenic and in-silico studies of C-6 substituted dihydropyrimidines. Bioorg Chem 2018; 80:99-111. [PMID: 29894893 DOI: 10.1016/j.bioorg.2018.05.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 01/15/2023]
Abstract
Thymidine phosphorylase (TP) is an angiogenic enzyme. It plays an important role in angiogenesis, tumour growth, invasion and metastasis. In current research work, we study the effect of structural modification of dihydropyrimidine-2-ones (DHPM-2-ones) on TP inhibition. A series of eighteen new derivatives of 3,4-dihydropyrimidone-2-one were designed and synthesized through the structural modification at C-6 position. All these new derivatives were then assessed for in-vitro inhibition of thymidine phosphorylase (TP) from E. coli. Oxadiazole derivatives 4a-e exhibited excellent TP-inhibition at low micromolar concentration levels better than standard drug 7-deazaxanthine (7-DX). Among all these compounds, 4b was found to be the most potent with IC50 = 1.09 ± 0.004 μM. Anti-angiogenesis potential of representative compounds were also studied in a chorioallantoic membrane (CAM) assay. Here again, compound 4b was found to be the potent anti-angiogenesis compound in a CAM assay. Docking studies were also performed with Molecular Operating Environment (MOE) to further analyse the mode of inhibition of these compounds. Binding mode analysis of the most active inhibitors showed that these are well accommodated into the binding site of enzyme though stable hydrogen bonding and hydrophobic interactions.
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Affiliation(s)
- Fatima Iftikhar
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Farhana Yaqoob
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | - Nida Tabassum
- Department of Pharmacology, Rawalpindi Medical University, Rawalpindi 463000, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, University of Malakand, Chakdara 18000, Dir (L), Pakistan
| | - Abdul Sadiq
- Department of Pharmacy, University of Malakand, Chakdara 18000, Dir (L), Pakistan
| | - Saba Tahir
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus 22060, Pakistan
| | - Tahira Batool
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biotechnology, University of Azad Jammu & Kashmir Bagh, Pakistan
| | - Basit Niaz
- Department of Chemistry, Hazara University, Mansehra 21120, Pakistan
| | | | - Muhammad Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus 22060, Pakistan.
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23
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Balaev VV, Prokofev II, Gabdoulkhakov AG, Betzel C, Lashkov AA. Crystal structure of pyrimidine-nucleoside phosphorylase from Bacillus subtilis in complex with imidazole and sulfate. Acta Crystallogr F Struct Biol Commun 2018; 74:193-197. [PMID: 29633966 PMCID: PMC5894104 DOI: 10.1107/s2053230x18002935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/19/2018] [Indexed: 11/10/2022] Open
Abstract
Pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity. Investigation of this protein is essential for anticancer drug design. Here, the structure of this protein from Bacillus subtilis in complex with imidazole and sulfate is reported at 1.9 Å resolution, which is an improvement on the previously reported structure at 2.6 Å resolution. The localization and position of imidazole in the nucleoside-binding site reflects the possible binding of ligands that possess an imidazole ring.
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Affiliation(s)
- V. V. Balaev
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - I. I. Prokofev
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - A. G. Gabdoulkhakov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - C. Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Institute of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 83, Hamburg, Germany
| | - A. A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
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24
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Li W, Yue H. Thymidine phosphorylase: A potential new target for treating cardiovascular disease. Trends Cardiovasc Med 2017; 28:157-171. [PMID: 29108898 DOI: 10.1016/j.tcm.2017.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022]
Abstract
We recently found that thymidine phosphorylase (TYMP), also known as platelet-derived endothelial cell growth factor, plays an important role in platelet activation in vitro and thrombosis in vivo by participating in multiple signaling pathways. Platelets are a major source of TYMP. Since platelet-mediated clot formation is a key event in several fatal diseases, such as myocardial infarction, stroke and pulmonary embolism, understanding TYMP in depth may lead to uncovering novel mechanisms in the development of cardiovascular diseases. Targeting TYMP may become a novel therapeutic for cardiovascular disorders. In this review article, we summarize the discovery of TYMP and the potential molecular mechanisms of TYMP involved in the development of various diseases, especially cardiovascular diseases. We also offer insights regarding future studies exploring the role of TYMP in the development of cardiovascular disease as well as in therapy.
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Affiliation(s)
- Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall, University, Huntington, WV; Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, WV.
| | - Hong Yue
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall, University, Huntington, WV
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25
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Tomoike F, Nakagawa N, Fukui K, Yano T, Kuramitsu S, Masui R. Indispensable residue for uridine binding in the uridine-cytidine kinase family. Biochem Biophys Rep 2017; 11:93-98. [PMID: 28955773 PMCID: PMC5614712 DOI: 10.1016/j.bbrep.2017.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 06/09/2017] [Accepted: 07/03/2017] [Indexed: 10/31/2022] Open
Abstract
Uridine-cytidine kinase (UCK), including human UCK2, are a family of enzymes that generally phosphorylate both uridine and cytidine. However, UCK of Thermus thermophilus HB8 (ttCK) phosphorylates only cytidine. This cytidine-restricted activity is thought to depend on Tyr93, although the precise mechanism remains unresolved. Exhaustive mutagenesis of Tyr93 in ttCK revealed that the uridine phosphorylation activity was restored only by replacement of Tyr93 with His or Gln. Replacement of His117 in human UCK2, corresponding to residue Tyr93 in ttCK, by Tyr resulted in a loss of uridine phosphorylation activity. These findings indicated that uridine phosphorylation activity commonly depends on a single residue in the UCK family.
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Affiliation(s)
- Fumiaki Tomoike
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- Research Center for Materials Science, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Noriko Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Kenji Fukui
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Takato Yano
- Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Ryoji Masui
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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Tada Y, Kazuno H, Sato T, Suzuki N, Emura T, Yano S. Molecular modeling study of the thymidine phosphorylase inhibitor by SBDD and classical QSAR analysis. CHEM-BIO INFORMATICS JOURNAL 2017. [DOI: 10.1273/cbij.17.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yukio Tada
- Department of Computational Intelligence and System Science, Tokyo Institute of Technology
| | - Hideki Kazuno
- Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd
| | - Tsutomu Sato
- Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd
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Bera H, Chigurupati S. Recent discovery of non-nucleobase thymidine phosphorylase inhibitors targeting cancer. Eur J Med Chem 2016; 124:992-1003. [PMID: 27783978 DOI: 10.1016/j.ejmech.2016.10.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 01/19/2023]
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Balaev VV, Lashkov AA, Prokofev II, Gabdulkhakov AG, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. Acta Crystallogr F Struct Biol Commun 2016; 72:224-33. [PMID: 26919527 PMCID: PMC4774882 DOI: 10.1107/s2053230x1600162x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/26/2016] [Indexed: 11/10/2022] Open
Abstract
Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-α-D-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of the thymidine phosphorylase from Salmonella typhimurium were solved and refined: the unliganded structure at 2.05 Å resolution (PDB entry 4xr5), the structure of the complex with thymidine at 2.55 Å resolution (PDB entry 4yek) and that of the complex with uridine at 2.43 Å resolution (PDB entry 4yyy). The various structural features of the enzyme which might be responsible for the specificity for thymidine and not for uridine were identified. The presence of the 2'-hydroxyl group in uridine results in a different position of the uridine furanose moiety compared with that of thymidine. This feature may be the key element of the substrate specificity. The specificity might also be associated with the opening/closure mechanism of the two-domain subunit structure of the enzyme.
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Affiliation(s)
- Vladislav V. Balaev
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Maria V. Dontsova
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Tatiana A. Seregina
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Alexander S. Mironov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Institute of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
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Discovery of mixed type thymidine phosphorylase inhibitors endowed with antiangiogenic properties: Synthesis, pharmacological evaluation and molecular docking study of 2-thioxo-pyrazolo[1,5-a][1,3,5]triazin-4-ones. Part II. Eur J Med Chem 2014; 78:294-303. [DOI: 10.1016/j.ejmech.2014.03.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 11/23/2022]
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31
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Bera H, Dolzhenko AV, Sun L, Dutta Gupta S, Chui WK. Synthesis and in vitro evaluation of 1,2,4-triazolo[1,5-a][1,3,5]triazine derivatives as thymidine phosphorylase inhibitors. Chem Biol Drug Des 2014; 82:351-60. [PMID: 23758794 DOI: 10.1111/cbdd.12171] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 05/15/2013] [Accepted: 06/06/2013] [Indexed: 11/29/2022]
Abstract
In our lead finding program, a series of 1,2,4-triazolo[1,5-a][1,3,5]triazine derivatives were synthesized, and their in vitro thymidine phosphorylase inhibitory potential was explored. Among the different derivatives, compounds having keto group (C = O) at C7 and thioketo group (C = S) at C5 positions showed varying degrees of TP inhibitory activity comparable with positive control, 7-deazaxanthine (7-DX, 2) (IC50 value = 42.63 μm). Enzyme inhibition kinetics study suggested that compound IVn behaved as a mixed-type inhibitor of the enzyme with respect to thymidine (dThd) as a variable substrate. Compound IVn was also found to inhibit PMA-induced MMP-9 expression in MDA-MB-231 cells at sublethal concentrations. Computational docking study was performed to illustrate the enzyme inhibition kinetics and to explore the ligand-enzyme interactions.
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Affiliation(s)
- Hriday Bera
- Gokaraju Rangaraju College of Pharmacy, Bachupally, Hyderabad, 500090, India; Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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Timofeev V, Abramchik Y, Zhukhlistova N, Muravieva T, Fateev I, Esipov R, Kuranova I. 3'-Azidothymidine in the active site of Escherichia coli thymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study. ACTA ACUST UNITED AC 2014; 70:1155-65. [PMID: 24699659 DOI: 10.1107/s1399004714001904] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/27/2014] [Indexed: 11/10/2022]
Abstract
The structural study of complexes of thymidine phosphorylase (TP) with nucleoside analogues which inhibit its activity is of special interest because many of these compounds are used as chemotherapeutic agents. Determination of kinetic parameters showed that 3'-azido-3'-deoxythymidine (3'-azidothymidine; AZT), which is widely used for the treatment of human immunodeficiency virus, is a reversible noncompetitive inhibitor of Escherichia coli thymidine phosphorylase (TP). The three-dimensional structure of E. coli TP complexed with AZT was solved by the molecular-replacement method and was refined at 1.52 Å resolution. Crystals for X-ray study were grown in microgravity by the counter-diffusion technique from a solution of the protein in phosphate buffer with ammonium sulfate as a precipitant. The AZT molecule was located with full occupancy in the electron-density maps in the nucleoside-binding pocket of TP, whereas the phosphate-binding pocket of the enzyme was occupied by phosphate (or sulfate) ion. The structure of the active-site cavity and conformational changes of the enzyme upon AZT binding are described in detail. It is found that the position of AZT differs remarkably from the positions of the pyrimidine bases and nucleoside analogues in other known complexes of pyrimidine phosphorylases, but coincides well with the position of 2'-fluoro-3'-azido-2',3'-dideoxyuridine (N3FddU) in the recently investigated complex of E. coli TP with this ligand (Timofeev et al., 2013). The peculiarities of the arrangement of N3FddU and 3'-azidothymidine in the nucleoside binding pocket of TP and correlations between the arrangement and inhibitory properties of these compounds are discussed.
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Affiliation(s)
- Vladimir Timofeev
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Yulia Abramchik
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Nadezda Zhukhlistova
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Tatiana Muravieva
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Ilya Fateev
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Roman Esipov
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Inna Kuranova
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
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33
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Košiová I, Šimák O, Panova N, Buděšínský M, Petrová M, Rejman D, Liboska R, Páv O, Rosenberg I. Inhibition of human thymidine phosphorylase by conformationally constrained pyrimidine nucleoside phosphonic acids and their “open-structure” isosteres. Eur J Med Chem 2014; 74:145-68. [DOI: 10.1016/j.ejmech.2013.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/12/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022]
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Synthesis and biological evaluation of novel oxadiazole derivatives: A new class of thymidine phosphorylase inhibitors as potential anti-tumor agents. Bioorg Med Chem 2014; 22:1008-15. [DOI: 10.1016/j.bmc.2013.12.043] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 02/06/2023]
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Deves C, Rostirolla DC, Martinelli LKB, Bizarro CV, Santos DS, Basso LA. The kinetic mechanism of Human Thymidine Phosphorylase - a molecular target for cancer drug development. MOLECULAR BIOSYSTEMS 2014; 10:592-604. [PMID: 24407036 DOI: 10.1039/c3mb70453j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human Thymidine Phosphorylase (HTP), also known as the platelet-derived endothelial cell growth factor (PD-ECGF) or gliostatin, catalyzes the reversible phosphorolysis of thymidine (dThd) to thymine and 2-deoxy-α-d-ribose-1-phosphate (2dR1P). HTP is a key enzyme in the pyrimidine salvage pathway involved in dThd homeostasis in cells. HTP is a target for anticancer drug development as its enzymatic activity promotes angiogenesis. Here, we describe cloning, expression, and purification to homogeneity of recombinant TYMP-encoded HTP. Peptide fingerprinting and the molecular mass value of the homogenous protein confirmed its identity as HTP assessed by mass spectrometry. Size exclusion chromatography showed that HTP is a dimer in solution. Kinetic studies revealed that HTP displayed substrate inhibition for dThd. Initial velocity and isothermal titration calorimetry (ITC) studies suggest that HTP catalysis follows a rapid-equilibrium random bi-bi kinetic mechanism. ITC measurements also showed that dThd and Pi binding are favorable processes. The pH-rate profiles indicated that maximal enzyme activity was achieved at low pH values. Functional groups with apparent pK values of 5.2 and 9.0 are involved in dThd binding and groups with pK values of 6.1 and 7.8 are involved in phosphate binding.
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Affiliation(s)
- Candida Deves
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A Av. Ipiranga, 90619-900, Porto Alegre, RS, Brazil.
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Timofeev VI, Abramchik YA, Fateev IV, Zhukhlistova NE, Murav’eva TI, Kuranova IP, Esipov RS. Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3′-azido-2′-fluoro-2′,3′-dideoxyuridine. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s1063774513060230] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Bera H, Lee MH, Sun L, Dolzhenko AV, Chui WK. Synthesis, anti-thymidine phosphorylase activity and molecular docking of 5-thioxo-[1,2,4]triazolo[1,5-a][1,3,5]triazin-7-ones. Bioorg Chem 2013; 50:34-40. [PMID: 23968897 DOI: 10.1016/j.bioorg.2013.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 07/17/2013] [Accepted: 07/24/2013] [Indexed: 11/16/2022]
Abstract
In our lead finding program, a series of 5-thioxo-[1,2,4]triazolo[1,5-a][1,3,5]triazin-7-ones and their 5-thio-alkyl derivatives were designed and synthesized which contained different substituents at ortho-position of 2-phenyl ring attached to the fused ring structure. The preliminary pharmacological evaluation demonstrated that the synthesized compounds exhibited a varying degree of inhibitory activity towards thymidine phosphorylase (TP), comparable to reference compound, 7-Deazaxanthine (7-DX, 2) (IC50 value=42.63 μM). The study also inferred that the ortho-substituted group at the phenyl ring and 5-thio-alkyl moiety imparted steric hindrance effects in the binding site of the enzyme, leading to a reduced inhibitory response. In addition, compound 3a was identified as a mixed-type inhibitor of TP. Moreover, computational docking study was performed to illustrate the important structural information on the plausible ligand-enzyme binding interactions.
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Affiliation(s)
- Hriday Bera
- Gokaraju Rangaraju College of Pharmacy, Bachupally, Hyderabad 500090, India; Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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38
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Nishitani Y, Aono R, Nakamura A, Sato T, Atomi H, Imanaka T, Miki K. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J Mol Biol 2013; 425:2709-21. [PMID: 23659790 DOI: 10.1016/j.jmb.2013.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/11/2013] [Accepted: 04/25/2013] [Indexed: 11/29/2022]
Abstract
AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macromolecular structure (>40-mers) in solution. To investigate its unique multimerization feature, we determined the first crystal structures of Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseΔN84 and Tk-AMPpaseΔC10) clarified that this multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Moreover, biochemical analysis demonstrated that the macromolecular assembly of Tk-AMPpase contributes to its high thermostability, essential for an enzyme from a hyperthermophile. Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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39
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Bera H, Chui WK, Gupta SD, Dolzhenko AV, Sun L. Synthesis, in vitro evaluation of thymidine phosphorylase inhibitory activity, and in silico study of 1,3,5-triazin-2,4-dione and its fused analogues. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0589-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Abstract
Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states bind tightly to enzymes by stabilizing the conformation optimized through evolution for transition state formation. Instead of forming the transient transition state geometry, transition state analogues convert the short-lived transition state to a stable thermodynamic state. Enzymatic transition states are understood by combining kinetic isotope effects and computational chemistry. Analogues of the transition state can bind millions of times more tightly than substrates and show promise for drug development for several targets.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx New York 10461, United States.
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41
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Characterization of pyrimidine nucleoside phosphorylase of Mycoplasma hyorhinis: implications for the clinical efficacy of nucleoside analogues. Biochem J 2012; 445:113-23. [PMID: 22475552 DOI: 10.1042/bj20112225] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present paper we demonstrate that the cytostatic and antiviral activity of pyrimidine nucleoside analogues is markedly decreased by a Mycoplasma hyorhinis infection and show that the phosphorolytic activity of the mycoplasmas is responsible for this. Since mycoplasmas are (i) an important cause of secondary infections in immunocompromised (e.g. HIV infected) patients and (ii) known to preferentially colonize tumour tissue in cancer patients, catabolic mycoplasma enzymes may compromise efficient chemotherapy of virus infections and cancer. In the genome of M. hyorhinis, a TP (thymidine phosphorylase) gene has been annotated. This gene was cloned, expressed in Escherichia coli and kinetically characterized. Whereas the mycoplasma TP efficiently catalyses the phosphorolysis of thymidine (Km=473 μM) and deoxyuridine (Km=578 μM), it prefers uridine (Km=92 μM) as a substrate. Our kinetic data and sequence analysis revealed that the annotated M. hyorhinis TP belongs to the NP (nucleoside phosphorylase)-II class PyNPs (pyrimidine NPs), and is distinct from the NP-II class TP and NP-I class UPs (uridine phosphorylases). M. hyorhinis PyNP also markedly differs from TP and UP in its substrate specificity towards therapeutic nucleoside analogues and susceptibility to clinically relevant drugs. Several kinetic properties of mycoplasma PyNP were explained by in silico analyses.
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Pomeisl K, Horská K, Pohl R, Blažek J, Krečmerová M. Syntheses of 1-[2-(Phosphonomethoxy)Alkyl] thymine monophosphates and an evaluation of their inhibitory activity toward human thymidine phosphorylase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:159-71. [PMID: 22356232 DOI: 10.1080/15257770.2011.648361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A series of new monophosphates of 1-[2-(phosphonomethoxy)alkyl]thymines, such as PMPTp(,) 3-MeO-PMPTp, HPMPTp, and FPMPTp, were synthesized and tested for their ability to inhibit human thymidine phosphorylase. Kinetic measurements of enzyme activity were performed using thymidine and inorganic phosphate as the substrates. The data show that some monophosphates provide a considerable increase of the multisubstrate inhibitory effect. The highest inhibitory potency was found with (R)-FPMPTp 4c (K (i) (dT) = 4.09 ± 0.47 μM, K (i)(P(i)) = 2.13 ± 0.29 μM) and (R) 3-MeO-PMPTp 4d (K (i) (dT) = 5.78 ± 0.71 μM, K (i)(P(i)) = 2.71 ± 0.37 μM).
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Affiliation(s)
- Karel Pomeisl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. , Prague, Czech Republic.
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43
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Jansa P, Špaček P, Votruba I, Břehová P, Dračínský M, Klepetářová B, Janeba Z. Efficient one-pot synthesis of polysubstituted 6-[(1H-1,2,3-triazol-1-yl)methyl]uracils through the “click” protocol. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The preparation of several triazolo acyclic nucleosides and triazolo acyclic nucleoside phosphonates is described. The synthetic methodology has been developed as an efficient one-pot Cu(I)-catalyzed azide alkyne Huisgen “click” cycloaddition. A novel Cu(I)-catalyzed decarboxylation reaction of 1-substituted 1H-1,2,3-triazole-4-carboxylic acids at room temperature was observed and used for the preparation of 1-substituted 1H-1,2,3-triazoles. As congeners of TPI (Taiho pharmaceutical inhibitor), the prepared compounds were screened as potential inhibitors of human thymidine phosphorylase, but no inhibitory activity was observed.
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Rajabi M, Mansell D, Freeman S, Bryce RA. Structure–activity relationship of 2,4,5-trioxoimidazolidines as inhibitors of thymidine phosphorylase. Eur J Med Chem 2011; 46:1165-71. [DOI: 10.1016/j.ejmech.2011.01.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 10/14/2010] [Accepted: 01/22/2011] [Indexed: 10/18/2022]
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45
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McNally VA, Rajabi M, Gbaj A, Stratford IJ, Edwards PN, Douglas KT, Bryce RA, Jaffar M, Freeman S. Design, synthesis and enzymatic evaluation of 6-bridged imidazolyluracil derivatives as inhibitors of human thymidine phosphorylase. J Pharm Pharmacol 2010; 59:537-47. [PMID: 17430637 DOI: 10.1211/jpp.59.4.0008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Abstract
A series of novel imidazolyluracil conjugates were rationally designed and synthesised to probe the active site constraints of the angiogenic enzyme, thymidine phosphorylase (TP, E.C. 2.4.2.4). The lead compound in the series, 15d, showed good binding in the active site of human TP with an inhibition in the low μM range. The absence of a methylene bridge between the uracil and the imidazolyl sub-units (series 16) decreased potency (up to 3-fold). Modelling suggested that active site residues Arg202, Ser217 and His116 are important for inhibitor binding.
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Affiliation(s)
- Virginia A McNally
- School of Pharmacy & Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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46
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The role of phosphate in the action of thymidine phosphorylase inhibitors: Implications for the catalytic mechanism. Bioorg Med Chem Lett 2010; 20:1648-51. [PMID: 20138520 DOI: 10.1016/j.bmcl.2010.01.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 01/11/2010] [Indexed: 11/24/2022]
Abstract
The design and synthesis of 5-fluoro-6-[(2-aminoimidazol-1-yl)methyl]uracil (AIFU), a potent inhibitor of thymidine phosphorylase (TP) with K(i)-values of 11nM (ecTP) and 17nM (hTP), are described. Kinetic studies established that the type of inhibition of TP by AIFU is uncompetitive with respect to inorganic phosphate (or arsenate). The results obtained suggest that AIFU and other zwitterionic thymine analog inhibitors of TP act as transition state analogs, mimicking the anionic thymine leaving group, consistent with an S(N)2-type catalytic mechanism, and anchored by their protonated side chains to the enzyme-bound phosphate by electrostatic and H-bonding interactions.
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47
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Bronckaers A, Gago F, Balzarini J, Liekens S. The dual role of thymidine phosphorylase in cancer development and chemotherapy. Med Res Rev 2009; 29:903-53. [PMID: 19434693 PMCID: PMC7168469 DOI: 10.1002/med.20159] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thymidine phosphorylase (TP), also known as "platelet-derived endothelial cell growth factor" (PD-ECGF), is an enzyme, which is upregulated in a wide variety of solid tumors including breast and colorectal cancers. TP promotes tumor growth and metastasis by preventing apoptosis and inducing angiogenesis. Elevated levels of TP are associated with tumor aggressiveness and poor prognosis. Therefore, TP inhibitors are synthesized in an attempt to prevent tumor angiogenesis and metastasis. TP is also indispensable for the activation of the extensively used 5-fluorouracil prodrug capecitabine, which is clinically used for the treatment of colon and breast cancer. Clinical trials that combine capecitabine with TP-inducing therapies (such as taxanes or radiotherapy) suggest that increasing TP expression is an adequate strategy to enhance the antitumoral efficacy of capecitabine. Thus, TP plays a dual role in cancer development and therapy: on the one hand, TP inhibitors can abrogate the tumorigenic and metastatic properties of TP; on the other, TP activity is necessary for the activation of several chemotherapeutic drugs. This duality illustrates the complexity of the role of TP in tumor progression and in the clinical response to fluoropyrimidine-based chemotherapy.
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Affiliation(s)
| | - Federico Gago
- Departamento de Farmacología, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
| | - Jan Balzarini
- Rega Institute for Medical Research, K.U.Leuven, B‐3000 Leuven, Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research, K.U.Leuven, B‐3000 Leuven, Belgium
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Use of Pd-catalyzed Suzuki–Miyaura coupling reaction in the rapid synthesis of 5-aryl-6-(phosphonomethoxy)uracils and evaluation of their inhibitory effect towards human thymidine phosphorylase. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.08.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Bronckaers A, Aguado L, Negri A, Camarasa MJ, Balzarini J, Pérez-Pérez MJ, Gago F, Liekens S. Identification of aspartic acid-203 in human thymidine phosphorylase as an important residue for both catalysis and non-competitive inhibition by the small molecule “crystallization chaperone” 5′-O-tritylinosine (KIN59). Biochem Pharmacol 2009; 78:231-40. [DOI: 10.1016/j.bcp.2009.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 04/03/2009] [Accepted: 04/06/2009] [Indexed: 11/27/2022]
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50
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Mitsiki E, Papageorgiou AC, Iyer S, Thiyagarajan N, Prior SH, Sleep D, Finnis C, Acharya KR. Structures of native human thymidine phosphorylase and in complex with 5-iodouracil. Biochem Biophys Res Commun 2009; 386:666-70. [PMID: 19555658 PMCID: PMC2719695 DOI: 10.1016/j.bbrc.2009.06.104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 06/19/2009] [Indexed: 11/28/2022]
Abstract
Thymidine phosphorylase (TP) first identified as platelet derived endothelial cell growth factor (PD-ECGF) plays a key role in nucleoside metabolism. Human TP (hTP) is implicated in angiogenesis and is overexpressed in several solid tumors. Here, we report the crystal structures of recombinant hTP and its complex with a substrate 5-iodouracil (5IUR) at 3.0 and 2.5A, respectively. In addition, we provide information on the role of specific residues in the enzymatic activity of hTP through mutagenesis and kinetic studies.
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Affiliation(s)
- Eirini Mitsiki
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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