1
|
Hatano A, Matsuzaka R, Shimane G, Wakana H, Suzuki K, Nishioka C, Kojima A, Kidowaki M. Introduction of pseudo-base benzimidazole derivatives into nucleosides via base exchange by a nucleoside metabolic enzyme. Bioorg Med Chem 2023; 91:117411. [PMID: 37451053 DOI: 10.1016/j.bmc.2023.117411] [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: 05/29/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
In alternate organic synthesis, biocatalysis using enzymes provides a more stereoselective and cost-effective approach. Synthesis of unnatural nucleosides by nucleoside base exchange reactions using nucleoside-metabolizing enzymes has previously shown that the 5-position recognition of pyrimidine bases on nucleoside substrates is loose and can be used to introduce functional molecules into pyrimidine nucleosides. Here we explored the incorporation of purine pseudo bases into nucleosides by the base exchange reaction of pyrimidine nucleoside phosphorylase (PyNP), demonstrating that an imidazole five-membered ring is an essential structure for the reaction. In the case of benzimidazole, the base exchange proceeded to give the deoxyribose form in 96 % yield, and the ribose form in 23 % yield. The reaction also proceeded with 1H-imidazo[4,5-b]phenazine, a benzimidazole analogue with an additional ring, although the yield of nucleoside was only 31 %. Docking simulations between 1H and imidazo[4,5-b]phenazine nucleoside and the active site of PyNP (PDB 1BRW) supported our observation that 1H-imidazo[4,5-b]phenazine can be used as a substrate by PyNP. Thus, the enzymatic substitution reaction using PyNP can be used to incorporate many purine pseudo bases and benzimidazole derivatives with various functional groups into nucleoside structures, which have potential utility as diagnostic or therapeutic agents.
Collapse
Affiliation(s)
- Akihiko Hatano
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.
| | - Riki Matsuzaka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Genki Shimane
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hiroyuki Wakana
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kou Suzuki
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Chisato Nishioka
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Aoi Kojima
- Department of Materials Science and Engineering, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Masatoshi Kidowaki
- Department of Applied Chemistry, Shibaura Institute of Technology, 3-7-5, Toyosu, Koto-ku, Tokyo 135-8548, Japan
| |
Collapse
|
2
|
Abstract
This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.
Collapse
Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
3
|
Kaspar F, Brandt F, Westarp S, Eilert L, Kemper S, Kurreck A, Neubauer P, Jacob CR, Schallmey A. Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications. Angew Chem Int Ed Engl 2023; 62:e202218492. [PMID: 36655928 DOI: 10.1002/anie.202218492] [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: 12/14/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/20/2023]
Abstract
Biocatalytic nucleoside (trans-)glycosylations catalyzed by nucleoside phosphorylases have evolved into a practical and convenient approach to the preparation of modified nucleosides, which are important pharmaceuticals for the treatment of various cancers and viral infections. However, the obtained yields in these reactions are generally determined exclusively by the innate thermodynamic properties of the nucleosides involved, hampering the biocatalytic access to many sought-after target nucleosides. We herein report an additional means for reaction engineering of these systems. We show how apparent equilibrium shifts in phosphorolysis and glycosylation reactions can be effected through entropically driven, biased esterification of nucleosides and ribosyl phosphates with inorganic borate. Our multifaceted analysis further describes the kinetic implications of this in situ reactant esterification for a model phosphorylase.
Collapse
Affiliation(s)
- Felix Kaspar
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.,Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Brandt
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Lea Eilert
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.,Present address: Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Sebastian Kemper
- Institute for Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106, Braunschweig, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| |
Collapse
|
4
|
Feng Q, Yang W, Peng Z, Wang G. Recent advances in the synthetic thymidine phosphorylase inhibitors for cancer therapy. Eur J Pharmacol 2022; 934:175319. [DOI: 10.1016/j.ejphar.2022.175319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/03/2022]
|
5
|
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.
Collapse
|
6
|
Antipov AN, Mordkovich NN, Khijniak TV, Okorokova NA, Veiko VP. Cloning of Nucleoside Phosphorylase Genes from the Extremophilic Bacterium Halomonas chromatireducens AGD 8-3 with the Construction of Recombinant Producer Strains of These Proteins and the Study of Their Enzymatic Properties. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Dorababu A. Evolution of uracil based thymidine phosphorylase inhibitors, SAR and electronic correlation: revisit. Drug Dev Res 2019. [DOI: 10.1002/ddr.21592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Atukuri Dorababu
- Department of Studies in ChemistrySRMPP Govt. First Grade College Huvinahadagali Karnataka India
| |
Collapse
|
9
|
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]
|
10
|
Prokofev II, Lashkov AA, Gabdulkhakov AG, Balaev VV, Mironov AS, Betzel C, Mikhailov AM. Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518030239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
11
|
Lettieri R, D'Abramo M, Stella L, La Bella A, Leonelli F, Giansanti L, Venanzi M, Gatto E. Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 195:84-94. [PMID: 29414586 DOI: 10.1016/j.saa.2018.01.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
Thymidine phosphorylase (TP) is an enzyme that is up-regulated in a wide variety of solid tumors, including breast and colorectal cancers. It is involved in tumor growth and metastasis, for this reason it is one of the key enzyme to be inhibited, in an attempt to prevent tumor proliferation. However, it also plays an active role in cancer treatment, through its contribution in the conversion of the anti-cancer drug 5-fluorouracil (5-FU) to an irreversible inhibitor of thymidylate synthase (TS), responsible of the inhibition of the DNA synthesis. In this work, the intrinsic TP fluorescence has been investigated for the first time and exploited to study TP binding affinity for the unsubstituted 5-FU and for two 5-FU derivatives, designed to expose this molecule on liposomal membranes. These molecules were obtained by functionalizing the nitrogen atom with a chain consisting of six (1) or seven (2) units of glycol, linked to an alkyl moiety of 12 carbon atoms. Derivatives (1) and (2) exhibited an affinity for TP in the micromolar range, 10 times higher than the parent compound, irrespective of the length of the polyoxyethylenic spacer. This high affinity was maintained also when the compounds were anchored in liposomal membranes. Experimental results were supported by molecular dynamics simulations and docking calculations, supporting a feasible application of the designed supramolecular lipid structure in selective targeting of TP, to be potentially used as a drug delivery system or sensor device.
Collapse
Affiliation(s)
- R Lettieri
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - M D'Abramo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Roma, Italy
| | - L Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - A La Bella
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Roma, Italy
| | - F Leonelli
- Dipartimento di Biologia Ambientale, Università degli Studi di Roma "La Sapienza", Roma, Italy
| | - L Giansanti
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell'Aquila, Aquila, Italy; CNR, Istituto di Metodologie Chimiche, Monterotondo Scalo, Rome, Italy
| | - M Venanzi
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - E Gatto
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Stepchenko VA, Miroshnikov AI, Seela F, Mikhailopulo IA. Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases. Beilstein J Org Chem 2016; 12:2588-2601. [PMID: 28144328 PMCID: PMC5238616 DOI: 10.3762/bjoc.12.254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/17/2016] [Indexed: 11/23/2022] Open
Abstract
The trans-2-deoxyribosylation of 4-thiouracil (4SUra) and 2-thiouracil (2SUra), as well as 6-azauracil, 6-azathymine and 6-aza-2-thiothymine was studied using dG and E. coli purine nucleoside phosphorylase (PNP) for the in situ generation of 2-deoxy-α-D-ribofuranose-1-phosphate (dRib-1P) followed by its coupling with the bases catalyzed by either E. coli thymidine (TP) or uridine (UP) phosphorylases. 4SUra revealed satisfactory substrate activity for UP and, unexpectedly, complete inertness for TP; no formation of 2'-deoxy-2-thiouridine (2SUd) was observed under analogous reaction conditions in the presence of UP and TP. On the contrary, 2SU, 2SUd, 4STd and 2STd are good substrates for both UP and TP; moreover, 2SU, 4STd and 2'-deoxy-5-azacytidine (Decitabine) are substrates for PNP and the phosphorolysis of the latter is reversible. Condensation of 2SUra and 5-azacytosine with dRib-1P (Ba salt) catalyzed by the accordant UP and PNP in Tris∙HCl buffer gave 2SUd and 2'-deoxy-5-azacytidine in 27% and 15% yields, respectively. 6-Azauracil and 6-azathymine showed good substrate properties for both TP and UP, whereas only TP recognizes 2-thio-6-azathymine as a substrate. 5-Phenyl and 5-tert-butyl derivatives of 6-azauracil and its 2-thioxo derivative were tested as substrates for UP and TP, and only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed.
Collapse
Affiliation(s)
- Vladimir A Stepchenko
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus
| | - Anatoly I Miroshnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 GSP, Moscow B-437, Russia
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, D-48149 Münster, Germany
| | - Igor A Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus
| |
Collapse
|
16
|
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]
|
17
|
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]
|
18
|
Petaccia M, Gentili P, Bešker N, D'Abramo M, Giansanti L, Leonelli F, La Bella A, Gradella Villalva D, Mancini G. Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives. Colloids Surf B Biointerfaces 2016; 140:121-127. [PMID: 26752208 DOI: 10.1016/j.colsurfb.2015.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/01/2015] [Accepted: 12/13/2015] [Indexed: 11/28/2022]
Abstract
In a previous investigation, cationic liposomes formulated with new 5-FU derivatives, differing for the length of the polyoxyethylenic spacer that links the N(3) position of 5-FU to an alkyl chain of 12 carbon atoms, showed a higher cytotoxicity compared to free 5-FU, the cytotoxic effect being directly related to the length of the spacer. To better understand the correlation of the spacer length with toxicity, we carried out initial rate studies to determine inhibition, equilibrium and kinetic constants (KI, KM, kcat), and get inside inhibition activity of the 5-FU derivatives and their mechanism of action, a crucial information to design structural variations for improving the anticancer activity. The experimental investigation was supported by docking simulations based on the X-ray structure of thymidine phosphorylase (TP) from Escherichia coli complexed with 3'-azido-2'-fluoro-dideoxyuridin. Theoretical and experimental results showed that all the derivatives exert the same inhibition activity of 5-FU either as monomer and when embedded in lipid bilayer.
Collapse
Affiliation(s)
- Manuela Petaccia
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell'Aquila, Via Vetoio, 67100 Coppito (Aq), Italy
| | - Patrizia Gentili
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy
| | - Neva Bešker
- CINECA, SCAI-Super Computing Applications and Innovation Department, Via dei Tizii, 6, 00185 Rome, Italy
| | - Marco D'Abramo
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy
| | - Luisa Giansanti
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell'Aquila, Via Vetoio, 67100 Coppito (Aq), Italy.
| | - Francesca Leonelli
- Dipartimento di Biologia Ambientale, Università degli Studi di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy
| | - Angela La Bella
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy
| | - Denise Gradella Villalva
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy
| | - Giovanna Mancini
- CNR-Istituto di Metodologie Chimiche, Via Salaria km 29.300, Monterotondo Scalo, 00016 Rome, Italy
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
Collapse
|
21
|
Schneider D, Kaiser W, Stutz C, Holinski A, Mayans O, Babinger P. YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins. J Biol Chem 2015; 290:19527-39. [PMID: 26063803 DOI: 10.1074/jbc.m114.620575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 12/28/2022] Open
Abstract
We present the crystal structure and biochemical characterization of Escherichia coli YbiB, a member of the hitherto uncharacterized TrpD2 protein family. Our results demonstrate that the functional diversity of proteins with a common fold can be far greater than predictable by computational annotation. The TrpD2 proteins show high structural homology to anthranilate phosphoribosyltransferase (TrpD) and nucleoside phosphorylase class II enzymes but bind with high affinity (KD = 10-100 nM) to nucleic acids without detectable sequence specificity. The difference in affinity between single- and double-stranded DNA is minor. Results suggest that multiple YbiB molecules bind to one longer DNA molecule in a cooperative manner. The YbiB protein is a homodimer that, therefore, has two electropositive DNA binding grooves. But due to negative cooperativity within the dimer, only one groove binds DNA in in vitro experiments. A monomerized variant remains able to bind DNA with similar affinity, but the negative cooperative effect is eliminated. The ybiB gene forms an operon with the DNA helicase gene dinG and is under LexA control, being induced by DNA-damaging agents. Thus, speculatively, the TrpD2 proteins may be part of the LexA-controlled SOS response in bacteria.
Collapse
Affiliation(s)
- Daniel Schneider
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Wolfgang Kaiser
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Cian Stutz
- the Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland, and
| | - Alexandra Holinski
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Olga Mayans
- the Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland, and the Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Patrick Babinger
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany,
| |
Collapse
|
22
|
Li W, Gigante A, Perez-Perez MJ, Yue H, Hirano M, McIntyre TM, Silverstein RL. Thymidine phosphorylase participates in platelet signaling and promotes thrombosis. Circ Res 2014; 115:997-1006. [PMID: 25287063 DOI: 10.1161/circresaha.115.304591] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Platelets contain abundant thymidine phosphorylase (TYMP), which is highly expressed in diseases with high risk of thrombosis, such as atherosclerosis and type II diabetes mellitus. OBJECTIVE To test the hypothesis that TYMP participates in platelet signaling and promotes thrombosis. METHODS AND RESULTS By using a ferric chloride (FeCl3)-induced carotid artery injury thrombosis model, we found time to blood flow cessation was significantly prolonged in Tymp(-/-) and Tymp(+/-) mice compared with wild-type mice. Bone marrow transplantation and platelet transfusion studies demonstrated that platelet TYMP was responsible for the antithrombotic phenomenon in the TYMP-deficient mice. Collagen-, collagen-related peptide-, adenosine diphosphate-, or thrombin-induced platelet aggregation were significantly attenuated in Tymp(+/-) and Tymp(-/-) platelets, and in wild type or human platelets pretreated with TYMP inhibitor KIN59. Tymp deficiency also significantly decreased agonist-induced P-selectin expression. TYMP contains an N-terminal SH3 domain-binding proline-rich motif and forms a complex with the tyrosine kinases Lyn, Fyn, and Yes in platelets. TYMP-associated Lyn was inactive in resting platelets, and TYMP trapped and diminished active Lyn after collagen stimulation. Tymp/Lyn double haploinsufficiency diminished the antithrombotic phenotype of Tymp(+/-) mice. TYMP deletion or inhibition of TYMP with KIN59 dramatically increased platelet-endothelial cell adhesion molecule 1 tyrosine phosphorylation and diminished collagen-related peptide- or collagen-induced AKT phosphorylation. In vivo administration of KIN59 significantly inhibited FeCl3-induced carotid artery thrombosis without affecting hemostasis. CONCLUSIONS TYMP participates in multiple platelet signaling pathways and regulates platelet activation and thrombosis. Targeting TYMP might be a novel antiplatelet and antithrombosis therapy.
Collapse
Affiliation(s)
- Wei Li
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Alba Gigante
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Maria-Jesus Perez-Perez
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Hong Yue
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Michio Hirano
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Thomas M McIntyre
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| | - Roy L Silverstein
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute, The Cleveland Clinic, OH (W.L., T.M.M.); Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, OH (W.L., T.M.M.); Instituto de Quimica Medica, Consejo Superior De Investigaciones Cientificas (IQM-CSIC), Madrid, Spain (A.G.,M.-J.P.-P.); Department of Biological Sciences, Case Western Reserve University, Cleveland, OH (H.Y.); Department of Neurology, Columbia University Medical Center, New York, NY (M.H.); and Department of Medicine, Medical College of Wisconsin and Blood Research Institute, Blood Center of Wisconsin, Milwaukee (R.L.S.)
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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]
|
25
|
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]
|
26
|
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.
Collapse
Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | | | | | | | | | | | | |
Collapse
|
27
|
Hatano A, Kurosu M, Yonaha S, Okada M, Uehara S. One-pot approach to functional nucleosides possessing a fluorescent group using nucleobase-exchange reaction by thymidine phosphorylase. Org Biomol Chem 2013; 11:6900-5. [DOI: 10.1039/c3ob41605d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
28
|
Serra I, Ubiali D, Piškur J, Christoffersen S, Lewkowicz ES, Iribarren AM, Albertini AM, Terreni M. Developing a Collection of Immobilized Nucleoside Phosphorylases for the Preparation of Nucleoside Analogues: Enzymatic Synthesis of Arabinosyladenine and 2′,3′-Dideoxyinosine. Chempluschem 2012. [DOI: 10.1002/cplu.201200278] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
29
|
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.
Collapse
|
30
|
Serra I, Serra CD, Rocchietti S, Ubiali D, Terreni M. Stabilization of thymidine phosphorylase from Escherichia coli by immobilization and post immobilization techniques. Enzyme Microb Technol 2011; 49:52-8. [DOI: 10.1016/j.enzmictec.2011.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 03/24/2011] [Accepted: 03/30/2011] [Indexed: 10/18/2022]
|
31
|
Biologically important nucleosides: modern trends in biotechnology and application. MENDELEEV COMMUNICATIONS 2011. [DOI: 10.1016/j.mencom.2011.03.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
32
|
Schwartz PA, Vetticatt MJ, Schramm VL. Transition state analysis of the arsenolytic depyrimidination of thymidine by human thymidine phosphorylase. Biochemistry 2011; 50:1412-20. [PMID: 21222488 DOI: 10.1021/bi101900b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, promotes angiogenesis, and is involved in metabolic inactivation of antiproliferative agents that inhibit thymidylate synthase. Understanding its transition state structure is on the path to design transition state analogues. Arsenolysis of dT by hTP permits kinetic isotope effect (KIE) analysis of the reaction by forming thymine and the chemically unstable 2-deoxyribose 1-arsenate. The transition state for the arsenolytic reaction was characterized using multiple KIEs and computational analysis. Transition state analysis revealed a concerted bimolecular (A(N)D(N)) mechanism. A transition state constrained to match the intrinsic KIE values was found using density functional theory (B3LYP/6-31G*). An active site histidine is implicated as the catalytic base responsible for activation of the arsenate nucleophile and stabilization of the thymine leaving group during the isotopically sensitive step. At the transition state, the deoxyribose ring exhibits significant oxocarbenium ion character with bond breaking (r(C-N) = 2.45 Å) nearly complete and minimal bond making to the attacking nucleophile (r(C-O) = 2.95 Å). The transition state model predicts a deoxyribose conformation with a 2'-endo ring geometry. Transition state structure for the slow hydrolytic reaction of hTP involves a stepwise mechanism [Schwartz, P. A., Vetticatt, M. J., and Schramm, V. L. (2010) J. Am. Chem. Soc. 132, 13425-13433], in contrast to the concerted mechanism described here for arsenolysis.
Collapse
Affiliation(s)
- Phillip A Schwartz
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | |
Collapse
|
33
|
Schwartz PA, Vetticatt MJ, Schramm VL. Transition state analysis of thymidine hydrolysis by human thymidine phosphorylase. J Am Chem Soc 2010; 132:13425-33. [PMID: 20804144 DOI: 10.1021/ja105041j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose, and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1'-(14)C]-, [1-(15)N]-, [1'-(3)H]-, [2'R-(3)H]-, [2'S-(3)H]-, [4'-(3)H]-, and [5'-(3)H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (r(C-O)) is predicted to be 2.3 A at the transition state. The transition state model predicts that deoxyribose adopts a mild 3'-endo conformation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction (Birck, M. R.; Schramm, V. L. J. Am. Chem. Soc. 2004, 126, 2447-2453).
Collapse
Affiliation(s)
- Phillip A Schwartz
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | | | | |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
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]
|
36
|
Panova NG, Alexeev CS, Polyakov KM, Gavryushov SA, Kritzyn AM, Mikhailov SN. Substrate specificity of thymidine phosphorylase of E. coli: role of hydroxyl groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2009; 27:1211-4. [PMID: 19003566 DOI: 10.1080/15257770802257895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Substrate specificity of E. coli thymidine phosphorylase to pyrimidine nucleoside modified at 5'-, 3'-, and 2'-positions of sugar moiety has been studied. Equilibrium (K(eq)) and kinetics constants of phosphorolysis reaction of nucleosides were measured. The most important hydrogen bonds in enzyme-substrate complex have been determined.
Collapse
Affiliation(s)
- Natalya G Panova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
37
|
Hussain S, Gaffney J, Ahmed N, Slevin M, Iqbal Choudhary M, Ahmad VU, Qasmi Z, Abbasi MA. An investigation of the kinetic and anti-angiogenic properties of plant glycoside inhibitors of thymidine phosphorylase. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2009; 11:159-167. [PMID: 19219729 DOI: 10.1080/10286020802618860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We investigated the potential of symplocomoside (1) and symponoside (2), glycosides isolated from the bark of Symplocos racemosa to inhibit thymidine phosphorylase (TP) activity and associated angiogenesis. Compound 1 was a reversible, noncompetitive inhibitor of deoxythymidine binding to TP (IC(50) = 65.45 +/- 5.08 microM; K(i) = 62.83 +/- 2.10 microM) and 2 was a reversible, uncompetitive inhibitor (IC(50) = 94.17 +/- 4.05 microM; K(i) = 101.95 +/- 1.65 microM). Molecular modeling analysis indicated that both compounds bound at the active site of the enzyme but not solely to amino acid residues involved in catalysis. Both compounds were active in in vitro angiogenic assays inhibiting endothelial cell migration and invasion in Matrigel, but did not inhibit growth factor-induced proliferation and were not cytotoxic. Compound 1 may have potential as an anti-angiogenic and anti-tumor agent.
Collapse
Affiliation(s)
- S Hussain
- School of Biology, Chemistry and Health Science, Manchester Metropolitan University, Manchester, UK
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Edwards PN. A kinetic, modeling and mechanistic re-analysis of thymidine phosphorylase and some related enzymes. J Enzyme Inhib Med Chem 2008; 21:483-99. [PMID: 17194017 DOI: 10.1080/14756360600721075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Thymidine phosphorylase (TP) is an important target enzyme for cancer chemotherapy but currently available inhibitors lack in vivo potency. Related enzymes also are therapeutic targets. A greater understanding of enzyme structure and mechanism may help in the design of improved drugs and this work assists in that regard. Also important is the correct identification of the ionization states and tautomeric forms of substrates and products when bound to the enzyme and during the course of the reaction. Approximate methods for estimating some deltapK(a)s between aqueous and protein-bound substrates are exemplified for nucleobases and nucleosides. The estimates demonstrate that carbonyl-protonated thymidine and hydroxy tautomers of thymine are not involved in TP's actions. Other estimates indicate that purine nucleoside phosphorylase binds inosine and guanosine as zwitterionic tautomers and that phosphorolysis proceeds through these forms. Extensive molecular modeling based on an X-ray structure of human TP indicates that TP is likely to be mechanistically similar to all other natural members of the class in proceeding through a alpha-oxacarbenium-like transition state or states.
Collapse
Affiliation(s)
- Philip N Edwards
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| |
Collapse
|
39
|
Gbaj A, Edwards PN, Reigan P, Freeman S, Jaffar M, Douglas KT. Thymidine phosphorylase fromEscherichia coli: Tight-binding inhibitors as enzyme active-site titrants. J Enzyme Inhib Med Chem 2008; 21:69-73. [PMID: 16570508 DOI: 10.1080/14756360500424010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Thymidine phosphorylase (EC 2.4.2.4) catalyses the reversible phosphorolysis of pyrimidine 2'-deoxynucleosides, forming 2-deoxyribose-1-phosphate and pyrimidine. 5-Chloro-6-(2-imino-pyrrolidin-1-yl)methyl-uracil hydrochloride (TPI, 1) and its 5-bromo analogue (2), 6-(2-amino-imidazol-1-yl)methyl-5-bromo-uracil (3) and its 5-chloro analogue (4) act as tight-binding stoichiometric inhibitors of recombinant E. coli thymidine phosphorylase, and thus can be used as the first active-site titrants for it using either thymidine or 5-nitro-2'-deoxyuridine as substrate.
Collapse
Affiliation(s)
- Abdul Gbaj
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester M13 9PL, UK
| | | | | | | | | | | |
Collapse
|
40
|
Schwab T, Skegro D, Mayans O, Sterner R. A Rationally Designed Monomeric Variant of Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus is as Active as the Dimeric Wild-type Enzyme but Less Thermostable. J Mol Biol 2008; 376:506-16. [DOI: 10.1016/j.jmb.2007.11.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 11/14/2007] [Accepted: 11/23/2007] [Indexed: 11/28/2022]
|
41
|
Nencka R, Votruba I, Hřebabecký H, Jansa P, Tloušt'ová E, Horská K, Masojídková M, Holý A. Discovery of 5-Substituted-6-chlorouracils as Efficient Inhibitors of Human Thymidine Phosphorylase. J Med Chem 2007; 50:6016-23. [DOI: 10.1021/jm070644i] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Radim Nencka
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Ivan Votruba
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Hubert Hřebabecký
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Petr Jansa
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Eva Tloušt'ová
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Květa Horská
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Milena Masojídková
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| | - Antonín Holý
- Gilead Sciences & IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Centre for New Antivirals and Antineoplastics (IOCB), Flemingovo nám. 2, CZ-166 10, Prague 6, Czech Republic
| |
Collapse
|
42
|
Panova NG, Alexeev CS, Kuzmichov AS, Shcheveleva EV, Gavryushov SA, Polyakov KM, Kritzyn AM, Mikhailov SN, Esipov RS, Miroshnikov AI. Substrate specificity of Escherichia coli thymidine phosphorylase. BIOCHEMISTRY (MOSCOW) 2007; 72:21-8. [PMID: 17309433 DOI: 10.1134/s0006297907010026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Substrate specificity of Escherichia coli thymidine phosphorylase to thymidine derivatives modified at 5' -, 3' -, and 2' ,3' - positions of the sugar moiety was studied. Equilibrium and kinetic constants (K(m), K(I), k(cat)) of the phosphorolysis reaction have been determined for 20 thymidine analogs. The results are compared with X-ray and molecular dynamics data. The most important hydrogen bonds in the enzyme-substrate complex are revealed.
Collapse
Affiliation(s)
- N G Panova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Allan AL, Gladstone PL, Price MLP, Hopkins SA, Juarez JC, Doñate F, Ternansky RJ, Shaw DE, Ganem B, Li Y, Wang W, Ealick S. Synthesis and Evaluation of Multisubstrate Bicyclic Pyrimidine Nucleoside Inhibitors of Human Thymidine Phosphorylase. J Med Chem 2006; 49:7807-15. [PMID: 17181163 DOI: 10.1021/jm060428u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of novel, multisubstrate, bicyclic pyrimidine nucleoside inhibitors of human thymidine phosphorylase (TP) is described. Thymidine phosphorylase has been implicated in angiogenesis and plays a significant role in tumor progression and metastasis. The presence and orientation of the phosphonate moiety (acting as a phosphate mimic) in these derivatives were critical for inhibitory activity. The most active compounds possessed a phosphonate group in an endo orientation. This was consistent with molecular modeling results that showed the endo isomer protein-ligand complex to be lower in energy than the exo complex.
Collapse
Affiliation(s)
- Amy L Allan
- Attenuon, LLC, 11535 Sorrento Valley Road Suite 401, San Diego, CA 92121, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Omari K, Bronckaers A, Liekens S, Pérez-Pérez MJ, Balzarini J, Stammers D. Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design. Biochem J 2006; 399:199-204. [PMID: 16803458 PMCID: PMC1609907 DOI: 10.1042/bj20060513] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end complex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406-415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs.
Collapse
Affiliation(s)
- Kamel EL Omari
- *Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
| | | | - Sandra Liekens
- †Rega Institute for Medical Research, K.U.Leuven, B-3000 Leuven, Belgium
| | | | - Jan Balzarini
- †Rega Institute for Medical Research, K.U.Leuven, B-3000 Leuven, Belgium
| | - David K. Stammers
- *Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- To whom correspondence should be addressed (email )
| |
Collapse
|
45
|
Gao XF, Huang XR, Sun CC. Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis: A hybrid QM/MM study. J Struct Biol 2006; 154:20-6. [PMID: 16469506 DOI: 10.1016/j.jsb.2005.11.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 07/15/2005] [Accepted: 11/15/2005] [Indexed: 11/24/2022]
Abstract
Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. We have built a model of a closed active conformation of the three-dimensional structure of PYNP from Bacillus subtilis. Using docking, molecular dynamics, and hybrid quantum-mechanical/molecular-mechanical methods to study the reaction mechanics between PYNP and a substrate, we identified the role of each residue in the active site during the entire catalytic process. The results indicate that the function of His(82), Arg(169), and Lys(188) is to stabilize the uridine in a high-energy conformation by means of electrostatic interactions and that these residues are involved in catalysis. In addition, the function of Asp(162) is likely to activate Lys(188) for phosphorolytic catalysis through polarization effects.
Collapse
Affiliation(s)
- Xue-Feng Gao
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, PR China
| | | | | |
Collapse
|
46
|
Kalman TI, Lai L. 6-substituted 5-fluorouracil derivatives as transition state analogue inhibitors of thymidine phosphorylase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:367-73. [PMID: 16247953 DOI: 10.1081/ncn-200059790] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A combination of mechanism-based and structure-based design strategies led to the synthesis of a series of 5- and 6-substituted uracil derivatives as potential inhibitors of thymidine phosphorlase/platelet derived endothelial cell growth factor (TP/PD-ECGF). Among those tested, 6-imidazolylmethyl-5-fluorouracil was found to be the most potent inhibitor with a Ki-value of 51 nM, representing a new class of 5-fluoropyrimidines with a novel mechanism of action.
Collapse
Affiliation(s)
- Thomas I Kalman
- Department of Chemistry, University at Buffalo, Amherst, NY 14260, USA.
| | | |
Collapse
|
47
|
Mendieta J, Martín-Santamaría S, Priego EM, Balzarini J, Camarasa MJ, Pérez-Pérez MJ, Gago F. Role of histidine-85 in the catalytic mechanism of thymidine phosphorylase as assessed by targeted molecular dynamics simulations and quantum mechanical calculations. Biochemistry 2004; 43:405-14. [PMID: 14717594 DOI: 10.1021/bi034793o] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural changes taking place in the enzyme thymidine phosphorylase (TPase, also known as PD-ECGF) that are required to achieve catalytic competence upon binding thymidine and phosphate have been simulated by means of targeted molecular dynamics (tMD). The hinge regions were characterized by structural homology comparisons with pyrimidine nucleoside phosphorylase, whose X-ray structure has been solved both in a closed and in an open form. The rearrangement of residues around the substrate that was observed during the tMD trajectory suggested that His-85 could be playing an important role in the catalytic mechanism. A quantum mechanical study of the reaction in the presence of the most relevant active site residues was then performed at the semiempirical level. The results revealed that His-85 could be involved in the protonation of the pyrimidine base at the O2 position to yield the enol tautomer of the base. To establish the role of this oxygen atom in the reaction, ground states, transition states, and final products were studied using higher level ab initio methods starting from both thymidine and 2-thiothymidine as alternative substrates. Comparison of both transition states showed that replacing the oxygen at position 2 of the pyrimidine base by sulfur should accelerate the reaction rate. Consistent with this result, 2-thiothymidine was shown to be a better substrate for TPase than the natural substrate, thymidine. For simulating the final step of the reaction, tMD simulations were used to study domain opening upon product formation considering both the enol and keto tautomers of thymine. Product release from the enzyme was easiest in the simulation that incorporated the keto tautomer of thymine, suggesting that the enol intermediate spontaneously tautomerizes back to the more energetically stable keto form. These results highlight a previously unreported role for His-85 in the catalytic mechanism of TPase and can have important implications for the design of novel TPase inhibitors.
Collapse
Affiliation(s)
- Jesús Mendieta
- Departamento de Farmacología, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain, Instituto de Química Médica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
48
|
Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF. Crystal Structures of Escherichia coli Uridine Phosphorylase in Two Native and Three Complexed Forms Reveal Basis of Substrate Specificity, Induced Conformational Changes and Influence of Potassium. J Mol Biol 2004; 337:337-54. [PMID: 15003451 DOI: 10.1016/j.jmb.2004.01.039] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 12/23/2003] [Accepted: 01/09/2004] [Indexed: 11/18/2022]
Abstract
Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective effect ("uridine rescue") against the toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its antitumour activity. We have investigated UP-substrate interactions by determining the crystal structures of native Escherichia coli UP (two forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric structures confirm the overall structural similarity of UP to E.coli purine nucleoside phosphorylase (PNP) whereby, in the presence of substrate, each displays a closed conformation resulting from a concerted movement that closes the active site cleft. However, in contrast to PNP where helix segmentation is the major conformational change between the open and closed forms, in UP more extensive changes are observed. In particular a swinging movement of a flap region consisting of residues 224-234 seals the active site. This overall change in conformation results in compression of the active site cleft. Gln166 and Arg168, part of an inserted segment not seen in PNP, are key residues in the uracil binding pocket and together with a tightly bound water molecule are seen to be involved in the substrate specificity of UP. Enzyme activity shows a twofold dependence on potassium ion concentration. The presence of a potassium ion at the monomer/monomer interface induces some local rearrangement, which results in dimer stabilisation. The conservation of key residues and interactions with substrate in the phosphate and ribose binding pockets suggest that ribooxocarbenium ion formation during catalysis of UP may be similar to that proposed for E.coli PNP.
Collapse
Affiliation(s)
- Tom T Caradoc-Davies
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin 9001, New Zealand.
| | | | | | | |
Collapse
|
49
|
Norman RA, Barry ST, Bate M, Breed J, Colls JG, Ernill RJ, Luke RWA, Minshull CA, McAlister MSB, McCall EJ, McMiken HHJ, Paterson DS, Timms D, Tucker JA, Pauptit RA. Crystal Structure of Human Thymidine Phosphorylase in Complex with a Small Molecule Inhibitor. Structure 2004; 12:75-84. [PMID: 14725767 DOI: 10.1016/j.str.2003.11.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human thymidine phosphorylase (HTP), also known as platelet-derived endothelial cell growth factor (PD-ECGF), is overexpressed in certain solid tumors where it is linked to poor prognosis. HTP expression is utilized for certain chemotherapeutic strategies and is also thought to play a role in tumor angiogenesis. We determined the structure of HTP bound to the small molecule inhibitor 5-chloro-6-[1-(2-iminopyrrolidinyl) methyl] uracil hydrochloride (TPI). The inhibitor appears to mimic the substrate transition state, which may help explain the potency of this inhibitor and the catalytic mechanism of pyrimidine nucleotide phosphorylases (PYNPs). Further, we have confirmed the validity of the HTP structure as a template for structure-based drug design by predicting binding affinities for TPI and other known HTP inhibitors using in silico docking techniques. This work provides the first structural insight into the binding mode of any inhibitor to this important drug target and forms the basis for designing novel inhibitors for use in anticancer therapy.
Collapse
|
50
|
McNally VA, Gbaj A, Douglas KT, Stratford IJ, Jaffar M, Freeman S, Bryce RA. Identification of a novel class of inhibitor of human and Escherichia coli thymidine phosphorylase by in silico screening. Bioorg Med Chem Lett 2003; 13:3705-9. [PMID: 14552762 DOI: 10.1016/j.bmcl.2003.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Structure-based computational screening of the National Cancer Institute database of anticancer compounds identified novel non-nucleobase-derived inhibitors of human thymidine phosphorylase as candidates for lead optimization. The hierarchical in silico screening strategy predicted potentially strong low molecular weight ligands exhibiting a range of molecular scaffolds. Of the thirteen ligands assayed for activity, all displayed inhibitory activity against Escherichia coli thymidine phosphorylase. One compound, hydrazine carboxamide 2-[(1-methyl-2,5-dioxo-4-pentyl-4-imidazolidinyl)methylene], was found to inhibit E. coli thymidine phosphorylase with an IC(50) value of 20 microM and an IC(50) value of 77 microM against human thymidine phosphorylase. As this hydantoin derivative lacks the undesirable ionic sites of existing tight-binding nucleobase-derived inhibitors, such as 5-chloro-6-[(2-iminopyrrolidin-1-yl)methyl]uracil hydrochloride, it provides an opportunity for the design of potent thymidine phosphorylase inhibitors with improved pharmacokinetic properties.
Collapse
Affiliation(s)
- V A McNally
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | | | | | | | | | | | | |
Collapse
|