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Rai S, Bishnoi A, Devi P, Afza N. Computational and Experimental Investigations of 7-(4-nitrophenyl)benzo[6,7]chromeno[3,2-e]pyrido[1,2-a]pyrimidin-6(7h)-one. LETT ORG CHEM 2022. [DOI: 10.2174/1570178619666220113112355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Acstract:
In-silico studies are used for the prediction of the properties of several novel materials using computer simulation technique. The present study describes the complete description of the molecular vibrations and electronic feature of the title compound by this technique. 7-(4-nitrophenyl)benzo[6,7]chromeno[3,2-e]pyrido[1,2-a]pyrimidin-6(7H)-one was prepared by the multicomponent reaction of 2H-pyrido[1,2-a]pyrimidine-2,4(3H)-dione, 2-naphthol and p-nitrobenzaldehyde. The structure of the compound was confirmed by UV, IR, NMR (1H, 13C) and mass spectroscopic studies. The compound was further subjected to quantum chemical calculations at the level of Hartee-Fock (HF) method using Lan2DZ basis set to compute polarizability, hyperpolarizabilities, AIM approach, Natural bond orbital analysis, complete vibrational assignments, Mulliken charges, spectral analysis and HOMO-LUMO energies
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Affiliation(s)
- Sonam Rai
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Abha Bishnoi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Poornima Devi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Nisha Afza
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
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2
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Very N, Hardivillé S, Decourcelle A, Thévenet J, Djouina M, Page A, Vergoten G, Schulz C, Kerr-Conte J, Lefebvre T, Dehennaut V, El Yazidi-Belkoura I. Thymidylate synthase O-GlcNAcylation: a molecular mechanism of 5-FU sensitization in colorectal cancer. Oncogene 2022; 41:745-756. [PMID: 34845374 DOI: 10.1038/s41388-021-02121-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022]
Abstract
Alteration of O-GlcNAcylation, a dynamic posttranslational modification, is associated with tumorigenesis and tumor progression. Its role in chemotherapy response is poorly investigated. Standard treatment for colorectal cancer (CRC), 5-fluorouracil (5-FU), mainly targets Thymidylate Synthase (TS). TS O-GlcNAcylation was reported but not investigated yet. We hypothesize that O-GlcNAcylation interferes with 5-FU CRC sensitivity by regulating TS. In vivo, we observed that combined 5-FU with Thiamet-G (O-GlcNAcase (OGA) inhibitor) treatment had a synergistic inhibitory effect on grade and tumor progression. 5-FU decreased O-GlcNAcylation and, reciprocally, elevation of O-GlcNAcylation was associated with TS increase. In vitro in non-cancerous and cancerous colon cells, we showed that 5-FU impacts O-GlcNAcylation by decreasing O-GlcNAc Transferase (OGT) expression both at mRNA and protein levels. Reciprocally, OGT knockdown decreased 5-FU-induced cancer cell apoptosis by reducing TS protein level and activity. Mass spectrometry, mutagenesis and structural studies mapped O-GlcNAcylated sites on T251 and T306 residues and deciphered their role in TS proteasomal degradation. We reveal a crosstalk between O-GlcNAcylation and 5-FU metabolism in vitro and in vivo that converges to 5-FU CRC sensitization by stabilizing TS. Overall, our data propose that combining 5-FU-based chemotherapy with Thiamet-G could be a new way to enhance CRC response to 5-FU.
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Affiliation(s)
- Ninon Very
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Stéphan Hardivillé
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Amélie Decourcelle
- Université de Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Julien Thévenet
- Universté de Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1190-EGID, F-59000, Lille, France
| | - Madjid Djouina
- Université de Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research In Inflammation, F-59000, Lille, France
| | - Adeline Page
- Protein Science Facility, CNRS UMS3444, INSERM US8, UCBL, ENS de Lyon, SFR BioSciences, Lyon, France
| | - Gérard Vergoten
- Université de Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research In Inflammation, F-59000, Lille, France
| | - Céline Schulz
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Julie Kerr-Conte
- Universté de Lille, Inserm, CHU Lille, Institut Pasteur Lille, U1190-EGID, F-59000, Lille, France
| | - Tony Lefebvre
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Vanessa Dehennaut
- Université de Lille, CNRS, INSERM, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Ikram El Yazidi-Belkoura
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
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Guo J, Janet JP, Bauer MR, Nittinger E, Giblin KA, Papadopoulos K, Voronov A, Patronov A, Engkvist O, Margreitter C. DockStream: a docking wrapper to enhance de novo molecular design. J Cheminform 2021; 13:89. [PMID: 34789335 PMCID: PMC8596819 DOI: 10.1186/s13321-021-00563-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/29/2021] [Indexed: 01/09/2023] Open
Abstract
Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-made protocols to maximize impact in small molecule drug discovery projects. A major obstacle of generative models is producing active compounds, in which predictive (QSAR) models have been applied to enrich target activity. However, QSAR models are inherently limited by their applicability domains. To overcome these limitations, we introduce a structure-based scoring component for REINVENT. DockStream is a flexible, stand-alone molecular docking wrapper that provides access to a collection of ligand embedders and docking backends. Using the benchmarking and analysis workflow provided in DockStream, execution and subsequent analysis of a variety of docking configurations can be automated. Docking algorithms vary greatly in performance depending on the target and the benchmarking and analysis workflow provides a streamlined solution to identifying productive docking configurations. We show that an informative docking configuration can inform the REINVENT agent to optimize towards improving docking scores using public data. With docking activated, REINVENT is able to retain key interactions in the binding site, discard molecules which do not fit the binding cavity, harness unused (sub-)pockets, and improve overall performance in the scaffold-hopping scenario. The code is freely available at https://github.com/MolecularAI/DockStream .
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Affiliation(s)
- Jeff Guo
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Jon Paul Janet
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Matthias R Bauer
- Structure & Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Eva Nittinger
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kathryn A Giblin
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Alexey Voronov
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Atanas Patronov
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Spizzichino S, Boi D, Boumis G, Lucchi R, Liberati FR, Capelli D, Montanari R, Pochetti G, Piacentini R, Parisi G, Paone A, Rinaldo S, Contestabile R, Tramonti A, Paiardini A, Giardina G, Cutruzzolà F. Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex. FEBS J 2021; 289:1625-1649. [PMID: 34694685 PMCID: PMC9299187 DOI: 10.1111/febs.16248] [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] [Received: 08/21/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT1), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5‐fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex. We report the intracellular dynamics of the complex in cancer cells by an in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the thymidylate synthesis complex assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human thymidylate synthase and dihydrofolate reductase. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein–protein interactions. Lastly, our results regarding the activity of the complete thymidylate cycle in vitro may provide a useful tool with respect to developing drugs targeting the entire complex instead of the individual components.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Dalila Boi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
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Fahim AM, Ismael EHI, Elsayed GH, Farag AM. Synthesis, antimicrobial, anti-proliferative activities, molecular docking and DFT studies of novel pyrazolo[5,1-c][1, 2, 4]triazine-3-carboxamide derivatives. J Biomol Struct Dyn 2021; 40:9177-9193. [PMID: 34106038 DOI: 10.1080/07391102.2021.1930582] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this investigation, we studied the reactivity of 5-aminouracil (1) with ethyl cyanoacetate (2) utilizing microwave irradiation to afford the corresponding 2-cyano-N-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acetamide (3) in excellent yield. The electrophilic azo-coupling reaction of acetamide 3 with aromatic diazonium salts afforded the corresponding hydrazone derivatives 4a-d. The Michael addition cyclization of hydrazone in pyridine to give pyrazolo[5,1-c][1, 2, 4]triazine-3-carboxamide 5a-d derivatives. The obtained compounds were elucidated against antimicrobial activity and antitumor activity breast cancer cells (MCF-7) and liver cancer cells (HepG2) utilized MTT assay. Compounds 5b, 5c and 5d revealed more inhibitory influence on MCF7 and HepG2 growth than the reference drug doxorubicin (Dox) after 48 h incubation. Furthermore, molecular docking studies were carried out on one of the most effective compound 4-amino-N-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-7-(4-fluorophenyl) pyrazole [5,1-c][1, 2, 4]triazine-3-carboxamide (5c) (TFC) with (PDB: 3t88), (PDB: 2wje) , (PDB: 4ynt), (PDB: 1tgh), (PDB: 4hdq) and (PDB: 3pxe) which attached with different proteins with different energies and shortage bond distance. Also; the comprehensive theoretical and experimental mechanical studies of compound TFC and TMC were compatible with FTIR and 1H NMR spectral data. The optimized molecular structure of TFC with FTIR was examined via DFT/ B3LYP/6-31G (d) level.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asmaa M Fahim
- Department of Green Chemistry, National Research Center, Dokki, Cairo, Egypt
| | - Eman H I Ismael
- Department of Organometallic and Organ Metalloid Chemistry, National Research Centre, Dokki, Cairo, Egypt
| | - Ghada H Elsayed
- Hormones Department, National Research Centre, Dokki, Cairo, Egypt
| | - Ahmad M Farag
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Cairo, Egypt
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6
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Synthesis, antimicrobial and antiproliferative activities, molecular docking, and computational studies of novel heterocycles. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02251-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Structural Bases for the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth by Drug Combinations. Cancers (Basel) 2021; 13:cancers13092061. [PMID: 33923290 PMCID: PMC8123127 DOI: 10.3390/cancers13092061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Drug combinations may help overcome drug resistance, a relevant cause of failure of ovarian cancer therapy. However, designing successful combinations requires a lengthy preclinical validation process. We have analyzed combinations of 5-fluorouracil and raltitrexed, two anticancer drugs that target thymidylate synthase, a key enzyme for the nucleotide synthesis. We have observed administration sequence specific and synergistic combined effects of the two drugs against cisplatin sensitive and resistant ovarian cancer cells. However, the focus of this work was to show that a high stability of the complex of the enzyme with the two drugs, as highlighted by X-ray crystallography, and synergistic inhibition of the enzyme represent indicators, if not prerequisites, for this drug combination to be synergistically active against sensitive and resistant ovarian cancer cells. We thus propose that structural and mechanistic information acquired during the preclinical research can help predict a successful therapeutic application of a drug combination. Abstract Combining drugs represent an approach to efficiently prevent and overcome drug resistance and to reduce toxicity; yet it is a highly challenging task, particularly if combinations of inhibitors of the same enzyme target are considered. To show that crystallographic and inhibition kinetic information can provide indicators of cancer cell growth inhibition by combinations of two anti-human thymidylate synthase (hTS) drugs, we obtained the X-ray crystal structure of the hTS:raltitrexed:5-fluorodeoxyuridine monophosphate (FdUMP) complex. Its analysis showed a ternary complex with both molecules strongly bound inside the enzyme catalytic cavity. The synergistic inhibition of hTS and its mechanistic rationale were consistent with the structural analysis. When administered in combination to A2780 and A2780/CP ovarian cancer cells, the two drugs inhibited ovarian cancer cell growth additively/synergistically. Together, these results support the idea that X-ray crystallography can provide structural indicators for designing combinations of hTS (or any other target)-directed drugs to accelerate preclinical research for therapeutic application.
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8
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Ruiz VG, Czyzyk DJ, Kumar VP, Jorgensen WL, Anderson KS. Targeting the TS dimer interface in bifunctional Cryptosporidium hominis TS-DHFR from parasitic protozoa: Virtual screening identifies novel TS allosteric inhibitors. Bioorg Med Chem Lett 2020; 30:127292. [PMID: 32631514 PMCID: PMC7376443 DOI: 10.1016/j.bmcl.2020.127292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
Effective therapies are lacking to treat gastrointestinal infections caused by the genus Cryptosporidium, which can be fatal in the immunocompromised. One target of interest is Cryptosporidium hominis (C. hominis) thymidylate synthase-dihydrofolate reductase (ChTS-DHFR), a bifunctional enzyme necessary for DNA biosynthesis. Targeting the TS-TS dimer interface is a novel strategy previously used to identify inhibitors against the related bifunctional enzyme in Toxoplasma gondii. In the present study, we target the ChTS dimer interface through homology modeling and high-throughput virtual screening to identifying allosteric, ChTS-specific inhibitors. Our work led to the discovery of methylenedioxyphenyl-aminophenoxypropanol analogues which inhibit ChTS activity in a manner that is both dose-dependent and influenced by the conformation of the enzyme. Preliminary results presented here include an analysis of structure activity relationships and a ChTS-apo crystal structure of ChTS-DHFR supporting the continued development of inhibitors that stabilize a novel pocket formed in the open conformation of ChTS-TS.
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Affiliation(s)
- Victor G Ruiz
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Daniel J Czyzyk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Vidya P Kumar
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520-8107, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - William L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520-8107, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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Czyzyk DJ, Valhondo M, Jorgensen WL, Anderson KS. Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase. FEBS Lett 2019; 593:2069-2078. [PMID: 31172516 DOI: 10.1002/1873-3468.13474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 11/08/2022]
Abstract
Thymidylate synthase (TS), found in all organisms, is an essential enzyme responsible for the de novo synthesis of deoxythymidine monophosphate. The TS active sites of the protozoal parasite Cryptosporidium hominis and human are relatively conserved. Evaluation of antifolate compound 1 and its R-enantiomer 2 against both enzymes reveals divergent inhibitor selectivity and enzyme stereospecificity. To establish how C. hominis and human TS (ChTS and hTS) selectively discriminate 1 and 2, respectively, we determined crystal structures of ChTS complexed with 2 and hTS complexed with 1 or 2. Coupled with the previously determined structure of ChTS complexed with 1, we discuss a possible mechanism for enzyme stereospecificity and inhibitor selectivity.
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Affiliation(s)
- Daniel J Czyzyk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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10
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Pozzi C, Ferrari S, Luciani R, Costi MP, Mangani S. Structural and Functional Characterization of the Human Thymidylate Synthase (hTS) Interface Variant R175C, New Perspectives for the Development of hTS Inhibitors. Molecules 2019; 24:molecules24071362. [PMID: 30959951 PMCID: PMC6479699 DOI: 10.3390/molecules24071362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is pivotal for cell survival and proliferation, indeed it provides the only synthetic source of dTMP, required for DNA biosynthesis. hTS represents a validated target for anticancer chemotherapy. However, active site-targeting drugs towards hTS have limitations connected to the onset of resistance. Thus, new strategies have to be applied to effectively target hTS without inducing resistance in cancer cells. Here, we report the generation and the functional and structural characterization of a new hTS interface variant in which Arg175 is replaced by a cysteine. Arg175 is located at the interface of the hTS obligate homodimer and protrudes inside the active site of the partner subunit, in which it provides a fundamental contribution for substrate binding. Indeed, the R175C variant results catalytically inactive. The introduction of a cysteine at the dimer interface is functional for development of new hTS inhibitors through innovative strategies, such as the tethering approach. Structural analysis, performed through X-ray crystallography, has revealed that a cofactor derivative is entrapped inside the catalytic cavity of the hTS R175C variant. The peculiar binding mode of the cofactor analogue suggests new clues exploitable for the design of new hTS inhibitors.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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11
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Pozzi C, Lopresti L, Santucci M, Costi MP, Mangani S. Evidence of Destabilization of the Human Thymidylate Synthase (hTS) Dimeric Structure Induced by the Interface Mutation Q62R. Biomolecules 2019; 9:biom9040134. [PMID: 30987202 PMCID: PMC6523895 DOI: 10.3390/biom9040134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022] Open
Abstract
In human cells, thymidylate synthase (TS) provides the only source of 2′-deoxythymidyne-5′-monophosphate (dTMP), which is required for DNA biosynthesis. Because of its pivotal role, human TS (hTS) represents a validated target for anticancer chemotherapy. Nonetheless, the efficacy of drugs blocking the hTS active site has limitations due to the onset of resistance in cancer cells, requiring the identification of new strategies to effectively inhibit this enzyme. Human TS works as an obligate homodimer, making the inter-subunit interface an attractive targetable area. Here, we report the design and investigation of a new hTS variant, in which Gln62, located at the dimer interface, has been replaced by arginine in order to destabilize the enzyme quaternary assembly. The hTS Q62R variant has been characterized though kinetic assay, thermal denaturation analysis and X-ray crystallography. Our results provide evidence that hTS Q62R has a reduced melting temperature. The effective destabilization of the TS quaternary structure is also confirmed by structural analysis, showing that the introduced mutation induces a slight aperture of the hTS dimer. The generation of hTS variants having a more accessible interface area can facilitate the screening of interface-targeting molecules, providing key information for the rational design of innovative hTS interface inhibitors.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2020, University of Siena, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2020, University of Siena, 53100 Siena, Italy.
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2020, University of Siena, 53100 Siena, Italy.
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Fahim AM, Shalaby MA. Synthesis, biological evaluation, molecular docking and DFT calculations of novel benzenesulfonamide derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.087] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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New Insight into the Octamer of TYMS Stabilized by Intermolecular Cys43-Disulfide. Int J Mol Sci 2018; 19:ijms19051393. [PMID: 29735940 PMCID: PMC5983622 DOI: 10.3390/ijms19051393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 01/04/2023] Open
Abstract
Thymidylate synthase (TYMS) is an essential enzyme for the de novo synthesis of deoxythymidine monophosphate (dTMP) and has been a primary target for cancer chemotherapy. Although the physical structure of TYMS and the molecular mechanisms of TYMS catalyzing the conversion of deoxyuridine monophosphate (dUMP) to dTMP have been the subject of thorough studies, its oligomeric structure remains unclear. Here, we show that human TYMS not only exists in dimer form but also as an octamer by intermolecular Cys43-disulfide formation. We optimized the expression conditions of recombinant human TYMS using the Escherichia coli system. Using high-performance liquid chromatography⁻tandem mass spectrometry (HPLC⁻MS/MS), we have shown that purified TYMS has catalytic activity for producing dTMP. In the absence of reductant β-mercaptoethanol, SDS-PAGE and size exclusion chromatography (SEC) showed that the size of the TYMS protein is about 35 kDa, 70 kDa, and 280 kDa. When the Cys43 was mutated to Gly, the band of ~280 kDa and the peak of the octamer disappeared. Therefore, TYMS was determined to form an octamer, depending on the presence of Cys43-disulfide. By measuring steady-state parameters for the monomer, dimer, and octamer, we found the kcat of the octamer was increased slightly more than the monomer. On the basis of these findings, we suggest that the octamer in the active state might have a potential influence on the design of new drug targets.
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Ferrari S, Severi L, Pozzi C, Quotadamo A, Ponterini G, Losi L, Marverti G, Costi MP. Human Thymidylate Synthase Inhibitors Halting Ovarian Cancer Growth. VITAMINS AND HORMONES 2018; 107:473-513. [PMID: 29544641 DOI: 10.1016/bs.vh.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human thymidylate synthase (hTS) has an important role in DNA biosynthesis, thus it is essential for cell survival. TS is involved in the folate pathways, specifically in the de novo pyrimidine biosynthesis. Structure and functions are intimately correlated, account for cellular activity and, in a broader view, with in vivo mechanisms. hTS is a target for anticancer agents, some of which are clinical drugs. The understanding of the detailed mechanism of TS inhibition by currently used drugs and of the interaction with the mechanism of action of other anticancer agents can suggest new perspective of TS inhibition able to improve the anticancer effect and to overcome drug resistance. TS-targeting drugs in therapy today are inhibitors that bind at the active site and that mostly resemble the substrates. Nonsubstrate analogs offer an opportunity for allosteric binding and novel mode of inhibition in the cancer cells. This chapter illustrates the relationship among the large number of hTS actions at molecular and clinical levels, its role as a target for ovarian cancer therapy, in particular in cases of overexpression of hTS and other folate proteins such as those induced by platinum drug treatments, and address the potential combination of TS inhibitors with other suitable anticancer agents.
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Affiliation(s)
| | - Leda Severi
- University of Modena and Reggio Emilia, Modena, Italy
| | | | | | | | - Lorena Losi
- University of Modena and Reggio Emilia, Modena, Italy
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15
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Jarmuła A, Wilk P, Maj P, Ludwiczak J, Dowierciał A, Banaszak K, Rypniewski W, Cieśla J, Dąbrowska M, Frączyk T, Bronowska AK, Jakowiecki J, Filipek S, Rode W. Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS. J Mol Graph Model 2017; 77:33-50. [PMID: 28826032 DOI: 10.1016/j.jmgm.2017.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 01/01/2023]
Abstract
Three crystal structures are presented of nematode thymidylate synthases (TS), including Caenorhabditis elegans (Ce) enzyme without ligands and its ternary complex with dUMP and Raltitrexed, and binary complex of Trichinella spiralis (Ts) enzyme with dUMP. In search of differences potentially relevant for the development of species-specific inhibitors of the nematode enzyme, a comparison was made of the present Ce and Ts enzyme structures, as well as binary complex of Ce enzyme with dUMP, with the corresponding mammalian (human, mouse and rat) enzyme crystal structures. To complement the comparison, tCONCOORD computations were performed to evaluate dynamic behaviors of mammalian and nematode TS structures. Finally, comparative molecular docking combined with molecular dynamics and free energy of binding calculations were carried out to search for ligands showing selective affinity to T. spiralis TS. Despite an overall strong similarity in structure and dynamics of nematode vs mammalian TSs, a pool of ligands demonstrating predictively a strong and selective binding to TsTS has been delimited. These compounds, the E63 family, locate in the dimerization interface of TsTS where they exert species-specific interactions with certain non-conserved residues, including hydrogen bonds with Thr174 and hydrophobic contacts with Phe192, Cys191 and Tyr152. The E63 family of ligands opens the possibility of future development of selective inhibitors of TsTS and effective agents against trichinellosis.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Macromolecular Crystallography (BESSY-MX), Berlin, Germany
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Jan Ludwiczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tomasz Frączyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | | | | | | | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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16
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Chen D, Jansson A, Sim D, Larsson A, Nordlund P. Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states. J Biol Chem 2017; 292:13449-13458. [PMID: 28634233 PMCID: PMC5555203 DOI: 10.1074/jbc.m117.787267] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/18/2017] [Indexed: 12/16/2022] Open
Abstract
Thymidylate synthase (TS) is the sole enzyme responsible for de novo biosynthesis of thymidylate (TMP) and is essential for cell proliferation and survival. Inhibition of human TS (hTS) has been extensively investigated for cancer chemotherapy, but several aspects of its activity and regulation are still uncertain. In this study, we performed comprehensive structural and biophysical studies of hTS using crystallography and thermal shift assay and provided the first detailed structural information on the conformational changes induced by ligand binding to the hTS active site. We found that upon binding of the antifolate agents raltitrexed and nolatrexed, the two insert regions in hTS, the functions of which are unclear, undergo positional shifts toward the catalytic center. We investigated the inactive conformation of hTS and found that the two insert regions are also involved in the conformational transition between the active and inactive state of hTS. Moreover, we identified a ligand-binding site in the dimer interface, suggesting that the cavity in the dimer interface could serve as an allosteric site of hTS to regulate the conformational switching between the active and inactive states. On the basis of these findings, we propose a regulatory mechanism of hTS activity that involves allosteric regulation of interactions of hTS with its own mRNA depending on cellular demands for TMP.
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Affiliation(s)
- Dan Chen
- From the School of Biological Sciences, Lab 07-02 and
| | - Anna Jansson
- From the School of Biological Sciences, Lab 07-02 and
| | - Daniel Sim
- Lab 07-01, Nanyang Technological University, 61 Biopolis Drive (Proteos), Singapore 138673
| | | | - Pär Nordlund
- From the School of Biological Sciences, Lab 07-02 and
- the Institute of Cellular and Molecular Biology, A*STAR, 61 Biopolis Drive (Proteos), Singapore 138673, and
- the Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 17177, Sweden
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17
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Deschamps P, Réty S, Bareille J, Leulliot N. Crystal structure of the active form of native human thymidylate synthase in the absence of bound substrates. Acta Crystallogr F Struct Biol Commun 2017; 73:336-341. [PMID: 28580921 PMCID: PMC5458390 DOI: 10.1107/s2053230x17007233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022] Open
Abstract
Human thymidylate synthase (hTS) provides the sole de novo intracellular source of thymidine 5'-monophosphate (dTMP). hTS is required for DNA replication prior to cell division, making it an attractive target for anticancer chemotherapy and drug discovery. hTS binds 2'-deoxyuridine 5'-monophosphate (dUMP) and the folate co-substrate N5,N10-methylenetetrahydrofolate (meTHF) in a pocket near the catalytic residue Cys195. The catalytic loop, which is composed of amino-acid residues 181-197, can adopt two distinct conformations related by a 180° rotation. In the active conformation Cys195 is close to the active site, while in the inactive conformation it is rotated and Cys195 is too distant from the active site for catalysis. Several hTS structures, either native or engineered, have been solved in the active conformation in complex with ligands or inhibitors and at different salt concentrations. However, apo hTS structures have been solved in an inactive conformation in high-salt and low-salt conditions (PDB entries 1ypv, 4h1i, 4gyh, 3egy and 3ehi). Here, the structure of apo hTS crystallized in the active form with sulfate ions coordinated by the arginine residue that binds dUMP is reported.
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Affiliation(s)
- P. Deschamps
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - S. Réty
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - J. Bareille
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - N. Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie de Paris, Paris, France
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18
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Choi YM, Yeo HK, Park YW, Lee JY. Structural Analysis of Thymidylate Synthase from Kaposi's Sarcoma-Associated Herpesvirus with the Anticancer Drug Raltitrexed. PLoS One 2016; 11:e0168019. [PMID: 27936107 PMCID: PMC5148040 DOI: 10.1371/journal.pone.0168019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/25/2016] [Indexed: 01/07/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a highly infectious human herpesvirus that causes Kaposi's sarcoma. KSHV encodes functional thymidylate synthase, which is a target for anticancer drugs such as raltitrexed or 5-fluorouracil. Thymidylate synthase catalyzes the conversion of 2'-deoxyuridine-5'-monophosphate (dUMP) to thymidine-5'-monophosphate (dTMP) using 5,10-methylenetetrahydrofolate (mTHF) as a co-substrate. The crystal structures of thymidylate synthase from KSHV (apo), complexes with dUMP (binary), and complexes with both dUMP and raltitrexed (ternary) were determined at 1.7 Å, 2.0 Å, and 2.4 Å, respectively. While the ternary complex structures of human thymidylate synthase and E. coli thymidylate synthase had a closed conformation, the ternary complex structure of KSHV thymidylate synthase was observed in an open conformation, similar to that of rat thymidylate synthase. The complex structures of KSHV thymidylate synthase did not have a covalent bond between the sulfhydryl group of Cys219 and C6 atom of dUMP, unlike the human thymidylate synthase. The catalytic Cys residue demonstrated a dual conformation in the apo structure, and its sulfhydryl group was oriented toward the C6 atom of dUMP with no covalent bond upon ligand binding in the complex structures. These structural data provide the potential use of antifolates such as raltitrexed as a viral induced anticancer drug and structural basis to design drugs for targeting the thymidylate synthase of KSHV.
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Affiliation(s)
- Yong Mi Choi
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hyun Ku Yeo
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Young Woo Park
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
- * E-mail:
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19
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Dowierciał A, Jarmuła A, Wilk P, Rypniewski W, Kowalska M, Frączyk T, Cieśla J, Rode W. Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme. Struct Chem 2016. [DOI: 10.1007/s11224-016-0840-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Almqvist H, Axelsson H, Jafari R, Dan C, Mateus A, Haraldsson M, Larsson A, Martinez Molina D, Artursson P, Lundbäck T, Nordlund P. CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil. Nat Commun 2016; 7:11040. [PMID: 27010513 PMCID: PMC4820820 DOI: 10.1038/ncomms11040] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/15/2016] [Indexed: 02/06/2023] Open
Abstract
Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.
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Affiliation(s)
- Helena Almqvist
- Laboratories for Chemical Biology, Karolinska Institutet, Science for Life Laboratory Stockholm, Division of Translational Medicine &Chemical Biology, Department of Medical Biochemistry &Biophysics, Karolinska Institutet, Tomtebodavägen 23A, Solna 171 65, Sweden
| | - Hanna Axelsson
- Laboratories for Chemical Biology, Karolinska Institutet, Science for Life Laboratory Stockholm, Division of Translational Medicine &Chemical Biology, Department of Medical Biochemistry &Biophysics, Karolinska Institutet, Tomtebodavägen 23A, Solna 171 65, Sweden
| | - Rozbeh Jafari
- Department of Medical Biochemistry &Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 171 77, Sweden
| | - Chen Dan
- School of Biological Sciences, Nanyang Technological University, 61 Biopolis Drive (Proteos), Singapore 138673, Singapore
| | - André Mateus
- Department of Pharmacy, Uppsala University, BMC, Box 580, Uppsala SE-751 23, Sweden
| | - Martin Haraldsson
- Laboratories for Chemical Biology, Karolinska Institutet, Science for Life Laboratory Stockholm, Division of Translational Medicine &Chemical Biology, Department of Medical Biochemistry &Biophysics, Karolinska Institutet, Tomtebodavägen 23A, Solna 171 65, Sweden
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, SBS-04s-45, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Daniel Martinez Molina
- Department of Medical Biochemistry &Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 171 77, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, BMC, Box 580, Uppsala SE-751 23, Sweden.,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, BMC, Box 580, Uppsala SE-751 23, Sweden.,Science for Life Laboratory Drug Discovery and Development platform, Uppsala University, Uppsala SE-751 23, Sweden
| | - Thomas Lundbäck
- Laboratories for Chemical Biology, Karolinska Institutet, Science for Life Laboratory Stockholm, Division of Translational Medicine &Chemical Biology, Department of Medical Biochemistry &Biophysics, Karolinska Institutet, Tomtebodavägen 23A, Solna 171 65, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry &Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 171 77, Sweden.,School of Biological Sciences, Nanyang Technological University, 61 Biopolis Drive (Proteos), Singapore 138673, Singapore.,Institute of Cellular and Molecular Biology, ASTAR, 61 Biopolis Drive (Proteos), Singapore 138673, Singapore
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21
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Synthesis, Biological Evaluation and Molecular Docking Studies of 6-Aryl-2-Styrylquinazolin-4(3H)-Ones. Molecules 2015; 21:E28. [PMID: 26712730 PMCID: PMC6274206 DOI: 10.3390/molecules21010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/19/2015] [Accepted: 12/22/2015] [Indexed: 11/17/2022] Open
Abstract
Suzuki-Miyaura cross-coupling of 6-bromo-2-styrylquinazolin-4(3H)-ones with arylboronic acids afforded a series of novel 6-aryl-2-styrylquinazolin-4(3H)-ones. These compounds were evaluated for potential anticancer properties against the human renal (TK-10), melanoma (UACC-62) and breast cancer (MCF-7) cell lines. Their antimicrobial properties were also evaluated against six Gram-positive and four Gram-negative bacteria, as well as two strains of fungi. Molecular docking studies (in silico) were conducted on compounds 5a, b, d and 6a, b, d–f to recognize the hypothetical binding motif of the title compounds within the active site of the dihydrofolate reductase and thymidylate synthase enzymes.
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22
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Hew K, Dahlroth SL, Veerappan S, Pan LX, Cornvik T, Nordlund P. Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine. PLoS One 2015; 10:e0143947. [PMID: 26630264 PMCID: PMC4668047 DOI: 10.1371/journal.pone.0143947] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/11/2015] [Indexed: 12/19/2022] Open
Abstract
Varicella zoster virus (VZV) is a highly infectious human herpesvirus that is the causative agent for chicken pox and shingles. VZV encodes a functional thymidylate synthase (TS), which is the sole enzyme that produces dTMP from dUMP de novo. To study substrate binding, the complex structure of TSVZV with dUMP was determined to a resolution of 2.9 Å. In the absence of a folate co-substrate, dUMP binds in the conserved TS active site and is coordinated similarly as in the human encoded TS (TSHS) in an open conformation. The interactions between TSVZV with dUMP and a cofactor analog, raltitrexed, were also studied using differential scanning fluorimetry (DSF), suggesting that TSVZV binds dUMP and raltitrexed in a sequential binding mode like other TS. The DSF also revealed interactions between TSVZV and in vitro phosphorylated brivudine (BVDUP), a highly potent anti-herpesvirus drug against VZV infections. The binding of BVDUP to TSVZV was further confirmed by the complex structure of TSVZV and BVDUP solved at a resolution of 2.9 Å. BVDUP binds similarly as dUMP in the TSHS but it induces a closed conformation of the active site. The structure supports that the 5-bromovinyl substituent on BVDUP is likely to inhibit TSVZV by preventing the transfer of a methylene group from its cofactor and the subsequent formation of dTMP. The interactions between TSVZV and BVDUP are consistent with that TSVZV is indeed a target of brivudine in vivo. The work also provided the structural basis for rational design of more specific TSVZV inhibitors.
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Affiliation(s)
- Kelly Hew
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sue-Li Dahlroth
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Saranya Veerappan
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Lucy Xin Pan
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Tobias Cornvik
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Pär Nordlund
- Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail:
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23
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Frączyk T, Ruman T, Wilk P, Palmowski P, Rogowska-Wrzesinska A, Cieśla J, Zieliński Z, Nizioł J, Jarmuła A, Maj P, Gołos B, Wińska P, Ostafil S, Wałajtys-Rode E, Shugar D, Rode W. Properties of phosphorylated thymidylate synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1922-1934. [PMID: 26315778 DOI: 10.1016/j.bbapap.2015.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/24/2015] [Accepted: 08/18/2015] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TS) may undergo phosphorylation endogenously in mammalian cells, and as a recombinant protein expressed in bacterial cells, as indicated by the reaction of purified enzyme protein with Pro-Q® Diamond Phosphoprotein Gel Stain (PGS). With recombinant human, mouse, rat, Trichinella spiralis and Caenorhabditis elegans TSs, expressed in Escherichia coli, the phosphorylated, compared to non-phosphorylated recombinant enzyme forms, showed a decrease in Vmax(app), bound their cognate mRNA (only rat enzyme studied), and repressed translation of their own and several heterologous mRNAs (human, rat and mouse enzymes studied). However, attempts to determine the modification site(s), whether endogenously expressed in mammalian cells, or recombinant proteins, did not lead to unequivocal results. Comparative ESI-MS/analysis of IEF fractions of TS preparations from parental and FdUrd-resistant mouse leukemia L1210 cells, differing in sensitivity to inactivation by FdUMP, demonstrated phosphorylation of Ser(10) and Ser(16) in the resistant enzyme only, although PGS staining pointed to the modification of both L1210 TS proteins. The TS proteins phosphorylated in bacterial cells were shown by (31)P NMR to be modified only on histidine residues, like potassium phosphoramidate (KPA)-phosphorylated TS proteins. NanoLC-MS/MS, enabling the use of CID and ETD peptide fragmentation methods, identified several phosphohistidine residues, but certain phosphoserine and phosphothreonine residues were also implicated. Molecular dynamics studies, based on the mouse TS crystal structure, allowed one to assess potential of several phosphorylated histidine residues to affect catalytic activity, the effect being phosphorylation site dependent.
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Affiliation(s)
- Tomasz Frączyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Ruman
- Rzeszów University of Technology, Faculty of Chemistry, Rzeszów, Poland
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Palmowski
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Nizioł
- Rzeszów University of Technology, Faculty of Chemistry, Rzeszów, Poland
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Gołos
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Patrycja Wińska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sylwia Ostafil
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Wałajtys-Rode
- Warsaw University of Technology, Faculty of Chemistry, Institute of Biotechnology, Warsaw, Poland
| | - David Shugar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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24
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Salo-Ahen OMH, Tochowicz A, Pozzi C, Cardinale D, Ferrari S, Boum Y, Mangani S, Stroud RM, Saxena P, Myllykallio H, Costi MP, Ponterini G, Wade RC. Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase. J Med Chem 2015; 58:3572-81. [PMID: 25798950 DOI: 10.1021/acs.jmedchem.5b00137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human thymidylate synthase (hTS), a target for antiproliferative drugs, is an obligate homodimer. Single-point mutations to alanine at the monomer-monomer interface may enable the identification of specific residues that delineate sites for drugs aimed at perturbing the protein-protein interactions critical for activity. We computationally identified putative hotspot residues at the interface and designed mutants to perturb the intersubunit interaction. Dimer dissociation constants measured by a FRET-based assay range from 60 nM for wild-type hTS up to about 1 mM for single-point mutants and agree with computational predictions of the effects of these mutations. Mutations that are remote from the active site retain full or partial activity, although the substrate KM values were generally higher and the dimer was less stable. The lower dimer stability of the mutants can facilitate access to the dimer interface by small molecules and thereby aid the design of inhibitors that bind at the dimer interface.
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Affiliation(s)
- Outi M H Salo-Ahen
- †Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Anna Tochowicz
- ‡Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California 94158, United States
| | - Cecilia Pozzi
- §Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Daniela Cardinale
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefania Ferrari
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Yap Boum
- ⊥Ecole Polytechnique, CNRS UMR7645, INSERM U696, 91128 Palaiseau, France
| | - Stefano Mangani
- §Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Robert M Stroud
- ‡Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California 94158, United States
| | - Puneet Saxena
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Hannu Myllykallio
- ⊥Ecole Polytechnique, CNRS UMR7645, INSERM U696, 91128 Palaiseau, France
| | - Maria Paola Costi
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Glauco Ponterini
- ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Rebecca C Wade
- †Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.,#Center for Molecular Biology, DKFZ-ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany
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25
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Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations. BIOMED RESEARCH INTERNATIONAL 2014; 2014:945803. [PMID: 24995339 PMCID: PMC4065713 DOI: 10.1155/2014/945803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/13/2014] [Accepted: 05/16/2014] [Indexed: 11/17/2022]
Abstract
The crystal structure of mouse thymidylate synthase (mTS) in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB) and thus supporting tighter binding of ligands, and the other being more open (dimer CD) and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed.
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26
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Lima A, Azevedo R, Sousa H, Seabra V, Medeiros R. Current approaches for TYMS polymorphisms and their importance in molecular epidemiology and pharmacogenetics. Pharmacogenomics 2013; 14:1337-51. [DOI: 10.2217/pgs.13.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
TS is critical for providing the requisite nucleotide precursors in order to maintain DNA synthesis and repair. Furthermore, it is an important target for several drugs such as 5-fluorouracil and methotrexate. However, several mechanisms of resistance to TS inhibitors have been explained as linked to TYMS overexpression. Some authors have described the relationship between genetic polymorphisms on TYMS, in particular rs34743033, rs2853542 and rs34489327, with the development of several diseases and with the clinical response to drug therapy and/or survival. Nevertheless, the obtained results described in the literature are controversial, which has lead to a search strategy to understand the impact of these polymorphisms on molecular epidemiology and pharmacogenetics. With the progress of these scientific areas, early identification of individuals at risk of disease along with improvement in the prediction of patients’ outcome will offer a powerful tool for the translation of TYMS polymorphisms into clinical practice and individualization of treatments.
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Affiliation(s)
- Aurea Lima
- Molecular Oncology Group CI, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
- CESPU, Health Sciences Research Center (CICS), Department of Pharmaceutical Sciences, Higher Institute of Health Sciences – North (ISCS-N), Rua Central de Gandra 1317, 4585-116, Gandra PRD, Portugal.
| | - Rita Azevedo
- Molecular Oncology Group CI, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
- Faculty of Medicine of University of Porto (FMUP), Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Hugo Sousa
- Molecular Oncology Group CI, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
- Faculty of Medicine of University of Porto (FMUP), Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Virology Service, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Vítor Seabra
- CESPU, Health Sciences Research Center (CICS), Department of Pharmaceutical Sciences, Higher Institute of Health Sciences – North (ISCS-N), Rua Central de Gandra 1317, 4585-116, Gandra PRD, Portugal
| | - Rui Medeiros
- Molecular Oncology Group CI, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
- Virology Service, Portuguese Institute of Oncology of Porto (IPO-Porto), Rua António Bernardino de Almeida, 4200-072, Porto, Portugal
- Research Department – Portuguese League Against Cancer (LPCC-NRNorte), Estrada Interior da Circunvalação, 6657, 4200-177, Porto, Portugal
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27
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Tochowicz A, Dalziel S, Eidam O, O'Connell JD, Griner S, Finer-Moore JS, Stroud RM. Development and binding mode assessment of N-[4-[2-propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-γ-glutamyl-D-glutamic acid (BGC 945), a novel thymidylate synthase inhibitor that targets tumor cells. J Med Chem 2013; 56:5446-55. [PMID: 23710599 DOI: 10.1021/jm400490e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta[g]quinazolin-6-yl]amino]benzoyl]-l-γ-glutamyl-d-glutamic acid 1 (BGC 945, now known as ONX 0801), is a small molecule thymidylate synthase (TS) inhibitor discovered at the Institute of Cancer Research in London. It is licensed by Onyx Pharmaceuticals and is in phase 1 clinical studies. It is a novel antifolate drug resembling TS inhibitors plevitrexed and raltitrexed that combines enzymatic inhibition of thymidylate synthase with α-folate receptor-mediated targeting of tumor cells. Thus, it has potential for efficacy with lower toxicity due to selective intracellular accumulation through α-folate receptor (α-FR) transport. The α-FR, a cell-surface receptor glycoprotein, which is overexpressed mainly in ovarian and lung cancer tumors, has an affinity for 1 similar to that for its natural ligand, folic acid. This study describes a novel synthesis of 1, an X-ray crystal structure of its complex with Escherichia coli TS and 2'-deoxyuridine-5'-monophosphate, and a model for a similar complex with human TS.
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Affiliation(s)
- Anna Tochowicz
- Department of Biochemistry and Biophysics, University of California-San Francisco , 600 16th Street, San Francisco, California 94158, United States
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28
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Erales J, Coffino P. Ubiquitin-independent proteasomal degradation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:216-21. [PMID: 23684952 DOI: 10.1016/j.bbamcr.2013.05.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 10/26/2022]
Abstract
Most proteasome substrates are marked for degradation by ubiquitin conjugation, but some are targeted by other means. The properties of these exceptional cases provide insights into the general requirements for proteasomal degradation. Here the focus is on three ubiquitin-independent substrates that have been the subject of detailed study. These are Rpn4, a transcriptional regulator of proteasome homeostasis, thymidylate synthase, an enzyme required for production of DNA precursors and ornithine decarboxylase, the initial enzyme committed to polyamine biosynthesis. It can be inferred from these cases that proteasome association and the presence of an unstructured region are the sole prerequisites for degradation. Based on that inference, artificial substrates have been designed to test the proteasome's capacity for substrate processing and its limitations. Ubiquitin-independent substrates may in some cases be a remnant of the pre-ubiquitome world, but in other cases could provide optimized regulatory solutions. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Jenny Erales
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94127, USA
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29
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Jarmuła A, Rode W. Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase. J Comput Aided Mol Des 2012; 27:45-66. [PMID: 23239172 DOI: 10.1007/s10822-012-9624-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 12/06/2012] [Indexed: 11/25/2022]
Abstract
Tyrosine nitration is a widespread post-translational modification capable of affecting both the function and structure of the host protein molecule. Enzyme thymidylate synthase (TS), a homodimer, is a molecular target for anticancer therapy. Recently purified TS preparations, isolated from mammalian tissues, were found to be nitrated, suggesting this modification to appear endogenously in normal and tumor tissues. Moreover, human TS (hTS) nitration in vitro led to a by twofold lowered catalytic activity following nitration in average of 1 tyrosine residue per monomer (Dąbrowska-Maś et al. in Org Biomol Chem 10:323-331, 2012), with the modification identified by mass spectrometry at seven different sites (Y33, Y65, Y135, Y213, Y230, Y258 and Y301). In the present paper, combined computational approach, including molecular and essential dynamics and free energy computations, was used to predict the influence on the activity of hTS of nitration of each of the seven tyrosine residues. The simulations were based on the crystal structure of hTS ternary complex with dUMP and Tomudex (PDB code: 1I00), with the Tomudex molecule replaced by the molecule of TS cofactor analogue, tetrahydrofolate. The present results indicate that while with nitration of five out of seven residues (Y33, Y135, Y230, Y258 and Y301), single residue modification appears to have a strong reducing effect on the activity, with the remaining two, Y65 and Y213, no or a weaker influence is apparent. Taken together, these results demonstrate that tyrosine nitrations in the hTS enzyme show clear tendency to influence the structure and dynamics and, in turn, catalytic properties of the host enzyme. These effects are overall distance-dependent.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland.
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30
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Carosati E, Tochowicz A, Marverti G, Guaitoli G, Benedetti P, Ferrari S, Stroud RM, Finer-Moore J, Luciani R, Farina D, Cruciani G, Costi MP. Inhibitor of Ovarian Cancer Cells Growth by Virtual Screening: A New Thiazole Derivative Targeting Human Thymidylate Synthase. J Med Chem 2012; 55:10272-6. [DOI: 10.1021/jm300850v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Emanuele Carosati
- Dipartimento
di Chimica, Università degli Studi di Perugia, Via Elce
di Sotto 10, 06123, Perugia, Italy
| | - Anna Tochowicz
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Gaetano Marverti
- Dipartimento di Scienze Biomediche,
Metaboliche e Neuroscienze, Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena,
Italy
| | - Giambattista Guaitoli
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Paolo Benedetti
- Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5
5NE, U.K
| | - Stefania Ferrari
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Robert M. Stroud
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Janet Finer-Moore
- Department of Biochemistry and
Biophysics, University of California—San Francisco, 600 16th Street, San Francisco 94158, California, United States
| | - Rosaria Luciani
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Davide Farina
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Gabriele Cruciani
- Dipartimento
di Chimica, Università degli Studi di Perugia, Via Elce
di Sotto 10, 06123, Perugia, Italy
| | - M. Paola Costi
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41125 Modena, Italy
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31
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The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations. Proteins 2011; 79:2886-99. [DOI: 10.1002/prot.23123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 05/13/2011] [Accepted: 06/15/2011] [Indexed: 12/11/2022]
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32
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Luo B, Repalli J, Yousef AM, Johnson SR, Lebioda L, Berger SH. Human thymidylate synthase with loop 181-197 stabilized in an inactive conformation: ligand interactions, phosphorylation, and inhibition profiles. Protein Sci 2011; 20:87-94. [PMID: 21064161 DOI: 10.1002/pro.539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thymidylate synthase (TS) is a well-validated cancer target that undergoes conformational switching between active and inactive states. Two mutant human TS (hTS) proteins are predicted from crystal structures to be stabilized in an inactive conformation to differing extents, with M190K populating the inactive conformation to a greater extent than A191K. Studies of intrinsic fluorescence and circular dichroism revealed that the structures of the mutants differ from those of hTS. Inclusion of the substrate dUMP was without effect on M190K but induced structural changes in A191K that are unique, relative to hTS. The effect of strong stabilization in an inactive conformation on protein phosphorylation by casein kinase 2 (CK2) was investigated. M190K was highly phosphorylated by CK2 relative to an active-stabilized mutant, R163K hTS. dUMP had no detectable effect on phosphorylation of M190K; however, dUMP inhibited phosphorylation of hTS and R163K. Studies of temperature dependence of catalysis revealed that the E(act) and temperature optimum are higher for A191K than hTS. The potency of the active-site inhibitor, raltitrexed, was lower for A191K than hTS. The response of A191K to the allosteric inhibitor, propylene diphosphonate (PDPA) was concentration dependent. Mixed inhibition was observed at low concentrations; at higher concentrations, A191K exhibited nonhyperbolic behavior with respect to dUMP and inhibition of catalysis was reversed by substrate saturation. In summary, inactive-stabilized mutants differ from hTS in thermal stability and response to substrates and PDPA. Importantly, phosphorylation of hTS by CK2 is selective for the inactive conformation, providing the first indication of physiological relevance for conformational switching.
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Affiliation(s)
- BeiBei Luo
- Department of Pharmaceutical Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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33
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Gibson LM, Celeste LR, Lovelace LL, Lebioda L. Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:60-6. [PMID: 21206062 PMCID: PMC3016017 DOI: 10.1107/s0907444910044732] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/01/2010] [Indexed: 11/10/2022]
Abstract
Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that hTS binds this ligand. Interestingly, the two types of binding observed are both asymmetric. In one subunit of the physiological dimer covalent modification of the catalytic nucleophile Cys195 takes place, while in another dimer a noncovalent adduct with reduced glutathione is formed in one of the active sites.
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Affiliation(s)
- Lydia M. Gibson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lesa R. Celeste
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Leslie L. Lovelace
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
- Center for Colon Cancer Research, University of South Carolina, Columbia, South Carolina 29208, USA
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34
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Jarmuła A, Fraczyk T, Cieplak P, Rode W. Mechanism of influence of phosphorylation on serine 124 on a decrease of catalytic activity of human thymidylate synthase. Bioorg Med Chem 2010; 18:3361-70. [PMID: 20430630 PMCID: PMC4127429 DOI: 10.1016/j.bmc.2010.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 04/01/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022]
Abstract
Regulation by phosphorylation is a well-established mechanism for controlling biological activity of proteins. Recently, phosphorylation of serine 124 in human thymidylate synthase (hTS) has been shown to lower the catalytic activity of the enzyme. To clarify a possible mechanism of the observed influence, molecular dynamics (MD), essential dynamics (ED) and MM-GBSA studies were undertaken. Structures derived from the MD trajectories reveal incorrect binding alignment between the pyrimidine ring of the substrate, dUMP, and the pterine ring of the cofactor analogue, THF, in the active site of the phosphorylated enzyme. The ED analysis indicates changes in the behavior of collective motions in the phosphorylated enzyme, suggesting that the formation of the closed ternary complex is hindered. Computed free energies, in agreement with structural analysis, predict that the binding of dUMP and THF to hTS is favored in the native compared to phosphorylated state of the enzyme. The paper describes at the structural level how phosphorylation at the distant site influences the ligand binding. We propose that the 'phosphorylation effect' is transmitted from the outside loop of Ser 124 into the active site via a subtle mechanism initiated by the long-range electrostatic repulsion between the phosphate groups of dUMP and Ser124. The mechanism can be described in terms of the interplay between the two groups of amino acids: the link (residues 125-134) and the patch (residues 189-192), resulting in the change of orientation of the pyrimidine ring of dUMP, which, in turn, prevents the correct alignment between the latter ring and the pterin ring of THF.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland.
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35
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Huang X, Gibson LM, Bell BJ, Lovelace LL, Peña MMO, Berger FG, Berger SH, Lebioda L. Replacement of Val3 in human thymidylate synthase affects its kinetic properties and intracellular stability . Biochemistry 2010; 49:2475-82. [PMID: 20151707 DOI: 10.1021/bi901457e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human and other mammalian thymidylate synthase (TS) enzymes have an N-terminal extension of approximately 27 amino acids that is not present in bacterial TSs. The extension, which is disordered in all reported crystal structures of TSs, has been considered to play a primary role in protein turnover but not in catalytic activity. In mammalian cells, the variant V3A has a half-life similar to that of wild-type human TS (wt hTS) while V3T is much more stable; V3L, V3F, and V3Y have half-lives approximately half of that for wt hTS. Catalytic turnover rates for most Val3 mutants are only slightly diminished, as expected. However, two mutants, V3L and V3F, have strongly compromised dUMP binding, with K(m,app) values increased by factors of 47 and 58, respectively. For V3L, this observation can be explained by stabilization of the inactive conformation of the loop of residues 181-197, which prevents substrate binding. In the crystal structure of V3L, electron density corresponding to a leucine residue is present in a position that stabilizes the loop of residues 181-197 in the inactive conformation. Since this density is not observed in other mutants and all other leucine residues are ordered in this structure, it is likely that this density represents Leu3. In the crystal structure of a V3F.FdUMP binary complex, the nucleotide is bound in an alternative mode to that proposed for the catalytic complex, indicating that the high K(m,app) value is caused not by stabilization of the inactive conformer but by substrate binding in a nonproductive, inhibitory site. These observations show that the N-terminal extension affects the conformational state of the hTS catalytic region. Each of the mechanisms leading to the high K(m,app) values can be exploited to facilitate design of compounds acting as allosteric inhibitors of hTS.
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Affiliation(s)
- Xiao Huang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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36
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Srivastava V, Gupta SP, Siddiqi MI, Mishra BN. Molecular docking studies on quinazoline antifolate derivatives as human thymidylate synthase inhibitors. Bioinformation 2010; 4:357-65. [PMID: 20975900 PMCID: PMC2951674 DOI: 10.6026/97320630004357] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 11/15/2009] [Indexed: 11/29/2022] Open
Abstract
We have performed molecular docking on quinazoline antifolates complexed with human thymidylate synthase to gain insight into the structural
preferences of these inhibitors. The study was conducted on a selected set of one hundred six compounds with variation in structure and activity.
The structural analyses indicate that the coordinate bond interactions, the hydrogen bond interactions, the van der Waals interactions as well as
the hydrophobic interactions between ligand and receptor are responsible simultaneously for the preference of inhibition and potency. In this
study, fast flexible docking simulations were performed on quinazoline antifolates derivatives as human thymidylate synthase inhibitors. The
results indicated that the quinazoline ring of the inhibitors forms hydrophobic contacts with Leu192, Leu221 and Tyr258 and stacking interaction
is conserved in complex with the inhibitor and cofactor.
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Affiliation(s)
- Vivek Srivastava
- Department of Biotechnology, Meerut Institute of Engineering & Technology, Meerut-250005; Department of Biotechnology, Institute of Engineering & Technology, UP Technical University, Sitapur Road, Lucknow 226021
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37
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Fraczyk T, Kubiński K, Masłyk M, Cieśla J, Hellman U, Shugar D, Rode W. Phosphorylation of thymidylate synthase from various sources by human protein kinase CK2 and its catalytic subunits. Bioorg Chem 2010; 38:124-31. [PMID: 20199796 DOI: 10.1016/j.bioorg.2010.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/06/2010] [Accepted: 02/09/2010] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) was found to be a substrate for both catalytic subunits of human CK2, with phosphorylation by CK2alpha and CK2alpha' characterized by similar K(m) values, 4.6microM and 4.2microM, respectively, but different efficiencies, the apparent turnover number with CK2alpha being 10-fold higher. With both catalytic subunits, phosphorylation of human TS, like calmodulin and BID, was strongly inhibited in the presence of the regulatory subunit CK2beta, the holoenzyme being activated by polylysine. Phosphorylation of recombinant human, rat, mouse and Trichinella spiralis TSs proteins was compared, with the human enzyme being apparently a much better substrate than the others. Following hydrolysis and TLC, phosphoserine was detected in human and rat, and phosphotyrosine in T. spiralis, TS, used as substrates for CK2alpha. MALDI-TOF MS analysis led to identification of phosphorylated Ser(124) in human TS, within a sequence LGFS(124)TREEGD, atypical for a CK2 substrate recognition site. The phosphorylation site is located in a region considered important for the catalytic mechanism or regulation of human TS, corresponding to the loop 107-128. Following phosphorylation by CK2alpha, resulting in incorporation of 0.4mol of phosphate per mol of dimeric TS, human TS exhibits unaltered K(m) values for dUMP and N(5,10)-methylenetetrahydrofolate, but a 50% lower turnover number, pointing to a strong influence of Ser(124) phosphorylation on its catalytic efficiency.
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Affiliation(s)
- Tomasz Fraczyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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38
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Lovelace LL, Johnson SR, Gibson LM, Bell BJ, Berger SH, Lebioda L. Variants of human thymidylate synthase with loop 181-197 stabilized in the inactive conformation. Protein Sci 2009; 18:1628-36. [PMID: 19569192 DOI: 10.1002/pro.171] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Loop 181-197 of human thymidylate synthase (hTS) populates two major conformations, essentially corresponding to the loop flipped by 180 degrees . In one of the conformations, the catalytic Cys195 residue lies distant from the active site making the enzyme inactive. Ligands stabilizing this inactive conformation may function as allosteric inhibitors. To facilitate the search for such inhibitors, we have expressed and characterized several mutants designed to shift the equilibrium toward the inactive conformer. In most cases, the catalytic efficiency of the mutants was only somewhat impaired with values of k(cat)/K(m) reduced by factors in a 2-12 range. One of the mutants, M190K, is however unique in having the value of k(cat)/K(m) smaller by a factor of approximately 7500 than the wild type. The crystal structure of this mutant is similar to that of the wt hTS with loop 181-197 in the inactive conformation. However, the direct vicinity of the mutation, residues 188-194 of this loop, assumes a different conformation with the positions of C(alpha) shifted up to 7.2 A. This affects region 116-128, which became ordered in M190K while it is disordered in wt. The conformation of 116-128 is however different than that observed in hTS in the active conformation. The side chain of Lys190 does not form contacts and is in solvent region. The very low activity of M190K as compared to another mutant with a charged residue in this position, M190E, suggests that the protein is trapped in an inactive state that does not equilibrate easily with the active conformer.
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Affiliation(s)
- Leslie L Lovelace
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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Martucci WE, Vargo MA, Anderson KS. Explaining an unusually fast parasitic enzyme: folate tail-binding residues dictate substrate positioning and catalysis in Cryptosporidium hominis thymidylate synthase. Biochemistry 2008; 47:8902-11. [PMID: 18672899 DOI: 10.1021/bi800466z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The essential enzyme TS-DHFR from Cryptosporidium hominis undergoes an unusually rapid rate of catalysis at the conserved TS domain, facilitated by two nonconserved residues, Ala287 and Ser290, in the folate tail-binding region. Mutation of these two residues to their conserved counterparts drastically affects multiple steps of the TS catalytic cycle. We have determined the crystal structures of all three mutants (A287F, S290G, and A287F/S290G) in complex with active site ligands dUMP and CB3717. The structural data show two effects of the mutations: an increased distance between the ligands in the active site and increased flexibility of the folate ligand in the partially open enzyme state that precedes conformational change to the active catalytic state. The latter effect is able to be rescued by the mutants containing the A287F mutation. In addition, the conserved water network of TS is altered in each of the mutants. The structural results point to a role of the folate tail-binding residues in closely positioning ChTS ligands and restricting ligand flexibility in the partially open state to allow for a rapid transition to the active closed state and enhanced rate of catalysis. These results provide an explanation on how folate tail-binding residues at one end of the active site affect long-range interactions throughout the TS active site and validate these residues as targets for species-specific drug design.
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Affiliation(s)
- W Edward Martucci
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
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40
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Jariel-Encontre I, Bossis G, Piechaczyk M. Ubiquitin-independent degradation of proteins by the proteasome. Biochim Biophys Acta Rev Cancer 2008; 1786:153-77. [PMID: 18558098 DOI: 10.1016/j.bbcan.2008.05.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 05/15/2008] [Accepted: 05/15/2008] [Indexed: 02/08/2023]
Abstract
The proteasome is the main proteolytic machinery of the cell and constitutes a recognized drugable target, in particular for treating cancer. It is involved in the elimination of misfolded, altered or aged proteins as well as in the generation of antigenic peptides presented by MHC class I molecules. It is also responsible for the proteolytic maturation of diverse polypeptide precursors and for the spatial and temporal regulation of the degradation of many key cell regulators whose destruction is necessary for progression through essential processes, such as cell division, differentiation and, more generally, adaptation to environmental signals. It is generally believed that proteins must undergo prior modification by polyubiquitin chains to be addressed to, and recognized by, the proteasome. In reality, however, there is accumulating evidence that ubiquitin-independent proteasomal degradation may have been largely underestimated. In particular, a number of proto-oncoproteins and oncosuppressive proteins are privileged ubiquitin-independent proteasomal substrates, the altered degradation of which may have tumorigenic consequences. The identification of ubiquitin-independent mechanisms for proteasomal degradation also poses the paramount question of the multiplicity of catabolic pathways targeting each protein substrate. As this may help design novel therapeutic strategies, the underlying mechanisms are critically reviewed here.
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Affiliation(s)
- Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR5535, IFR122, 1919 Route de Mende, Montpellier, F-34293, France
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41
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Gibson LM, Lovelace LL, Lebioda L. The R163K mutant of human thymidylate synthase is stabilized in an active conformation: structural asymmetry and reactivity of cysteine 195. Biochemistry 2008; 47:4636-43. [PMID: 18370400 DOI: 10.1021/bi7019386] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Loop 181-197 of human thymidylate synthase (hTS) populates two conformational states. In the first state, Cys195, a residue crucial for catalytic activity, is in the active site (active conformer); in the other conformation, it is about 10 A away, outside the active site (inactive conformer). We have designed and expressed an hTS variant, R163K, in which the inactive conformation is destabilized. The activity of this mutant is 33% higher than that of wt hTS, suggesting that at least one-third of hTS populates the inactive conformer. Crystal structures of R163K in two different crystal forms, with six and two subunits per asymmetric part of the unit cells, have been determined. All subunits of this mutant are in the active conformation while wt hTS crystallizes as the inactive conformer in similar mother liquors. The structures show differences in the environment of catalytic Cys195, which correlate with Cys195 thiol reactivity, as judged by its oxidation state. Calculations show that the molecular electrostatic potential at Cys195 differs between the subunits of the dimer. One of the dimers is asymmetric with a phosphate ion bound in only one of the subunits. In the absence of the phosphate ion, that is in the inhibitor-free enzyme, the tip of loop 47-53 is about 11 A away from the active site.
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Affiliation(s)
- Lydia M Gibson
- Department of Chemistry and Biochemistry and Center for Colon Cancer Research, University of South Carolina, Columbia, SC 29208, USA
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42
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Jarmuła A, Dowierciał A, Rode W. A molecular modeling study of the interaction of 2'-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase. Bioorg Med Chem Lett 2008; 18:2701-8. [PMID: 18362071 DOI: 10.1016/j.bmcl.2008.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 03/03/2008] [Accepted: 03/06/2008] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulations and free energy calculations are presented, exploring previously described experimentally studied interactions of a series of 2'-fluoro-substituted dUMP/FdUMP analogues with thymidylate synthase (TS). The results show the inhibitory behaviors of 2'-F-ara-UMP, 2',2''-diF-dUMP and 2',5-diF-ara-UMP to be dependent upon the binding positions and orientations adopted by the molecules of these compounds in the active site of TS. The binding mode of 2',5-diF-ara-UMP suggests a novel role of the active site residue Trp 80, stabilizing through hydrophobic stacking the binding position of the pyrimidine ring in 2',5-diF-ara-UMP.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warszawa, Poland.
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43
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Lovelace LL, Gibson LM, Lebioda L. Cooperative inhibition of human thymidylate synthase by mixtures of active site binding and allosteric inhibitors. Biochemistry 2007; 46:2823-30. [PMID: 17297914 PMCID: PMC2516748 DOI: 10.1021/bi061309j] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidylate synthase (TS) is a target in the chemotherapy of colorectal cancer and some other neoplasms. It catalyzes the transfer of a methyl group from methylenetetrahydrofolate to dUMP to form dTMP. On the basis of structural considerations, we have introduced 1,3-propanediphosphonic acid (PDPA) as an allosteric inhibitor of human TS (hTS); it is proposed that PDPA acts by stabilizing an inactive conformer of loop 181-197. Kinetic studies showed that PDPA is a mixed (noncompetitive) inhibitor versus dUMP. In contrast, versus methylenetrahydrofolate at concentrations lower than 0.25 microM, PDPA is an uncompetitive inhibitor, while at PDPA concentrations higher than 1 microM the inhibiton is noncompetive, as expected. At the concentrations corresponding to uncompetitive inhibition, PDPA shows positive cooperativity with an antifolate inhibitor, ZD9331, which binds to the active conformer. PDPA binding leads to the formation of hTS tetramers, but not higher oligomers. These data are consistent with a model in which hTS exists preferably as an asymmetric dimer with one subunit in the active conformation of loop 181-197 and the other in the inactive conformation.
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Affiliation(s)
- Leslie L. Lovelace
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Lydia M. Gibson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
- Center for Colon Cancer Research, University of South Carolina, Columbia, South Carolina 29208
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44
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Costi MP, Gelain A, Barlocco D, Ghelli S, Soragni F, Reniero F, Rossi T, Ruberto A, Guillou C, Cavazzuti A, Casolari C, Ferrari S. Antibacterial Agent Discovery Using Thymidylate Synthase Biolibrary Screening. J Med Chem 2006; 49:5958-68. [PMID: 17004711 DOI: 10.1021/jm051187d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TS, ThyA) catalyzes the reductive methylation of 2'-deoxyuridine 5'-monophosphate to 2'-deoxythymidine 5'-monophosphate, an essential precursor for DNA synthesis. A specific inhibition of this enzyme induces bacterial cell death. As a second round lead optimization design, new 1,2-naphthalein derivatives have been synthesized and tested against a TS-based biolibrary, including human thymidylate synthase (hTS). Docking studies have been performed to rationalize the experimentally observed affinity profiles of 1,2-naphthalein compounds toward Lactobacillus casei TS and hTS. The best TS inhibitors have been tested against a number of clinical isolates of Gram-positive-resistant bacterial strains. Compound 3,3-bis(3,5-dibromo-4-hydroxyphenyl)-1H,3H-naphtho[1,2-c]furan-1-one (5) showed significant antibacterial activity, no in vitro toxicity, and dose-response effects against Staphylococcus epidermidis (MIC=0.5-2.5 microg/mL) clinical isolate strains, which are resistant to at least 17 of the best known antibacterial agents, including vancomycin. So far this compound can be regarded as a leading antibacterial agent.
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Affiliation(s)
- M Paola Costi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia (UNIMORE), Via Campi 183, 41100 Modena, Italy.
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45
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Sotelo-Mundo RR, Changchien L, Maley F, Montfort WR. Crystal structures of thymidylate synthase mutant R166Q: structural basis for the nearly complete loss of catalytic activity. J Biochem Mol Toxicol 2006; 20:88-92. [PMID: 16615077 DOI: 10.1002/jbt.20122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Thymidylate synthase (TS) catalyzes the folate-dependent methylation of deoxyuridine monophosphate (dUMP) to form thymidine monophosphate (dTMP). We have investigated the role of invariant arginine 166, one of four arginines that contact the dUMP phosphate, using site-directed mutagenesis, X-ray crystallography, and TS from Escherichia coli. The R166Q mutant was crystallized in the presence of dUMP and a structure determined to 2.9 A resolution, but neither the ligand nor the sulfate from the crystallization buffer was found in the active site. A second structure determined with crystals prepared in the presence of dUMP and the antifolate 10-propargyl-5,8-dideazafolate revealed that the inhibitor was bound in an extended, nonproductive conformation, partially occupying the nucleotide-binding site. A sulfate ion, rather than dUMP, was found in the nucleotide phosphate-binding site. Previous studies have shown that the substitution at three of the four arginines of the dUMP phosphate-binding site is permissive; however; for Arg166, all the mutations lead to a near-inactive mutant. The present structures of TS R166Q reveal that the phosphate-binding site is largely intact, but with a substantially reduced affinity for phosphate, despite the presence of the three remaining arginines. The position of Cys146, which initiates catalysis, is shifted in the mutant and resides in a position that interferes with the binding of the dUMP pyrimidine moiety.
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Affiliation(s)
- Rogerio R Sotelo-Mundo
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.
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46
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Berger SH, Berger FG, Lebioda L. Effects of ligand binding and conformational switching on intracellular stability of human thymidylate synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1696:15-22. [PMID: 14726200 DOI: 10.1016/j.bbapap.2003.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thymidylate synthase (TS) is the target in colon cancer therapeutic protocols utilizing such drugs as 5-fluorouracil and raltitrexed. The effectiveness of these treatments is hampered by emerging drug resistance, usually related to increased levels of TS. Human TS (hTS) is unique among thymidylate synthases from all species examined as its loop 181-197 can assume two main conformations related by rotation of 180 degrees. In one conformation, "active", the catalytic Cys-195 is positioned in the active site; in the other conformation, "inactive", it is at the subunit interface. Also, in the active conformation, region 107-128 has one well-defined conformation while in the inactive conformation this region assumes multiple conformations and is disordered in crystals. The native protein exists in apparent equilibrium between the two conformational states, while the enzyme liganded with TS inhibitors assumes the active conformation. The native protein has been reported to bind to several mRNAs, including its own mRNA, but upon ligation, RNA binding activity is lost. Ligation of TS by inhibitors also stabilizes it to turnover. Since currently used TS-directed drugs stabilize the active conformation and slow down the enzyme degradation, it is postulated that inhibitors of hTS stabilizing the inactive conformation of hTS should cause a down-regulation in enzyme levels as well as inactivate the enzyme.
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Affiliation(s)
- Sondra H Berger
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC 29208, USA.
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47
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Abstract
Structure-based drug design of species-specific inhibitors generally exploits structural differences in proteins from different organisms. Here, we demonstrate how achieving specificity can be aided by targeting differences in the dynamics of proteins. Thymidylate synthase (TS) is a good target for anticancer agents and a potential target for antibacterial agents. Most inhibitors are folate-analogs that bind at the folate binding site and are not species specific. In contrast, alpha156 is not a folate-analog and is specific for bacterial TS; it has been shown crystallographically to bind in a nonconserved binding site. Docking calculations and crystal structure-based estimation of the essential dynamics of TSs from five different species show that differences in the dynamics of TSs make the active site more accessible to alpha156 in the prokaryotic than in the eukaryotic TSs and thereby enhance the specificity of alpha156.
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Affiliation(s)
- Stefania Ferrari
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy.
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O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. J Biol Chem 2003; 278:52980-7. [PMID: 14555647 DOI: 10.1074/jbc.m310328200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have determined the crystal structure of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis, revealing a unique linker domain containing an 11-residue alpha-helix that has extensive interactions with the opposite DHFR-TS monomer of the homodimeric enzyme. Analysis of the structure of DHFR-TS from C. hominis and of previously solved structures of DHFR-TS from Plasmodium falciparum and Leishmania major reveals that the linker domain primarily controls the relative orientation of the DHFR and TS domains. Using the tertiary structure of the linker domains, we have been able to place a number of protozoa in two distinct and dissimilar structural families corresponding to two evolutionary families and provide the first structural evidence validating the use of DHFR-TS as a tool of phylogenetic classification. Furthermore, the structure of C. hominis DHFR-TS calls into question surface electrostatic channeling as the universal means of dihydrofolate transport between TS and DHFR in the bifunctional enzyme.
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Affiliation(s)
- Robert H O'Neil
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA
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Lin X, Liu J, Maley F, Chu E. Role of cysteine amino acid residues on the RNA binding activity of human thymidylate synthase. Nucleic Acids Res 2003; 31:4882-7. [PMID: 12907731 PMCID: PMC169953 DOI: 10.1093/nar/gkg678] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Revised: 06/23/2003] [Accepted: 06/23/2003] [Indexed: 11/13/2022] Open
Abstract
The role of cysteine sulfhydryl residues on the RNA binding activity of human thymidylate synthase (TS) was investigated by mutating each cysteine residue on human TS to a corresponding alanine residue. Enzymatic activities of TS:C43A and TS:C210A mutant proteins were nearly identical to wild-type TS, while TS:C180A and TS:C199A mutants expressed >80% of wild-type enzyme activity. In contrast, TS:C195A was completely inactive. Mutant proteins, TS:C195A, TS:C199A and TS:C210A, retained RNA binding activity to nearly the same degree as wild-type human TS. RNA binding activity of TS:C43A was reduced by 30% when compared to wild-type TS, while TS:C180A was completely devoid of RNA binding activity. In vitro translation studies confirmed that mutant proteins TS:C43A, TS:C195A, TS:C199A and TS:C210A, significantly repressed human TS mRNA translation, while TS:C180A was unable to do so. To confirm the in vivo significance of the cysteine sulfhydryl residue, mutant proteins TS:C180A and TS:C195A were each expressed in human colon cancer HCT-C18:TS(-) cells that expressed a functionally inactive TS. A recombinant luciferase reporter gene under the control of a TS-response element was co-transfected into these same cells, and luciferase activity increased in the presence of the TS:C195A mutant TS protein to a level similar to that observed upon expression of wild-type TS protein. In contrast, luciferase activity remained unchanged in cells expressing the TS:C180A mutant protein. Taken together, these findings identify Cys-180 as a critical residue for the in vitro and in vivo translational regulatory effects of human TS.
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Affiliation(s)
- Xiukun Lin
- Department of Medicine and Pharmacology, Yale Cancer Center, Yale University School of Medicine and VA Connecticut Healthcare System, New Haven, CT 06520, USA
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50
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Birdsall DL, Finer-Moore J, Stroud RM. The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity. Protein Eng Des Sel 2003; 16:229-40. [PMID: 12702803 DOI: 10.1093/proeng/gzg020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.
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Affiliation(s)
- David L Birdsall
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143-0448, USA
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