1
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Bonin JP, Sapienza PJ, Lee AL. Dynamic allostery in substrate binding by human thymidylate synthase. eLife 2022; 11:79915. [PMID: 36200982 PMCID: PMC9536839 DOI: 10.7554/elife.79915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by 2H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
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2
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Costantino L, Ferrari S, Santucci M, Salo-Ahen OMH, Carosati E, Franchini S, Lauriola A, Pozzi C, Trande M, Gozzi G, Saxena P, Cannazza G, Losi L, Cardinale D, Venturelli A, Quotadamo A, Linciano P, Tagliazucchi L, Moschella MG, Guerrini R, Pacifico S, Luciani R, Genovese F, Henrich S, Alboni S, Santarem N, da Silva Cordeiro A, Giovannetti E, Peters GJ, Pinton P, Rimessi A, Cruciani G, Stroud RM, Wade RC, Mangani S, Marverti G, D'Arca D, Ponterini G, Costi MP. Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth. eLife 2022; 11:73862. [PMID: 36475542 PMCID: PMC9831607 DOI: 10.7554/elife.73862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression of this protein and development of drug resistance. We thus pursued an alternative strategy that led us to the discovery of TS-dimer destabilizers. These compounds bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. A structural, spectroscopic, and kinetic investigation has provided evidence and quantitative information on the effects of the interaction of these small molecules with hTS. Focusing on the best among them, E7, we have shown that it inhibits hTS in cancer cells and accelerates its proteasomal degradation, thus causing a decrease in the enzyme intracellular level. E7 also showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.
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Affiliation(s)
- Luca Costantino
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Outi MH Salo-Ahen
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Emanuele Carosati
- Department of Chemistry, Biology and Biotechnology, University of PerugiaPerugiaItaly
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Angela Lauriola
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of SienaSienaItaly
| | - Matteo Trande
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Gaia Gozzi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Puneet Saxena
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Giuseppe Cannazza
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Daniela Cardinale
- Respiratory, Critical Care & Anesthesia UCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Alberto Venturelli
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Antonio Quotadamo
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | | | - Maria Gaetana Moschella
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, ItalyModenaItaly
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Science, University of FerraraFerraraItaly
| | - Salvatore Pacifico
- Department of Chemical and Pharmaceutical Science, University of FerraraFerraraItaly
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Filippo Genovese
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Stefan Henrich
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Silvia Alboni
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | | | - Anabela da Silva Cordeiro
- IBMC I3SPortoPortugal,Department of Biological Sciences, Faculty of Pharmacy, University of PortoPortoPortugal
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081HV, Vrije Universiteit AmsterdamAmsterdamNetherlands,CancerPharmacology Lab, Fondazione Pisana per la ScienzaPisaItaly
| | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081HV, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Paolo Pinton
- Dept. of Medical Sciences and Laboratory for Technologies of Advanced Therapies (LTTA), University of FerraraFerraraItaly
| | - Alessandro Rimessi
- Dept. of Medical Sciences and Laboratory for Technologies of Advanced Therapies (LTTA), University of FerraraFerraraItaly
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of PerugiaPerugiaItaly
| | - Robert M Stroud
- Biochemistry and Biophysics Department, University of California San FranciscoSan FranciscoUnited States
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg UniversityHeidelbergGermany,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg UniversityHeidelbergGermany
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of SienaSienaItaly
| | - Gaetano Marverti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Domenico D'Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Glauco Ponterini
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio EmiliaModenaItaly
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3
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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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4
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Detection of Genomic Uracil Patterns. Int J Mol Sci 2021; 22:ijms22083902. [PMID: 33918885 PMCID: PMC8070346 DOI: 10.3390/ijms22083902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 01/06/2023] Open
Abstract
The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.
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5
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Detection of a G-Quadruplex as a Regulatory Element in Thymidylate synthase for Gene Silencing Using Polypurine Reverse Hoogsteen Hairpins. Int J Mol Sci 2020; 21:ijms21145028. [PMID: 32708710 PMCID: PMC7404261 DOI: 10.3390/ijms21145028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023] Open
Abstract
Thymidylate synthase (TYMS) enzyme is an anti-cancer target given its role in DNA biosynthesis. TYMS inhibitors (e.g., 5-Fluorouracil) can lead to drug resistance through an autoregulatory mechanism of TYMS that causes its overexpression. Since G-quadruplexes (G4) can modulate gene expression, we searched for putative G4 forming sequences (G4FS) in the TYMS gene that could be targeted using polypurine reverse Hoogsteen hairpins (PPRH). G4 structures in the TYMS gene were detected using the quadruplex forming G-rich sequences mapper and confirmed through spectroscopic approaches such as circular dichroism and NMR using synthetic oligonucleotides. Interactions between G4FS and TYMS protein or G4FS and a PPRH targeting this sequence (HpTYMS-G4-T) were studied by EMSA and thioflavin T staining. We identified a G4FS in the 5’UTR of the TYMS gene in both DNA and RNA capable of interacting with TYMS protein. The PPRH binds to its corresponding target dsDNA, promoting G4 formation. In cancer cells, HpTYMG-G4-T decreased TYMS mRNA and protein levels, leading to cell death, and showed a synergic effect when combined with 5-fluorouracil. These results reveal the presence of a G4 motif in the TYMS gene, probably involved in the autoregulation of TYMS expression, and the therapeutic potential of a PPRH targeted to the G4FS.
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6
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Wang X, Zhang L, Guan C, Dong Y, Liu H, Ma X, Xia H. The polymorphism of rs11614913 T/T in pri- miR-196a-2 alters the miRNA expression and associates with recurrent spontaneous abortion in a Han-Chinese population. Am J Transl Res 2020; 12:1928-1941. [PMID: 32509188 PMCID: PMC7269987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 01/17/2020] [Indexed: 06/11/2023]
Abstract
Rs11614913 in pri-miR-196a-2 is involved in the occurrence of many diseases, especially in cancers. However, it remains unknown whether miR-196a-2 is associated with human recurrent spontaneous abortion (RSA) in Chinese Han population. Our study found that rs11614913 T/T in pri-miR-196a-2 was associated with the increase risk of human unexplained RSA (URSA) in recessive mode in Chinese Han population. The T allele of rs11614913 increased the production of mature miR-196a-3p. Rs11614913 T/T inhibited HTR-8/SVneo cells proliferation and migration and promoted cells apoptosis. Further investigation discovered that dihydrofolate reductase (DHFR) was the target of miR-196a-3p and inversely regulated by miR-196a-3p. Dual-luciferase assay indicated that T allele in miR-196a-2 rs11614913 could more effectively suppress DHFR expression than C allele. In addition, C to T substitution in miR-196a-2 rs11614913 attenuated the sensibility of cells to mifepristone. Collectively, our data suggest that miR-196a-2 rs11614913 T/T in pri-miR-196a-2 may be conductive to the genetic predisposition to RSA by disrupting the production of mature miR-196a-3p and reinforcing the expression of DHFR.
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Affiliation(s)
- Xueqin Wang
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Department of Reproductive Medicine, Qingdao Municipal Hospital, Qingdao UniversityQingdao, Shandong, China
- Graduate School, Peking Union Medical CollegeBeijing, China
| | - Lu Zhang
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Graduate School, Peking Union Medical CollegeBeijing, China
| | - Chunyi Guan
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Graduate School, Peking Union Medical CollegeBeijing, China
| | - Yichao Dong
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Graduate School, Peking Union Medical CollegeBeijing, China
| | - Haining Liu
- Department of Reproductive Medicine, Qingdao Municipal Hospital, Qingdao UniversityQingdao, Shandong, China
| | - Xu Ma
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Graduate School, Peking Union Medical CollegeBeijing, China
| | - Hongfei Xia
- Reproductive and Genetic Center of National Research Institute for Family PlanningBeijing, China
- Graduate School, Peking Union Medical CollegeBeijing, China
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7
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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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8
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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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9
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The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity. Int J Mol Sci 2019; 20:ijms20061297. [PMID: 30875837 PMCID: PMC6471074 DOI: 10.3390/ijms20061297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/05/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled target proteins and RNA broaden in-cell NMR spectra yielding apparent megadalton molecular weights in-cell. The in-cell spectra can be resolved by using cross relaxation-induced polarization transfer (CRINEPT), heteronuclear multiple quantum coherence (HMQC), transverse relaxation-optimized, NMR spectroscopy (TROSY). The effect is reproduced in vitro by using reconstituted total cellular RNA and purified ribosome preparations. Furthermore, ribosomal binding antibiotics alter protein quinary structure through protein-ribosome and protein-mRNA-ribosome interactions. The quinary interactions of Adenylate kinase, Thymidylate synthase and Dihydrofolate reductase alter kinetic properties of the enzymes. The results demonstrate that ribosomes may specifically contribute to the regulation of biological activity.
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10
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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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11
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P53 represses pyrimidine catabolic gene dihydropyrimidine dehydrogenase (DPYD) expression in response to thymidylate synthase (TS) targeting. Sci Rep 2017; 7:9711. [PMID: 28851987 PMCID: PMC5575263 DOI: 10.1038/s41598-017-09859-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/12/2017] [Indexed: 12/29/2022] Open
Abstract
Nucleotide metabolism in cancer cells can influence malignant behavior and intrinsic resistance to therapy. Here we describe p53-dependent control of the rate-limiting enzyme in the pyrimidine catabolic pathway, dihydropyrimidine dehydrogenase (DPYD) and its effect on pharmacokinetics of and response to 5-fluorouracil (5-FU). Using in silico/chromatin-immunoprecipitation (ChIP) analysis we identify a conserved p53 DNA-binding site (p53BS) downstream of the DPYD gene with increased p53 occupancy following 5-FU treatment of cells. Consequently, decrease in Histone H3K9AC and increase in H3K27me3 marks at the DPYD promoter are observed concomitantly with reduced expression of DPYD mRNA and protein in a p53-dependent manner. Mechanistic studies reveal inhibition of DPYD expression by p53 is augmented following thymidylate synthase (TS) inhibition and DPYD repression by p53 is dependent on DNA-dependent protein kinase (DNA-PK) and Ataxia telangiectasia mutated (ATM) signaling. In-vivo, liver specific Tp53 loss increases the conversion of 5-FU to 5-FUH2 in plasma and elicits a diminished 5-FU therapeutic response in a syngeneic colorectal tumor model consistent with increased DPYD-activity. Our data suggest that p53 plays an important role in controlling pyrimidine catabolism through repression of DPYD expression, following metabolic stress imposed by nucleotide imbalance. These findings have implications for the toxicity and efficacy of the cancer therapeutic 5-FU.
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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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13
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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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14
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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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15
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Gibson MW, Dewar S, Ong HB, Sienkiewicz N, Fairlamb AH. Trypanosoma brucei DHFR-TS Revisited: Characterisation of a Bifunctional and Highly Unstable Recombinant Dihydrofolate Reductase-Thymidylate Synthase. PLoS Negl Trop Dis 2016; 10:e0004714. [PMID: 27175479 PMCID: PMC4866688 DOI: 10.1371/journal.pntd.0004714] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/25/2016] [Indexed: 11/19/2022] Open
Abstract
Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) is a chemically and genetically validated target in African trypanosomes, causative agents of sleeping sickness in humans and nagana in cattle. Here we report the kinetic properties and sensitivity of recombinant enzyme to a range of lipophilic and classical antifolate drugs. The purified recombinant enzyme, expressed as a fusion protein with elongation factor Ts (Tsf) in ThyA- Escherichia coli, retains DHFR activity, but lacks any TS activity. TS activity was found to be extremely unstable (half-life of 28 s) following desalting of clarified bacterial lysates to remove small molecules. Stability could be improved 700-fold by inclusion of dUMP, but not by other pyrimidine or purine (deoxy)-nucleosides or nucleotides. Inclusion of dUMP during purification proved insufficient to prevent inactivation during the purification procedure. Methotrexate and trimetrexate were the most potent inhibitors of DHFR (Ki 0.1 and 0.6 nM, respectively) and FdUMP and nolatrexed of TS (Ki 14 and 39 nM, respectively). All inhibitors showed a marked drop-off in potency of 100- to 1,000-fold against trypanosomes grown in low folate medium lacking thymidine. The most potent inhibitors possessed a terminal glutamate moiety suggesting that transport or subsequent retention by polyglutamylation was important for biological activity. Supplementation of culture medium with folate markedly antagonised the potency of these folate-like inhibitors, as did thymidine in the case of the TS inhibitors raltitrexed and pemetrexed.
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Affiliation(s)
- Marc W. Gibson
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Simon Dewar
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Han B. Ong
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Natasha Sienkiewicz
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alan H. Fairlamb
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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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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17
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Sapienza PJ, Falk BT, Lee AL. Bacterial Thymidylate Synthase Binds Two Molecules of Substrate and Cofactor without Cooperativity. J Am Chem Soc 2015; 137:14260-3. [PMID: 26517288 DOI: 10.1021/jacs.5b10128] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Thymidylate synthase (TSase) is a clinically important enzyme because it catalyzes synthesis of the sole de novo source of deoxy-thymidylate. Without this enzyme, cells die a "thymineless death" since they are starved of a crucial DNA synthesis precursor. As a drug target, TSase is well studied in terms of its structure and reaction mechanism. An interesting mechanistic feature of dimeric TSase is that it is "half-the-sites reactive", which is a form of negative cooperativity. Yet, the basis for this is not well-understood. Some experiments point to cooperativity at the binding steps of the reaction cycle as being responsible for the phenomenon, but the literature contains conflicting reports. Here we use ITC and NMR to resolve these inconsistencies. This first detailed thermodynamic dissection of multisite binding of dUMP to E. coli TSase shows the nucleotide binds to the free and singly bound forms of the enzyme with nearly equal affinity over a broad range of temperatures and in multiple buffers. While small but significant differences in ΔC°P for the two binding events show that the active sites are not formally equivalent, there is little-to-no allostery at the level of ΔG°bind. In addition NMR titration data reveal that there is minor intersubunit cooperativity in formation of a ternary complex with the mechanism based inhibitor, 5F-dUMP, and cofactor. Taken together, the data show that functional communication between subunits is minimal for both binding steps of the reaction coordinate.
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Affiliation(s)
- Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Bradley T Falk
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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