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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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Marverti G, Marraccini C, Martello A, D'Arca D, Pacifico S, Guerrini R, Spyrakis F, Gozzi G, Lauriola A, Santucci M, Cannazza G, Tagliazucchi L, Cazzato AS, Losi L, Ferrari S, Ponterini G, Costi MP. Folic Acid-Peptide Conjugates Combine Selective Cancer Cell Internalization with Thymidylate Synthase Dimer Interface Targeting. J Med Chem 2021; 64:3204-3221. [PMID: 33710891 PMCID: PMC8041318 DOI: 10.1021/acs.jmedchem.0c02107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Drug-target interaction, cellular internalization, and target engagement should be addressed to design a lead with high chances of success in further optimization stages. Accordingly, we have designed conjugates of folic acid with anticancer peptides able to bind human thymidylate synthase (hTS) and enter cancer cells through folate receptor α (FRα) highly expressed by several cancer cells. Mechanistic analyses and molecular modeling simulations have shown that these conjugates bind the hTS monomer-monomer interface with affinities over 20 times larger than the enzyme active site. When tested on several cancer cell models, these conjugates exhibited FRα selectivity at nanomolar concentrations. A similar selectivity was observed when the conjugates were delivered in synergistic or additive combinations with anticancer agents. At variance with 5-fluorouracil and other anticancer drugs that target the hTS catalytic pocket, these conjugates do not induce overexpression of this protein and can thus help combating drug resistance associated with high hTS levels.
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Affiliation(s)
- Gaetano Marverti
- Department Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Chiara Marraccini
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Andrea Martello
- Department Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Domenico D'Arca
- Department Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Salvatore Pacifico
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Fossato di Mortara, 44121 Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Fossato di Mortara, 44121 Ferrara, Italy
| | - Francesca Spyrakis
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Gaia Gozzi
- Department Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Angela Lauriola
- Department Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Matteo Santucci
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giuseppe Cannazza
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Lorenzo Tagliazucchi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | | | - Lorena Losi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefania Ferrari
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Glauco Ponterini
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Maria P Costi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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Affiliation(s)
- Vivian Tyng
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Michael E. Kellman
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
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Bacterial versus human thymidylate synthase: Kinetics and functionality. PLoS One 2018; 13:e0196506. [PMID: 29715278 PMCID: PMC5929524 DOI: 10.1371/journal.pone.0196506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Thymidylate Synthase (TSase) is a highly conserved enzyme that catalyzes the production of the DNA building block thymidylate. Structurally, functionally and mechanistically, bacterial and mammalian TSases share remarkable similarities. Because of this closeness, bacterial enzymes have long been used as model systems for human TSase. Furthermore, while TSase inhibitors have long served as chemotherapeutic drugs, no TSase inhibitor serves as an antibiotic. Despite their high resemblance, the mammalian TSases are distinct in a few known aspects, such as having a N-terminal tail and two insertions in the primary sequence and active/inactive conformations. Here, we aim to comprehensively characterize human (hs) TSase and delineate its contrasts and the similarities to the well-studied Escherichia coli (ec) TSase. We found that, in contrast to ecTSase, Mg2+ does not enhance reaction rates for hsTSase. The temperature dependence of intrinsic kinetic isotope effects (KIEs), on the other hand, suggests that Mg2+ has little or no impact on the transition state of hydride transfer in either enzyme, and that the transition state for the hydride transfer in hsTSase is looser than in ecTSase. Additionally, the substrates’ binding order is strictly ordered for ecTSase but slightly less ordered for hsTSase. The observed kinetic and functional differences between bacterial and human enzymes may aid in the development of antibiotic drugs with reduced toxicity.
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Intracellular quantitative detection of human thymidylate synthase engagement with an unconventional inhibitor using tetracysteine-diarsenical-probe technology. Sci Rep 2016; 6:27198. [PMID: 27250901 PMCID: PMC4890114 DOI: 10.1038/srep27198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/25/2022] Open
Abstract
Demonstrating a candidate drug's interaction with its target protein in live cells is of pivotal relevance to the successful outcome of the drug discovery process. Although thymidylate synthase (hTS) is an important anticancer target protein, the efficacy of the few anti-hTS drugs currently used in clinical practice is limited by the development of resistance. Hence, there is an intense search for new, unconventional anti-hTS drugs; there are approximately 1600 ongoing clinical trials involving hTS-targeting drugs, both alone and in combination protocols. We recently discovered new, unconventional peptidic inhibitors of hTS that are active against cancer cells and do not result in the overexpression of hTS, which is a known molecular source of resistance. Here, we propose an adaptation of the recently proposed tetracysteine-arsenic-binding-motif technology to detect and quantitatively characterize the engagement of hTS with one such peptidic inhibitor in cell lysates. This new model can be developed into a test for high-throughput screening studies of intracellular target-protein/small-molecule binding.
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Abstract
Expression of hTS (human thymidylate synthase), a key enzyme in thymidine biosynthesis, is regulated on the translational level through a feedback mechanism that is rarely found in eukaryotes. At low substrate concentrations, the ligand-free enzyme binds to its own mRNA and stabilizes a hairpin structure that sequesters the start codon. When in complex with dUMP (2'-deoxyuridine-5'-monophosphate) and a THF (tetrahydrofolate) cofactor, the enzyme adopts a conformation that is unable to bind and repress expression of mRNA. Here, we have used a combination of X-ray crystallography, RNA mutagenesis and site-specific cross-linking studies to investigate the molecular recognition of TS mRNA by the hTS enzyme. The interacting mRNA region was narrowed to the start codon and immediately flanking sequences. In the hTS enzyme, a helix-loop-helix domain on the protein surface was identified as the putative RNA-binding site.
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Pelà M, Saxena P, Luciani R, Santucci M, Ferrari S, Marverti G, Marraccini C, Martello A, Pirondi S, Genovese F, Salvadori S, D’Arca D, Ponterini G, Costi MP, Guerrini R. Optimization of Peptides That Target Human Thymidylate Synthase to Inhibit Ovarian Cancer Cell Growth. J Med Chem 2014; 57:1355-67. [DOI: 10.1021/jm401574p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michela Pelà
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100 Ferrara, Italy
| | - Puneet Saxena
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Gaetano Marverti
- Department of Biomedical Sciences, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Chiara Marraccini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Andrea Martello
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Silvia Pirondi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Filippo Genovese
- C.I.G.S. (Centro Interdipartimentale Grandi Strumenti), University of Modena and Reggio Emilia, via Campi 213/A, 41125 Modena, Italy
| | - Severo Salvadori
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100 Ferrara, Italy
- LTTA (Laboratorio per le Tecnologie delle Terapie Avanzate), via Fossato di Mortara 17-19, 44100 Ferrara, Italy
| | - Domenico D’Arca
- Department of Biomedical Sciences, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Glauco Ponterini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 183, 41125 Modena, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100 Ferrara, Italy
- LTTA (Laboratorio per le Tecnologie delle Terapie Avanzate), via Fossato di Mortara 17-19, 44100 Ferrara, Italy
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