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D’Arca D, Severi L, Ferrari S, Dozza L, Marverti G, Magni F, Chinello C, Pagani L, Tagliazucchi L, Villani M, d’Addese G, Piga I, Conteduca V, Rossi L, Gurioli G, De Giorgi U, Losi L, Costi MP. Serum Mass Spectrometry Proteomics and Protein Set Identification in Response to FOLFOX-4 in Drug-Resistant Ovarian Carcinoma. Cancers (Basel) 2023; 15:cancers15020412. [PMID: 36672361 PMCID: PMC9856519 DOI: 10.3390/cancers15020412] [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: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Ovarian cancer is a highly lethal gynecological malignancy. Drug resistance rapidly occurs, and different therapeutic approaches are needed. So far, no biomarkers have been discovered to predict early response to therapies in the case of multi-treated ovarian cancer patients. The aim of our investigation was to identify a protein panel and the molecular pathways involved in chemotherapy response through a combination of studying proteomics and network enrichment analysis by considering a subset of samples from a clinical setting. Differential mass spectrometry studies were performed on 14 serum samples from patients with heavily pretreated platinum-resistant ovarian cancer who received the FOLFOX-4 regimen as a salvage therapy. The serum was analyzed at baseline time (T0) before FOLFOX-4 treatment, and before the second cycle of treatment (T1), with the aim of understanding if it was possible, after a first treatment cycle, to detect significant proteome changes that could be associated with patients responses to therapy. A total of 291 shared expressed proteins was identified and 12 proteins were finally selected between patients who attained partial response or no-response to chemotherapy when both response to therapy and time dependence (T0, T1) were considered in the statistical analysis. The protein panel included APOL1, GSN, GFI1, LCATL, MNA, LYVE1, ROR1, SHBG, SOD3, TEC, VPS18, and ZNF573. Using a bioinformatics network enrichment approach and metanalysis study, relationships between serum and cellular proteins were identified. An analysis of protein networks was conducted and identified at least three biological processes with functional and therapeutic significance in ovarian cancer, including lipoproteins metabolic process, structural component modulation in relation to cellular apoptosis and autophagy, and cellular oxidative stress response. Five proteins were almost independent from the network (LYVE1, ROR1, TEC, GFI1, and ZNF573). All proteins were associated with response to drug-resistant ovarian cancer resistant and were mechanistically connected to the pathways associated with cancer arrest. These results can be the basis for extending a biomarker discovery process to a clinical trial, as an early predictive tool of chemo-response to FOLFOX-4 of heavily treated ovarian cancer patients and for supporting the oncologist to continue or to interrupt the therapy.
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Affiliation(s)
- Domenico D’Arca
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Leda Severi
- 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
| | - Luca Dozza
- Seràgnoli Institute of Hematology, Department of Experimental, Diagnostic and Specialty Medicine, Bologna University School of Medicine, S. Orsola Malpighi Hospital, 40138 Bologna, Italy
| | - Gaetano Marverti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20126 Vedano al Lambro, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20126 Vedano al Lambro, Italy
| | - Lisa Pagani
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20126 Vedano al Lambro, Italy
| | - Lorenzo Tagliazucchi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
- Clinical and Experimental Medicine (CEM) Doctorate School, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Marco Villani
- Department of Physics, Informatics and Mathematics, Modena and Reggio Emilia University, Via Campi 213/A, 41125 Modena, Italy
| | - Gianluca d’Addese
- Department of Physics, Informatics and Mathematics, Modena and Reggio Emilia University, Via Campi 213/A, 41125 Modena, Italy
| | - Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20126 Vedano al Lambro, Italy
| | - Vincenza Conteduca
- IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), 47014 Meldola, Italy
| | - Lorena Rossi
- IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), 47014 Meldola, Italy
| | - Giorgia Gurioli
- IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), 47014 Meldola, Italy
| | - Ugo De Giorgi
- IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), 47014 Meldola, Italy
| | - Lorena Losi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
- Correspondence: (L.L.); (M.P.C.)
| | - Maria Paola Costi
- Department Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
- Correspondence: (L.L.); (M.P.C.)
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2
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Zhang Y, Wright MA, Saar KL, Challa P, Morgunov AS, Peter QAE, Devenish S, Dobson CM, Knowles TPJ. Machine learning-aided protein identification from multidimensional signatures. LAB ON A CHIP 2021; 21:2922-2931. [PMID: 34109955 PMCID: PMC8314522 DOI: 10.1039/d0lc01148g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The ability to determine the identity of specific proteins is a critical challenge in many areas of cellular and molecular biology, and in medical diagnostics. Here, we present a macine learning aided microfluidic protein characterisation strategy that within a few minutes generates a three-dimensional fingerprint of a protein sample indicative of its amino acid composition and size and, thereby, creates a unique signature for the protein. By acquiring such multidimensional fingerprints for a set of ten proteins and using machine learning approaches to classify the fingerprints, we demonstrate that this strategy allows proteins to be classified at a high accuracy, even though classification using a single dimension is not possible. Moreover, we show that the acquired fingerprints correlate with the amino acid content of the samples, which makes it is possible to identify proteins directly from their sequence without requiring any prior knowledge about the fingerprints. These findings suggest that such a multidimensional profiling strategy can lead to the development of a novel method for protein identification in a microfluidic format.
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Affiliation(s)
- Yuewen Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Maya A Wright
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
| | - Pavankumar Challa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Alexey S Morgunov
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Fluidic Analytics Ltd., Cambridge, UK
| | - Quentin A E Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | | - Christopher M Dobson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK
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3
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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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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: 5] [Impact Index Per Article: 1.7] [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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5
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A Peptidic Thymidylate-Synthase Inhibitor Loaded on Pegylated Liposomes Enhances the Antitumour Effect of Chemotherapy Drugs in Human Ovarian Cancer Cells. Int J Mol Sci 2020; 21:ijms21124452. [PMID: 32585842 PMCID: PMC7352236 DOI: 10.3390/ijms21124452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/20/2020] [Accepted: 06/20/2020] [Indexed: 12/24/2022] Open
Abstract
There is currently no effective long-term treatment for ovarian cancer (OC) resistant to poly-chemotherapy regimens based on platinum drugs. Preclinical and clinical studies have demonstrated a strong association between development of Pt-drug resistance and increased thymidylate synthase (hTS) expression, and the consequent cross-resistance to the hTS inhibitors 5-fluorouracil (5-FU) and raltitrexed (RTX). In the present work, we propose a new tool to combat drug resistance. We propose to treat OC cell lines, both Pt-sensitive and -resistant, with dual combinations of one of the four chemotherapeutic agents that are widely used in the clinic, and the new peptide, hTS inhibitor, [D-Gln4]LR. This binds hTS allosterically and, unlike classical inhibitors that bind at the catalytic pocket, causes cell growth inhibition without inducing hTS overexpression. The dual drug combinations showed schedule-dependent synergistic antiproliferative and apoptotic effects. We observed that the simultaneous treatment or 24h pre-treatment of OC cells with the peptide followed by either agent produced synergistic effects even in resistant cells. Similar synergistic or antagonistic effects were obtained by delivering the peptide into OC cells either by means of a commercial delivery system (SAINT-PhD) or by pH sensitive PEGylated liposomes. Relative to non-PEGylated liposomes, the latter had been previously characterized and found to allow macrophage escape, thus increasing their chance to reach the tumour tissue. The transition from the SAINT-PhD delivery system to the engineered liposomes represents an advancement towards a more drug-like delivery system and a further step towards the use of peptides for in vivo studies. Overall, the results suggest that the association of standard drugs, such as cDDP and/or 5-FU and/or RTX, with the novel peptidic TS inhibitor encapsulated into PEGylated pH-sensitive liposomes can represent a promising strategy for fighting resistance to cDDP and anti-hTS drugs.
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6
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Pacifico S, Santucci M, Luciani R, Saxena P, Linciano P, Ponterini G, Lauriola A, D'Arca D, Marverti G, Guerrini R, Costi MP. Cyclic Peptides Acting as Allosteric Inhibitors of Human Thymidylate Synthase and Cancer Cell Growth. Molecules 2019; 24:molecules24193493. [PMID: 31561530 PMCID: PMC6804113 DOI: 10.3390/molecules24193493] [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: 07/20/2019] [Revised: 09/14/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022] Open
Abstract
Thymidylate synthase (TS) is a prominent drug target for different cancer types. However, the prolonged use of its classical inhibitors, substrate analogs that bind at the active site, leads to TS overexpression and drug resistance in the clinic. In the effort to identify anti-TS drugs with new modes of action and able to overcome platinum drug resistance in ovarian cancer, octapeptides with a new allosteric inhibition mechanism were identified as cancer cell growth inhibitors that do not cause TS overexpression. To improve the biological properties, 10 cyclic peptides (cPs) were designed from the lead peptides and synthesized. The cPs were screened for the ability to inhibit recombinant human thymidylate synthase (hTS), and peptide 7 was found to act as an allosteric inhibitor more potent than its parent open-chain peptide [Pro3]LR. In cytotoxicity studies on three human ovarian cancer cell lines, IGROV-1, A2780, and A2780/CP, peptide 5 and two other cPs, including 7, showed IC50 values comparable with those of the reference drug 5-fluorouracil, of the open-chain peptide [d-Gln4]LR, and of another seven prolyl derivatives of the lead peptide LR. These promising results indicate cP 7 as a possible lead compound to be chemically modified with the aim of improving both allosteric TS inhibitory activity and anticancer effectiveness.
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Affiliation(s)
- Salvatore Pacifico
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100 Ferrara, Italy.
| | - Matteo Santucci
- 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.
| | - Puneet Saxena
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 103, 41125 Modena, Italy.
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 103, 41125 Modena, Italy.
| | - Glauco Ponterini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 103, 41125 Modena, Italy.
| | - Angela Lauriola
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 103, 41125 Modena, Italy.
| | - Domenico D'Arca
- Department of Biomedical Sciences, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via Campi 287, 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.
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100 Ferrara, Italy.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi, 103, 41125 Modena, Italy.
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7
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Sacchetti F, Marverti G, D'Arca D, Severi L, Maretti E, Iannuccelli V, Pacifico S, Ponterini G, Costi MP, Leo E. pH-Promoted Release of a Novel Anti-Tumour Peptide by "Stealth" Liposomes: Effect of Nanocarriers on the Drug Activity in Cis-Platinum Resistant Cancer Cells. Pharm Res 2018; 35:206. [PMID: 30209680 DOI: 10.1007/s11095-018-2489-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022]
Abstract
PURPOSE To evaluate the potential effects of PEGylated pH-sensitive liposomes on the intracellular activity of a new peptide recently characterized as a novel inhibitor of the human thymidylate synthase (hTS) over-expressed in many drug-resistant human cancer cell lines. METHODS Peptide-loaded pH-sensitive PEGylated (PpHL) and non-PEGylated liposomes (nPpHL) were carefully characterized and delivered to cis-platinum resistant ovarian cancer C13* cells; the influence of the PpHL on the drug intracellular activity was investigated by the Western Blot analysis of proteins involved in the pathway affected by hTS inhibition. RESULTS Although PpHL and nPpHL showed different sizes, surface hydrophilicities and serum stabilities, both carriers entrapped the drug efficiently and stably demonstrating a pH dependent release; moreover, the different behavior against J774 macrophage cells confirmed the ability of PEGylation in protecting liposomes from the reticuloendothelial system. Comparable effects were instead observed against C13* cells and biochemical data by immunoblot analysis indicated that PEGylated pH-sensitive liposomes do not modify the proteomic profile of the cells, fully preserving the activity of the biomolecule. CONCLUSION PpHL can be considered as efficient delivery systems for the new promising anti-cancer peptide.
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Affiliation(s)
- Francesca Sacchetti
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Gaetano Marverti
- Department Biomedical, Metabolic and Neurosciences, University of Modena and Reggio Emilia, Via Campi, 287, Modena, Italy
| | - Domenico D'Arca
- Department Biomedical, Metabolic and Neurosciences, University of Modena and Reggio Emilia, Via Campi, 287, Modena, Italy
| | - Leda Severi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Eleonora Maretti
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Valentina Iannuccelli
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Salvatore Pacifico
- Department of Pharmaceutical Sciences, University of Ferrara, via Fossato di Mortara 17-19, 44100, Ferrara, Italy
| | - Glauco Ponterini
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Eliana Leo
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy.
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8
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Saxena P, Severi L, Santucci M, Taddia L, Ferrari S, Luciani R, Marverti G, Marraccini C, Tondi D, Mor M, Scalvini L, Vitiello S, Losi L, Fonda S, Pacifico S, Guerrini R, D’Arca D, Ponterini G, Costi MP. Conformational Propensity and Biological Studies of Proline Mutated LR Peptides Inhibiting Human Thymidylate Synthase and Ovarian Cancer Cell Growth. J Med Chem 2018; 61:7374-7380. [DOI: 10.1021/acs.jmedchem.7b01699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Puneet Saxena
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Leda Severi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Laura Taddia
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, 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
| | - 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 103, 41125 Modena, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Simone Vitiello
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
- Pathological Anatomy, Via del Pozzo 71, 41124 Modena, Italy
| | - Sergio Fonda
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Salvatore Pacifico
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 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 103, 41125 Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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9
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Severi L, Losi L, Fonda S, Taddia L, Gozzi G, Marverti G, Magni F, Chinello C, Stella M, Sheouli J, Braicu EI, Genovese F, Lauriola A, Marraccini C, Gualandi A, D'Arca D, Ferrari S, Costi MP. Proteomic and Bioinformatic Studies for the Characterization of Response to Pemetrexed in Platinum Drug Resistant Ovarian Cancer. Front Pharmacol 2018; 9:454. [PMID: 29867465 PMCID: PMC5952181 DOI: 10.3389/fphar.2018.00454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
Proteomics and bioinformatics are a useful combined technology for the characterization of protein expression level and modulation associated with the response to a drug and with its mechanism of action. The folate pathway represents an important target in the anticancer drugs therapy. In the present study, a discovery proteomics approach was applied to tissue samples collected from ovarian cancer patients who relapsed after the first-line carboplatin-based chemotherapy and were treated with pemetrexed (PMX), a known folate pathway targeting drug. The aim of the work is to identify the proteomic profile that can be associated to the response to the PMX treatment in pre-treatement tissue. Statistical metrics of the experimental Mass Spectrometry (MS) data were combined with a knowledge-based approach that included bioinformatics and a literature review through ProteinQuest™ tool, to design a protein set of reference (PSR). The PSR provides feedback for the consistency of MS proteomic data because it includes known validated proteins. A panel of 24 proteins with levels that were significantly different in pre-treatment samples of patients who responded to the therapy vs. the non-responder ones, was identified. The differences of the identified proteins were explained for the patients with different outcomes and the known PMX targets were further validated. The protein panel herein identified is ready for further validation in retrospective clinical trials using a targeted proteomic approach. This study may have a general relevant impact on biomarker application for cancer patients therapy selection.
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Affiliation(s)
- Leda Severi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Lorena Losi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sergio Fonda
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Taddia
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Gaia Gozzi
- Department of Biomedical Science, Metabolic Science and Neuroscience, University of Modena and Reggio Emilia, Modena, Italy
| | - Gaetano Marverti
- Department of Biomedical Science, Metabolic Science and Neuroscience, University of Modena and Reggio Emilia, Modena, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Martina Stella
- Department of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Jalid Sheouli
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elena I Braicu
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Filippo Genovese
- Centro Interdipartimentale Grandi Strumenti, University of Modena and Reggio Emilia, Modena, Italy
| | - Angela Lauriola
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Chiara Marraccini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Gualandi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Domenico D'Arca
- Department of Biomedical Science, Metabolic Science and Neuroscience, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maria P Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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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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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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12
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Inside the biochemical pathways of thymidylate synthase perturbed by anticancer drugs: Novel strategies to overcome cancer chemoresistance. Drug Resist Updat 2015; 23:20-54. [PMID: 26690339 DOI: 10.1016/j.drup.2015.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 10/08/2015] [Accepted: 10/23/2015] [Indexed: 12/11/2022]
Abstract
Our current understanding of the mechanisms of action of antitumor agents and the precise mechanisms underlying drug resistance is that these two processes are directly linked. Moreover, it is often possible to delineate chemoresistance mechanisms based on the specific mechanism of action of a given anticancer drug. A more holistic approach to the chemoresistance problem suggests that entire metabolic pathways, rather than single enzyme targets may better explain and educate us about the complexity of the cellular responses upon cytotoxic drug administration. Drugs, which target thymidylate synthase and folate-dependent enzymes, represent an important therapeutic arm in the treatment of various human malignancies. However, prolonged patient treatment often provokes drug resistance phenomena that render the chemotherapeutic treatment highly ineffective. Hence, strategies to overcome drug resistance are primarily designed to achieve either enhanced intracellular drug accumulation, to avoid the upregulation of folate-dependent enzymes, and to circumvent the impairment of DNA repair enzymes which are also responsible for cross-resistance to various anticancer drugs. The current clinical practice based on drug combination therapeutic regimens represents the most effective approach to counteract drug resistance. In the current paper, we review the molecular aspects of the activity of TS-targeting drugs and describe how such mechanisms are related to the emergence of clinical drug resistance. We also discuss the current possibilities to overcome drug resistance by using a molecular mechanistic approach based on medicinal chemistry methods focusing on rational structural modifications of novel antitumor agents. This paper also focuses on the importance of the modulation of metabolic pathways upon drug administration, their analysis and the assessment of their putative roles in the networks involved using a meta-analysis approach. The present review describes the main pathways that are modulated by TS-targeting anticancer drugs starting from the description of the normal functioning of the folate metabolic pathway, through the protein modulation occurring upon drug delivery to cultured tumor cells as well as cancer patients, finally describing how the pathways are modulated by drug resistance development. The data collected are then analyzed using network/netwire connecting methods in order to provide a wider view of the pathways involved and of the importance of such information in identifying additional proteins that could serve as novel druggable targets for efficacious cancer therapy.
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13
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Thongboonkerd V, LaBaer J, Domont GB. Recent Advances of Proteomics Applied to Human Diseases. J Proteome Res 2014; 13:4493-6. [DOI: 10.1021/pr501038g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit,
Office for Research and Development, Faculty of Medicine Siriraj Hospital,
and Center for Research in Complex Systems Science, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Joshua LaBaer
- Virginia G. Piper Center
for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287-6401, United States
| | - Gilberto B. Domont
- Proteomics Unit, Institute
of Chemistry, Federal University of Rio de Janeiro (UFRJ), Avenida
Athos da Silveira Ramos, Rio de Janeiro, 21941-909 RJ, Brazil
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