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Barbieri F, Carlen V, Martina MG, Sannio F, Cancade S, Perini C, Restori M, Crespan E, Maga G, Docquier JD, Cagno V, Radi M. 4-Trifluoromethyl bithiazoles as broad-spectrum antimicrobial agents for virus-related bacterial infections or co-infections. RSC Med Chem 2024; 15:1589-1600. [PMID: 38784463 PMCID: PMC11110737 DOI: 10.1039/d3md00686g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/07/2024] [Indexed: 05/25/2024] Open
Abstract
Respiratory tract infections involving a variety of microorganisms such as viruses, bacteria, and fungi are a prominent cause of morbidity and mortality globally, exacerbating various pre-existing respiratory and non-respiratory conditions. Moreover, the ability of bacteria and viruses to coexist might impact the development and severity of lung infections, promoting bacterial colonization and subsequent disease exacerbation. Secondary bacterial infections following viral infections represent a complex challenge to be overcome from a therapeutic point of view. We report herein our efforts in the development of new bithiazole derivatives showing broad-spectrum antimicrobial activity against both viruses and bacteria. A series of 4-trifluoromethyl bithiazole analogues was synthesized and screened against selected viruses (hRVA16, EVD68, and ZIKV) and a panel of Gram-positive and Gram-negative bacteria. Among them, two promising broad-spectrum antimicrobial compounds (8a and 8j) have been identified: both compounds showed low micromolar activity against all tested viruses, 8a showed synergistic activity against E. coli and A. baumannii in the presence of a subinhibitory concentration of colistin, while 8j showed a broader spectrum of activity against Gram-positive and Gram-negative bacteria. Activity against antibiotic-resistant clinical isolates is also reported. Given the ever-increasing need to adequately address viral and bacterial infections or co-infections, this study paves the way for the development of new agents with broad antimicrobial properties and synergistic activity with common antivirals and antibacterials.
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Affiliation(s)
- Francesca Barbieri
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Vincent Carlen
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Sacha Cancade
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Margherita Restori
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" Via Abbiategrasso 207 I-27100 Pavia Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena Viale Bracci 16 53100 Siena Italy
| | - Valeria Cagno
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne 1011 Lausanne Switzerland
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco (DipALIFAR), Università degli Studi di Parma Viale delle Scienze, 27/A 43124 Parma Italy
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Contadini C, Cirotti C, Carbone A, Norouzi M, Cianciusi A, Crespan E, Perini C, Maga G, Barilà D, Musumeci F, Schenone S. Identification and Biological Characterization of the Pyrazolo[3,4- d]pyrimidine Derivative SI388 Active as Src Inhibitor. Pharmaceuticals (Basel) 2023; 16:958. [PMID: 37513870 PMCID: PMC10384936 DOI: 10.3390/ph16070958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Src is a non-receptor tyrosine kinase (TK) whose involvement in cancer, including glioblastoma (GBM), has been extensively demonstrated. In this context, we started from our in-house library of pyrazolo[3,4-d]pyrimidines that are active as Src and/or Bcr-Abl TK inhibitors and performed a lead optimization study to discover a new generation derivative that is suitable for Src kinase targeting. We synthesized a library of 19 compounds, 2a-s. Among these, compound 2a (SI388) was identified as the most potent Src inhibitor. Based on the cell-free results, we investigated the effect of SI388 in 2D and 3D GBM cellular models. Interestingly, SI388 significantly inhibits Src kinase, and therefore affects cell viability, tumorigenicity and enhances cancer cell sensitivity to ionizing radiation.
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Affiliation(s)
- Claudia Contadini
- Laboratory of Cell Signaling, IRCCS-Fondazione Santa Lucia, 00179 Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Claudia Cirotti
- Laboratory of Cell Signaling, IRCCS-Fondazione Santa Lucia, 00179 Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Mehrdad Norouzi
- Laboratory of Cell Signaling, IRCCS-Fondazione Santa Lucia, 00179 Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Annarita Cianciusi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Daniela Barilà
- Laboratory of Cell Signaling, IRCCS-Fondazione Santa Lucia, 00179 Rome, Italy
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Francesca Musumeci
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
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Lodola C, Secchi M, Sinigiani V, De Palma A, Rossi R, Perico D, Mauri PL, Maga G. Interaction of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicases DDX1 and DDX3X Modulates Their Activities on Double-Stranded RNA. Int J Mol Sci 2023; 24:ijms24065784. [PMID: 36982856 PMCID: PMC10058294 DOI: 10.3390/ijms24065784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The nucleocapsid protein Np of SARS-CoV-2 is involved in the replication, transcription, and packaging of the viral genome, but it also plays a role in the modulation of the host cell innate immunity and inflammation response. Ectopic expression of Np alone was able to induce significant changes in the proteome of human cells. The cellular RNA helicase DDX1 was among the proteins whose levels were increased by Np expression. DDX1 and its related helicase DDX3X were found to physically interact with Np and to increase 2- to 4-fold its affinity for double-stranded RNA in a helicase-independent manner. Conversely, Np inhibited the RNA helicase activity of both proteins. These functional interactions among Np and DDX1 and DDX3X highlight novel possible roles played by these host RNA helicases in the viral life cycle.
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Affiliation(s)
- Camilla Lodola
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Massimiliano Secchi
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Virginia Sinigiani
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
| | - Antonella De Palma
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Rossana Rossi
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Davide Perico
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Pier Luigi Mauri
- Institute of Biomedical Technologies ITB-CNR, Via Fratelli Cervi 93, 20054 Segrate, MI, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100 Pavia, PV, Italy
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Princiotto S, Musso L, Manetti F, Marcellini V, Maga G, Crespan E, Perini C, Zaffaroni N, Beretta GL, Dallavalle S. Synthesis and biological activity evaluation of 3-(hetero) arylideneindolin-2-ones as potential c-Src inhibitors. J Enzyme Inhib Med Chem 2022; 37:2382-2394. [PMID: 36050846 PMCID: PMC9448371 DOI: 10.1080/14756366.2022.2117317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Inhibition of c-Src is considered one of the most studied approaches to cancer treatment, with several heterocyclic compounds approved during the last 15 years as chemotherapeutic agents. Starting from the biological evaluation of an in-house collection of small molecules, indolinone was selected as the most promising scaffold. In this work, several functionalised indolinones were synthesised and their inhibitory potency and cytotoxic activity were assayed. The pharmacological profile of the most active compounds, supported by molecular modelling studies, revealed that the presence of an amino group increased the affinity towards the ATP-binding site of c-Src. At the same time, bulkier derivatizations seemed to improve the interactions within the enzymatic pocket. Overall, these data represent an early stage towards the optimisation of new, easy-to-be functionalised indolinones as potential c-Src inhibitors.
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Affiliation(s)
- Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Siena, Italy
| | - Valentina Marcellini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Siena, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM, CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM, CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM, CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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Di Maria S, Picarazzi F, Mori M, Cianciusi A, Carbone A, Crespan E, Perini C, Sabetta S, Deplano S, Poggialini F, Molinari A, Aronne R, Maccioni E, Maga G, Angelucci A, Schenone S, Musumeci F, Dreassi E. Novel pyrazolo[3,4-d]pyrimidines as dual Src/Bcr-Abl kinase inhibitors: Synthesis and biological evaluation for chronic myeloid leukemia treatment. Bioorg Chem 2022; 128:106071. [PMID: 35932498 DOI: 10.1016/j.bioorg.2022.106071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/18/2022]
Abstract
The Bcr-Abl tyrosine kinase (TK) is the molecular hallmark of chronic myeloid leukemia (CML). Src is another TK kinase whose involvement in CML was widely demonstrated. Small molecules active as dual Src/Bcr-Abl inhibitors emerged as effective targeted therapies for CML and a few compounds are currently in clinical use. In this study, we applied a target-oriented approach to identify a family of pyrazolo[3,4-d]pyrimidines as dual Src/Bcr-Abl inhibitors as anti-leukemia agents. Considering the high homology between Src and Bcr-Abl, in-house Src inhibitors 8a-l and new analogue compounds 9a-n were screened as dual Src/Bcr-Abl inhibitors. The antiproliferative activity on K562 CML cells and the ADME profile were determined for the most promising compounds. Molecular modeling studies elucidated the binding mode of the inhibitors into the Bcr-Abl (wt) catalytic pocket. Compounds 8j and 8k showed nanomolar activities in enzymatic and cellular assays, together with favorable ADME properties, emerging as promising candidates for CML therapy. Finally, derivatives 9j and 9k, emerging as valuable inhibitors of the most aggressive Bcr-Abl mutation, T315I, constitute a good starting point in the search for compounds able to treat drug-resistant forms of CML. Overall, this study allowed us to identify more potent compounds than those previously reported by the group, marking a step forward in searching for new antileukemic agents.
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Affiliation(s)
- Salvatore Di Maria
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Annarita Cianciusi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Samantha Sabetta
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 Coppito, L'Aquila, Italy
| | - Serenella Deplano
- Department of Life and Environmental Sciences, University of Cagliari, Blocco A-Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, CA, Italy
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alessio Molinari
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Blocco A-Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, CA, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM), IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Adriano Angelucci
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Via Vetoio, 67100 Coppito, L'Aquila, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Francesca Musumeci
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy.
| | - Elena Dreassi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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Martina MG, Sannio F, Crespan E, Pavone M, Simoncini A, Barbieri F, Perini C, Pesce E, Maga G, Pedemonte N, Docquier JD, Radi M. Towards Innovative Antibacterial-Correctors for Cystic Fibrosis Targeting the Lung Microbiome with a Multifunctional Effect. ChemMedChem 2022; 17:e202200277. [PMID: 35638249 DOI: 10.1002/cmdc.202200277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/30/2022] [Indexed: 11/10/2022]
Abstract
Cystic Fibrosis (CF) is a genetic disease caused by loss-of-function mutations in the CFTR gene, which codes for a defective ion channel. This causes an electrolyte imbalance and results in a spiral of negative effects on multiple organs, most notably the accumulation of thick mucus in the lungs, chronic respiratory tract infections and inflammation leading to pulmonary exacerbation and premature death. Progressive decline of lung function is mainly linked to persistent or recurring infections, mostly caused by bacteria, which require treatments with antibiotics and represent one of the major life-limiting factors in subjects with CF. Treatment of such a complex disease require multiple drugs with a consequent therapeutic burden and complications caused by drug-drug interactions and rapid emergence of bacterial drug resistance. We report herein our recent efforts in developing innovative multifunctional antibiotics specifically tailored to CF by a direct action on bacterial topoisomerases and a potential indirect effect on the pulmonary mucociliary clearance mediated by ΔF508-CFTR correction. The obtained results may pave the way for the development of a simplified therapeutic approach with a single agent acting as multifunctional antibacterial-corrector.
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Affiliation(s)
- Maria Grazia Martina
- University of Parma: Universita degli Studi di Parma, Department of Food and Drug, ITALY
| | - Filomena Sannio
- University of Siena: Universita degli Studi di Siena, Dipartimento di Biotecnologie Mediche, ITALY
| | - Emmanuele Crespan
- CNR: Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", ITALY
| | - Marialaura Pavone
- University of Parma: Universita degli Studi di Parma, Department of Food and Drug, ITALY
| | - Alice Simoncini
- University of Parma: Universita degli Studi di Parma, Department of Food and Drug, ITALY
| | - Francesca Barbieri
- University of Parma: Universita degli Studi di Parma, Department of Food and Drug, ITALY
| | - Cecilia Perini
- CNR: Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", ITALY
| | - Emanuela Pesce
- Istituto Giannina Gaslini Istituto Pediatrico di Ricovero e Cura a Carattere Scientifico: Istituto Giannina Gaslini, U.O.C. Genetica Medica, ITALY
| | - Giovanni Maga
- CNR: Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", ITALY
| | - Nicoletta Pedemonte
- Istituto Giannina Gaslini Istituto Pediatrico di Ricovero e Cura a Carattere Scientifico: Istituto Giannina Gaslini, U.O.C. Genetica Medica, ITALY
| | - Jean-Denis Docquier
- University of Siena: Universita degli Studi di Siena, Dipartimento di Biotecnologie Mediche, ITALY
| | - Marco Radi
- University of Parma, Department of Food and Drug, Viale delle Scienze, 27/A, 43124, Parma, ITALY
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Grazia Martina M, Vicenti I, Bauer L, Crespan E, Rango E, Boccuto A, Olivieri N, Incerti M, Zwaagstra M, Allodi M, Bertoni S, Dreassi E, Zazzi M, Kuppeveld FJM, Maga G, Radi M. Front Cover: Bithiazole Inhibitors of Phosphatidylinositol 4‐Kinase (PI4KIIIβ) as Broad‐Spectrum Antivirals Blocking the Replication of SARS‐CoV‐2, Zika Virus, and Human Rhinoviruses (ChemMedChem 23/2021). ChemMedChem 2021. [DOI: 10.1002/cmdc.202100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Lisa Bauer
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
- Current address: Department of Viroscience Erasmus Medical Center 3015CA Rotterdam The Netherlands
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare IGM-CNR “Luigi Luca Cavalli-Sforza” Via Abbiategrasso 207 27100 Pavia Italy
| | - Enrico Rango
- Dipartimento Biotecnologie, Chimica e Farmacia Università degli Studi di Siena 53100 Siena Italy
- Current address: Dipartimento di Farmacia Università degli Studi di Genova 16132 Genoa Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Noemi Olivieri
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Matteo Incerti
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Marleen Zwaagstra
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
| | - Marika Allodi
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Simona Bertoni
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia Università degli Studi di Siena 53100 Siena Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies University of Siena 53100 Siena Italy
| | - Frank J. M. Kuppeveld
- Virology Section Infectious Disease and Immunology Division Department of Biomolecular Health Sciences Faculty of Veterinary Medicine Utrecht University Utrecht The Netherlands
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR “Luigi Luca Cavalli-Sforza” Via Abbiategrasso 207 27100 Pavia Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco Università degli Studi di Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
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Grazia Martina M, Vicenti I, Bauer L, Crespan E, Rango E, Boccuto A, Olivieri N, Incerti M, Zwaagstra M, Allodi M, Bertoni S, Dreassi E, Zazzi M, van Kuppeveld FJM, Maga G, Radi M. Bithiazole Inhibitors of Phosphatidylinositol 4-Kinase (PI4KIIIβ) as Broad-Spectrum Antivirals Blocking the Replication of SARS-CoV-2, Zika Virus, and Human Rhinoviruses. ChemMedChem 2021; 16:3548-3552. [PMID: 34382337 PMCID: PMC8427023 DOI: 10.1002/cmdc.202100483] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 12/14/2022]
Abstract
Over half a century since the description of the first antiviral drug, "old" re-emerging viruses and "new" emerging viruses still represent a serious threat to global health. Their high mutation rate and rapid selection of resistance toward common antiviral drugs, together with the increasing number of co-infections, make the war against viruses quite challenging. Herein we report a host-targeted approach, based on the inhibition of the lipid kinase PI4KIIIβ, as a promising strategy for inhibiting the replication of multiple viruses hijacking this protein. We show that bithiazole inhibitors of PI4KIIIβ block the replication of human rhinoviruses (hRV), Zika virus (ZIKV) and SARS-CoV-2 at low micromolar and sub-micromolar concentrations. However, while the anti-hRV/ZIKV activity can be directly linked to PI4KIIIβ inhibition, the role of PI4KIIIβ in SARS-CoV-2 entry/replication is debated.
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Affiliation(s)
- Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Lisa Bauer
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Current address: Department of Viroscience, Erasmus Medical Center, 3015CA, Rotterdam, The Netherlands
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Enrico Rango
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy.,Current address: Dipartimento di Farmacia, Università degli Studi di Genova, 16132, Genoa, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Noemi Olivieri
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Matteo Incerti
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Marleen Zwaagstra
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marika Allodi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Simona Bertoni
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100, Siena, Italy
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze, 27/A, 43124, Parma, Italy
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Vicenti I, Martina MG, Boccuto A, De Angelis M, Giavarini G, Dragoni F, Marchi S, Trombetta CM, Crespan E, Maga G, Eydoux C, Decroly E, Montomoli E, Nencioni L, Zazzi M, Radi M. System-oriented optimization of multi-target 2,6-diaminopurine derivatives: Easily accessible broad-spectrum antivirals active against flaviviruses, influenza virus and SARS-CoV-2. Eur J Med Chem 2021; 224:113683. [PMID: 34273661 PMCID: PMC8255191 DOI: 10.1016/j.ejmech.2021.113683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The worldwide circulation of different viruses coupled with the increased frequency and diversity of new outbreaks, strongly highlight the need for new antiviral drugs to quickly react against potential pandemic pathogens. Broad-spectrum antiviral agents (BSAAs) represent the ideal option for a prompt response against multiple viruses, new and re-emerging. Starting from previously identified anti-flavivirus hits, we report herein the identification of promising BSAAs by submitting the multi-target 2,6-diaminopurine chemotype to a system-oriented optimization based on phenotypic screening on cell cultures infected with different viruses. Among the synthesized compounds, 6i showed low micromolar potency against Dengue, Zika, West Nile and Influenza A viruses (IC50 = 0.5–5.3 μM) with high selectivity index. Interestingly, 6i also inhibited SARS-CoV-2 replication in different cell lines, with higher potency on Calu-3 cells that better mimic the SARS-CoV-2 infection in vivo (IC50 = 0.5 μM, SI = 240). The multi-target effect of 6i on flavivirus replication was also analyzed in whole cell studies (in vitro selection and immunofluorescence) and against isolated host/viral targets.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maria Grazia Martina
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Giavarini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | | | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Cecilia Eydoux
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Etienne Decroly
- AFMB, CNRS, Université Aix-Marseille, UMR 7257, Marseille, France
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy; VisMederi s.r.l, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124, Parma, Italy.
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11
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Mentegari E, Bertoletti F, Kissova M, Zucca E, Galli S, Tagliavini G, Garbelli A, Maffia A, Bione S, Ferrari E, d’Adda di Fagagna F, Francia S, Sabbioneda S, Chen LY, Lingner J, Bergoglio V, Hoffmann JS, Hübscher U, Crespan E, Maga G. A Role for Human DNA Polymerase λ in Alternative Lengthening of Telomeres. Int J Mol Sci 2021; 22:ijms22052365. [PMID: 33673424 PMCID: PMC7956399 DOI: 10.3390/ijms22052365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Telomerase negative cancer cell types use the Alternative Lengthening of Telomeres (ALT) pathway to elongate telomeres ends. Here, we show that silencing human DNA polymerase (Pol λ) in ALT cells represses ALT activity and induces telomeric stress. In addition, replication stress in the absence of Pol λ, strongly affects the survival of ALT cells. In vitro, Pol λ can promote annealing of even a single G-rich telomeric repeat to its complementary strand and use it to prime DNA synthesis. The noncoding telomeric repeat containing RNA TERRA and replication protein A negatively regulate this activity, while the Protection of Telomeres protein 1 (POT1)/TPP1 heterodimer stimulates Pol λ. Pol λ associates with telomeres and colocalizes with TPP1 in cells. In summary, our data suggest a role of Pol λ in the maintenance of telomeres by the ALT mechanism.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Federica Bertoletti
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Miroslava Kissova
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elisa Zucca
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Galli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Giulia Tagliavini
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Bione
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Fabrizio d’Adda di Fagagna
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- IFOM-The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sofia Francia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Liuh-Yow Chen
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Valerie Bergoglio
- UMR1037 INSERM, Cancer Research Center of Toulouse, 2 Avenue Curien, 31037 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
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Riva V, Garbelli A, Casiraghi F, Arena F, Trivisani CI, Gagliardi A, Bini L, Schroeder M, Maffia A, Sabbioneda S, Maga G. Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases. Nucleic Acids Res 2021; 48:11551-11565. [PMID: 33137198 PMCID: PMC7672437 DOI: 10.1093/nar/gkaa948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
Removal of ribonucleotides (rNMPs) incorporated into the genome by the ribonucleotide excision repair (RER) is essential to avoid genetic instability. In eukaryotes, the RNaseH2 is the only known enzyme able to incise 5' of the rNMP, starting the RER process, which is subsequently carried out by replicative DNA polymerases (Pols) δ or ϵ, together with Flap endonuclease 1 (Fen-1) and DNA ligase 1. Here, we show that the DEAD-box RNA helicase DDX3X has RNaseH2-like activity and can support fully reconstituted in vitro RER reactions, not only with Pol δ but also with the repair Pols β and λ. Silencing of DDX3X causes accumulation of rNMPs in the cellular genome. These results support the existence of alternative RER pathways conferring high flexibility to human cells in responding to the threat posed by rNMPs incorporation.
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Affiliation(s)
- Valentina Riva
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Federica Casiraghi
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Francesca Arena
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Claudia Immacolata Trivisani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Assunta Gagliardi
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Luca Bini
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Martina Schroeder
- Kathleen Lonsdale Institute for Human Health Research, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
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Lico C, Santi L, Baschieri S, Noris E, Marusic C, Donini M, Pedrazzini E, Maga G, Franconi R, Di Bonito P, Avesani L. Plant Molecular Farming as a Strategy Against COVID-19 - The Italian Perspective. Front Plant Sci 2020; 11:609910. [PMID: 33381140 PMCID: PMC7768017 DOI: 10.3389/fpls.2020.609910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/13/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed more than 37,000 people in Italy and has caused widespread socioeconomic disruption. Urgent measures are needed to contain and control the virus, particularly diagnostic kits for detection and surveillance, therapeutics to reduce mortality among the severely affected, and vaccines to protect the remaining population. Here we discuss the potential role of plant molecular farming in the rapid and scalable supply of protein antigens as reagents and vaccine candidates, antibodies for virus detection and passive immunotherapy, other therapeutic proteins, and virus-like particles as novel vaccine platforms. We calculate the amount of infrastructure and production capacity needed to deal with predictable subsequent waves of COVID-19 in Italy by pooling expertise in plant molecular farming, epidemiology and the Italian health system. We calculate the investment required in molecular farming infrastructure that would enable us to capitalize on this technology, and provide a roadmap for the development of diagnostic reagents and biopharmaceuticals using molecular farming in plants to complement production methods based on the cultivation of microbes and mammalian cells.
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Affiliation(s)
- Chiara Lico
- Laboratory of Biotechnology, Biotechnologies and Agroindustry Division, Department of Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Luca Santi
- Department of Agriculture and Forest Science, Tuscia University, Viterbo, Italy
| | - Selene Baschieri
- Laboratory of Biotechnology, Biotechnologies and Agroindustry Division, Department of Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council IPSP-CNR, Turin, Italy
| | - Carla Marusic
- Laboratory of Biotechnology, Biotechnologies and Agroindustry Division, Department of Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Marcello Donini
- Laboratory of Biotechnology, Biotechnologies and Agroindustry Division, Department of Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Emanuela Pedrazzini
- Institute for Sustainable Plant Protection, National Research Council IBBA-CNR, Turin, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza,”Pavia, Italy
| | - Rosella Franconi
- Laboratory of Biomedical Technologies, Health Technologies Division, Department of Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Paola Di Bonito
- Department of Infectious Diseases, Viral Hepatitis, Oncoviruses and Retroviruses (EVOR) Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Verona, Italy
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14
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Squeglia F, Romano M, Ruggiero A, Maga G, Berisio R. Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins. Front Chem 2020; 8:602162. [PMID: 33381492 PMCID: PMC7769135 DOI: 10.3389/fchem.2020.602162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
As intracellular parasites, viruses hijack the host cell metabolic machinery for their replication. Among other cellular proteins, the DEAD-box (DDX) RNA helicases have been shown to be hijacked by coronaviruses and to participate in essential DDX-mediated viral replication steps. Human DDX RNA helicases play essential roles in a broad array of biological processes and serve multiple roles at the virus-host interface. The viral proteins responsible for DDX interactions are highly conserved among coronaviruses, suggesting that they might also play conserved functions in the SARS-CoV-2 replication cycle. In this review, we provide an update of the structural and functional data of DDX as possible key factors involved in SARS-CoV-2 hijacking mechanisms. We also attempt to fill the existing gaps in the available structural information through homology modeling. Based on this information, we propose possible paths exploited by the virus to replicate more efficiently by taking advantage of host DDX proteins. As a general rule, sequestration of DDX helicases by SARS-CoV-2 is expected to play a pro-viral role in two ways: by enhancing key steps of the virus life cycle and, at the same time, by suppressing the host innate immune response.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics (IGM-CNR), Pavia, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB-CNR), Naples, Italy
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15
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Nalli M, Armijos Rivera JI, Masci D, Coluccia A, Badia R, Riveira-Muñoz E, Brambilla A, Cinquina E, Turriziani O, Falasca F, Catalano M, Limatola C, Esté JA, Maga G, Silvestri R, Crespan E, La Regina G. New indolylarylsulfone non-nucleoside reverse transcriptase inhibitors show low nanomolar inhibition of single and double HIV-1 mutant strains. Eur J Med Chem 2020; 208:112696. [DOI: 10.1016/j.ejmech.2020.112696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/16/2022]
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Bono B, Franco G, Riva V, Garbelli A, Maga G. Novel Insights into the Biochemical Mechanism of CK1ε and its Functional Interplay with DDX3X. Int J Mol Sci 2020; 21:ijms21176449. [PMID: 32899434 PMCID: PMC7503845 DOI: 10.3390/ijms21176449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 11/23/2022] Open
Abstract
Casein Kinase 1 epsilon (CK1ε) is a member of the serine (Ser)/threonine (Thr) CK1 family, known to have crucial roles in several biological scenarios and, ever more frequently, in pathological contexts, such as cancer. Recently, the human DEAD-box RNA helicase 3 X-linked (DDX3X), involved in cancer proliferation and viral infections, has been identified as one of CK1ε substrates and its positive regulator in the Wnt/β-catenin network. However, the way by which these two proteins influence each other has not been fully clarified. In order to further investigate their interplay, we defined the kinetic parameters of CK1ε towards its substrates: ATP, casein, Dvl2 and DDX3X. CK1ε affinity for ATP depends on the nature of the substrate: increasing of casein concentrations led to an increase of KmATP, while increasing DDX3X reduced it. In literature, DDX3X is described to act as an allosteric activator of CK1ε. However, when we performed kinase reactions combining DDX3X and casein, we did not find a positive effect of DDX3X on casein phosphorylation by CK1ε, while both substrates were phosphorylated in a competitive manner. Moreover, CK1ε positively stimulates DDX3X ATPase activity. Our data provide a more detailed kinetic characterization on the functional interplay of these two proteins.
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Riva V, Garbelli A, Brai A, Casiraghi F, Fazi R, Trivisani CI, Boccuto A, Saladini F, Vicenti I, Martelli F, Zazzi M, Giannecchini S, Dreassi E, Botta M, Maga G. Unique Domain for a Unique Target: Selective Inhibitors of Host Cell DDX3X to Fight Emerging Viruses. J Med Chem 2020; 63:9876-9887. [PMID: 32787106 DOI: 10.1021/acs.jmedchem.0c01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Emerging viruses like dengue, West Nile, chikungunya, and Zika can cause widespread viral epidemics. Developing novel drugs or vaccines against specific targets for each virus is a difficult task. As obligate parasites, all viruses exploit common cellular pathways, providing the possibility to develop broad-spectrum antiviral agents targeting host factors. The human DEAD-box RNA helicase DDX3X is an essential cofactor for viral replication but dispensable for cell viability. Herein, we exploited the presence of a unique structural motif of DDX3X not shared by other cellular enzymes to develop a theoretical model to aid in the design of a novel class of highly selective inhibitors acting against such specific targets, thus limiting off-targeting effects. High-throughput virtual screening led us to identify hit compound 5, endowed with promising antienzymatic activity. To improve its aqueous solubility, 5 and its two enantiomers were synthesized and converted into their corresponding acetate salts (compounds 11, 12, and 13). In vitro mutagenesis and biochemical and cellular assays further confirmed that the developed molecules were selective for DDX3X and were able to suppress replication of West Nile and dengue viruses in infected cells in the micromolar range while showing no toxicity for uninfected cells. These results provide proof of principle for a novel strategy in developing highly selective and broad-spectrum antiviral molecules active against emerging and dangerous viral pathogens. This study paves the way for the development of larger focused libraries targeting such domain to expand SAR studies and fully characterize their mode of interaction.
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Affiliation(s)
- Valentina Riva
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Federica Casiraghi
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Claudia I Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Martelli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Simone Giannecchini
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
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18
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Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells 2020; 9:E1267. [PMID: 32443810 PMCID: PMC7291026 DOI: 10.3390/cells9051267] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023] Open
Abstract
The current coronavirus disease-2019 (COVID-19) pandemic is due to the novel coronavirus SARS-CoV-2. The scientific community has mounted a strong response by accelerating research and innovation, and has quickly set the foundation for understanding the molecular determinants of the disease for the development of targeted therapeutic interventions. The replication of the viral genome within the infected cells is a key stage of the SARS-CoV-2 life cycle. It is a complex process involving the action of several viral and host proteins in order to perform RNA polymerization, proofreading and final capping. This review provides an update of the structural and functional data on the key actors of the replicatory machinery of SARS-CoV-2, to fill the gaps in the currently available structural data, which is mainly obtained through homology modeling. Moreover, learning from similar viruses, we collect data from the literature to reconstruct the pattern of interactions among the protein actors of the SARS-CoV-2 RNA polymerase machinery. Here, an important role is played by co-factors such as Nsp8 and Nsp10, not only as allosteric activators but also as molecular connectors that hold the entire machinery together to enhance the efficiency of RNA replication.
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Affiliation(s)
- Maria Romano
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
| | - Giovanni Maga
- Institute of Molecular Genetics, IGM, CNR, 27100 Pavia, Italy;
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, 80134 Naples, Italy; (M.R.); (A.R.); (F.S.)
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19
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Brai A, Boccuto A, Monti M, Marchi S, Vicenti I, Saladini F, Trivisani CI, Pollutri A, Trombetta CM, Montomoli E, Riva V, Garbelli A, Nola EM, Zazzi M, Maga G, Dreassi E, Botta M. Exploring the Implication of DDX3X in DENV Infection: Discovery of the First-in-Class DDX3X Fluorescent Inhibitor. ACS Med Chem Lett 2020; 11:956-962. [PMID: 32435411 DOI: 10.1021/acsmedchemlett.9b00681] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
In the absence of effective drugs or vaccines for the treatment of the five Dengue Virus serotypes, the search for novel antiviral drugs is of primary importance for the scientific community. In this context, drug repurposing represents the most used strategy; however, the study of host targets is now attracting attention since it allows identification of broad-spectrum drugs endowed with high genetic barrier. In the last ten years our research group identified several small molecules DDX3X inhibitors and proved their efficacy against different viruses including novel emerging ones. Herein, starting from a screening of our compounds, we designed and synthesized novel derivatives with potent activity and high selectivity. Finally, we synthesized a fluorescent inhibitor that allowed us to study DDX3X cellular localization during DENV infection in vitro. Immunofluorescence analysis showed that our inhibitor colocalized with DDX3X, promoting the reduction of infected cells and recovering the number of viable cells.
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Affiliation(s)
- Annalaura Brai
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Martina Monti
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Serena Marchi
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | | | - Alessandro Pollutri
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Claudia Maria Trombetta
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
| | - Emanuele Montomoli
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università degli Studi di Siena, 53100 Siena, Italy
- VisMederi Srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Valentina Riva
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emanuele Maria Nola
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elena Dreassi
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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20
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Brai A, Riva V, Saladini F, Zamperini C, Trivisani CI, Garbelli A, Pennisi C, Giannini A, Boccuto A, Bugli F, Martini M, Sanguinetti M, Zazzi M, Dreassi E, Botta M, Maga G. DDX3X inhibitors, an effective way to overcome HIV-1 resistance targeting host proteins. Eur J Med Chem 2020; 200:112319. [PMID: 32446036 DOI: 10.1016/j.ejmech.2020.112319] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
The huge resources that had gone into Human Immunodeficiency virus (HIV) research led to the development of potent antivirals able to suppress viral load in the majority of treated patients, thus dramatically increasing the life expectancy of people living with HIV. However, life-long treatments could result in the emergence of drug-resistant viruses that can progressively reduce the number of therapeutic options, facilitating the progression of the disease. In this scenario, we previously demonstrated that inhibitors of the human DDX3X helicase can represent an innovative approach for the simultaneous treatment of HIV and other viral infections such as Hepatitis c virus (HCV). We reported herein 6b, a novel DDX3X inhibitor that thanks to its distinct target of action is effective against HIV-1 strains resistant to currently approved drugs. Its improved in vitro ADME properties allowed us to perform preliminary in vivo studies in mice, which highlighted optimal biocompatibility and an improved bioavailability. These results represent a significant advancement in the development of DDX3X inhibitors as a novel class of broad spectrum and safe anti-HIV-1 drugs.
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Affiliation(s)
- Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Valentina Riva
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Claudia Immacolata Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Carla Pennisi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Alessia Giannini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Francesca Bugli
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, I-00168, Roma, Italy; Istituto di Microbiologia, Università Cattolica del SC, L.go F. Vito 1, I-00168, Roma, Italy
| | - Maurizio Martini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Servizio di Istopatologia e Citodiagnosi, Rome, Italy; Istituto di Patologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, I-00168, Roma, Italy; Istituto di Microbiologia, Università Cattolica del SC, L.go F. Vito 1, I-00168, Roma, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, I-53100, Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100, Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA, 19122, USA.
| | - Giovanni Maga
- Istituto di Genetica Molecolare "Luigi Luca Cavalli - Sforza", IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy.
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21
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Tassini S, Langron E, Delang L, Mirabelli C, Lanko K, Crespan E, Kissova M, Tagliavini G, Fontò G, Bertoni S, Palese S, Giorgio C, Ravanetti F, Ragionieri L, Zamperini C, Mancini A, Dreassi E, Maga G, Vergani P, Neyts J, Radi M. Multitarget CFTR Modulators Endowed with Multiple Beneficial Side Effects for Cystic Fibrosis Patients: Toward a Simplified Therapeutic Approach. J Med Chem 2019; 62:10833-10847. [DOI: 10.1021/acs.jmedchem.9b01416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Sabrina Tassini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Emily Langron
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E 6BT London, U.K
| | - Leen Delang
- Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Carmen Mirabelli
- Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Kristina Lanko
- Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Miroslava Kissova
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giulia Tagliavini
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Greta Fontò
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Simona Bertoni
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Simone Palese
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Carmine Giorgio
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Francesca Ravanetti
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Luisa Ragionieri
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Claudio Zamperini
- Lead Discovery Siena S.r.l., Via Vittorio Alfieri 31, Castelnuovo Berardenga, 53019 Siena, Italy
| | - Arianna Mancini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Paola Vergani
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E 6BT London, U.K
| | - Johan Neyts
- Laboratory of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
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22
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Geronikaki A, Petrou A, Kartsev V, Eleftheriou P, Boga R, Bartolo B, Crespan E, Franco G, Maga G. Molecular docking, design, synthesis and biological evaluation of novel 2,3-aryl-thiazolidin-4-ones as potent NNRTIs. SAR QSAR Environ Res 2019; 30:697-714. [PMID: 31542957 DOI: 10.1080/1062936x.2019.1653364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most promising anti-AIDS agents that target the HIV-1 reverse transcriptase enzyme (RT). However, the efficiency of approved NNRTI drugs has decreased by the appearance of drug-resistant viruses and side effects upon long-term usage. Thus, there is an urgent need for developing new, potent NNRTIs with broad spectrum against HIV-1 virus and with improved properties. In this study, a series of thiazolidinone derivatives was designed based on a butterfly mimicking scaffold consisting of a substituted benzothiazolyl moiety connected with a substituted phenyl ring via a thiazolidinone moiety. The most promising derivatives were selected using molecular docking analysis and PASS prediction program, synthesized and evaluated for HIV-1 RT inhibition. Five out of fifteen tested compounds exhibited good inhibitory action. It was observed that the presence of Cl or CN substituents at the position 6 of the benzothiazole ring in combination with two fluoro atoms at the ortho-positions or a hydrogen acceptor substituent at the 4-position of the phenyl ring are favourable for the HIV RT inhibitory activity.
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Affiliation(s)
- A Geronikaki
- School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - A Petrou
- School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | | | - P Eleftheriou
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University , Thessaloniki , Greece
| | - R Boga
- BogaR Laboratories LLC , Suwanee , USA
| | - B Bartolo
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - E Crespan
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - G Franco
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - G Maga
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
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23
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Fallacara AL, Passannanti R, Mori M, Iovenitti G, Musumeci F, Greco C, Crespan E, Kissova M, Maga G, Tarantelli C, Spriano F, Gaudio E, Bertoni F, Botta M, Schenone S. Identification of a new family of pyrazolo[3,4-d]pyrimidine derivatives as multitarget Fyn-Blk-Lyn inhibitors active on B- and T-lymphoma cell lines. Eur J Med Chem 2019; 181:111545. [PMID: 31400706 DOI: 10.1016/j.ejmech.2019.07.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/27/2022]
Abstract
Abnormal activation of B-cell receptor (BCR) signaling plays a key role in the development of lymphoid malignancies, and could be reverted by the simultaneous inhibition of Lyn, Fyn and Blk, three members of the Src family kinase (SFK). Fyn and Blk are also promising targets for the treatment of some forms of T-cell non-Hodgkin lymphoma which point to the druggability of SFKs for the treatment of these cancers. We recently identified Si308 as a potent Fyn inhibitor, while preliminary data showed that it might also inhibit Lyn and Blk. Here, molecular modelling studies were coupled with enzymatic assays to further investigate the effect of Si308 on Lyn and Blk. A small library of pyrazolo[3,4-d]pyrimidines structurally related to Si308 was synthesized and tested on human lymphoma cell lines. Compound 2h emerged as a new multitarget inhibitor of Lyn, Fyn and Blk endowed with remarkable antiproliferative effects on human B and T lymphoma cell lines. Its favorable ADME properties make the compound suitable for further developments.
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Affiliation(s)
- Anna Lucia Fallacara
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Raffaele Passannanti
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giulia Iovenitti
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Francesca Musumeci
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132, Genoa, Italy
| | - Chiara Greco
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132, Genoa, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Miroslava Kissova
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100, Pavia, Italy
| | - Chiara Tarantelli
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), via Vela 6, 6500, Bellinzona, Switzerland
| | - Filippo Spriano
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), via Vela 6, 6500, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), via Vela 6, 6500, Bellinzona, Switzerland
| | - Francesco Bertoni
- Università della Svizzera italiana (USI), Institute of Oncology Research (IOR), via Vela 6, 6500, Bellinzona, Switzerland
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100, Siena, Italy; Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA, 19122, United States; Lead Discovery Siena s.r.l., Via Vittorio Alfieri 31, 53019, Castelnuovo, Berardenga, Italy.
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132, Genoa, Italy
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24
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De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magaña A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A. p15PAF binding to PCNA modulates the DNA sliding surface. Nucleic Acids Res 2019; 46:9816-9828. [PMID: 30102405 PMCID: PMC6182140 DOI: 10.1093/nar/gky723] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF–PCNA–DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η–PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Susana Barrera-Vilarmau
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain
| | | | | | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alfredo De Biasio
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy.,Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
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25
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Brai A, Martelli F, Riva V, Garbelli A, Fazi R, Zamperini C, Pollutri A, Falsitta L, Ronzini S, Maccari L, Maga G, Giannecchini S, Botta M. DDX3X Helicase Inhibitors as a New Strategy To Fight the West Nile Virus Infection. J Med Chem 2019; 62:2333-2347. [PMID: 30721061 DOI: 10.1021/acs.jmedchem.8b01403] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Increased frequency of arbovirus outbreaks in the last 10 years represents an important emergence for global health. Climate warming, extensive urbanization of tropical regions, and human migration flows facilitate the expansion of anthropophilic mosquitos and the emerging or re-emerging of new viral infections. Only recently the human adenosinetriphosphatase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3X) emerged as a novel therapeutic target in the fight against infectious diseases. Herein, starting from our previous studies, a new family of DDX3X inhibitors was designed, synthesized, validated on the target enzyme, and evaluated against the West Nile virus (WNV) infection. Time of addition experiments after virus infection indicated that the compounds exerted their antiviral activities after the entry process, likely at the protein translation step of WNV replication. Finally, the most interesting compounds were then analyzed for their in vitro pharmacokinetic parameters, revealing favorable absorption, distribution, metabolism, and excretion values. The good safety profile together with a good activity against WNV for which no treatments are currently available, make this new class of molecules a good starting point for further in vivo studies.
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Affiliation(s)
- Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy.,Lead Discovery Siena S.r.l. , Castelnuovo Berardenga, I-53019 Siena , Italy
| | - Francesco Martelli
- Department of Experimental and Clinical Medicine , University of Florence , I-50134 Florence , Italy
| | - Valentina Riva
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207 , I-27100 Pavia , Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207 , I-27100 Pavia , Italy
| | - Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy.,Lead Discovery Siena S.r.l. , Castelnuovo Berardenga, I-53019 Siena , Italy
| | - Alessandro Pollutri
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy
| | - Lucia Falsitta
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy
| | - Stefania Ronzini
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy
| | - Laura Maccari
- Lead Discovery Siena S.r.l. , Castelnuovo Berardenga, I-53019 Siena , Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207 , I-27100 Pavia , Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine , University of Florence , I-50134 Florence , Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , Via A. De Gasperi 2 , I-53100 Siena , Italy.,Lead Discovery Siena S.r.l. , Castelnuovo Berardenga, I-53019 Siena , Italy.,Biotechnology College of Science and Technology , Temple University , BioLife Science Building, Suite 333, 1900 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
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26
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Nawrozkij MB, Forgione M, Yablokov AS, Lucidi A, Tomaselli D, Patsilinakos A, Panella C, Hailu GS, Kirillov IA, Badia R, Riveira-Muñoz E, Crespan E, Armijos Rivera JI, Cirilli R, Ragno R, Esté JA, Maga G, Mai A, Rotili D. Effect of α-Methoxy Substitution on the Anti-HIV Activity of Dihydropyrimidin-4(3H)-ones. J Med Chem 2018; 62:604-621. [DOI: 10.1021/acs.jmedchem.8b01238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Maxim B. Nawrozkij
- Volgograd State Technical University, Lenina Avenue 28, 400005 Volgograd, Russia
| | - Mariantonietta Forgione
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | | | - Alessia Lucidi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Daniela Tomaselli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Alexandros Patsilinakos
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Cristina Panella
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Gebremedhin S. Hailu
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Ivan A. Kirillov
- Volgograd State Technical University, Lenina Avenue 28, 400005 Volgograd, Russia
| | - Roger Badia
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | | | - Roberto Cirilli
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Rino Ragno
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - José A. Esté
- IrsiCaixa-AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
- Istituto Pasteur—Fondazione Cenci Bolognetti, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
| | - Dante Rotili
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy
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27
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Kaptein SJF, Vincetti P, Crespan E, Rivera JIA, Costantino G, Maga G, Neyts J, Radi M. Cover Feature: Identification of Broad-Spectrum Dengue/Zika Virus Replication Inhibitors by Functionalization of Quinoline and 2,6-Diaminopurine Scaffolds (ChemMedChem 14/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Suzanne J. F. Kaptein
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy; KU Leuven; B-3000 Leuven Belgium
| | - Paolo Vincetti
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
| | - Emmanuele Crespan
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Jorge I. Armijos Rivera
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Gabriele Costantino
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
| | - Giovanni Maga
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Johan Neyts
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy; KU Leuven; B-3000 Leuven Belgium
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
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28
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Kaptein SJF, Vincetti P, Crespan E, Rivera JIA, Costantino G, Maga G, Neyts J, Radi M. Identification of Broad-Spectrum Dengue/Zika Virus Replication Inhibitors by Functionalization of Quinoline and 2,6-Diaminopurine Scaffolds. ChemMedChem 2018; 13:1371-1376. [DOI: 10.1002/cmdc.201800178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/04/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Suzanne J. F. Kaptein
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy; KU Leuven; B-3000 Leuven Belgium
| | - Paolo Vincetti
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
| | - Emmanuele Crespan
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Jorge I. Armijos Rivera
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Gabriele Costantino
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
| | - Giovanni Maga
- National Research Council; Institute of Molecular Genetics IGM-CNR; Via Abbiategrasso 207 27100 Pavia Italy
| | - Johan Neyts
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy; KU Leuven; B-3000 Leuven Belgium
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco; Università degli Studi di Parma; Viale delle Scienze, 27/A 43124 Parma Italy
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29
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Affiliation(s)
- Barbara van Loon
- Department
of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Erling Skjalgssons gt 1, N-7491 Trondheim, Norway
- Department
of Pathology and Medical Genetics, St. Olavs Hospital, Trondheim University Hospital, 7491 Trondheim, Norway
| | - Ulrich Hübscher
- Department
of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Giovanni Maga
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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30
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Mentegari E, Crespan E, Bavagnoli L, Kissova M, Bertoletti F, Sabbioneda S, Imhof R, Sturla SJ, Nilforoushan A, Hübscher U, van Loon B, Maga G. Ribonucleotide incorporation by human DNA polymerase η impacts translesion synthesis and RNase H2 activity. Nucleic Acids Res 2017; 45:2600-2614. [PMID: 27994034 PMCID: PMC5389505 DOI: 10.1093/nar/gkw1275] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
Ribonucleotides (rNs) incorporated in the genome by DNA polymerases (Pols) are removed by RNase H2. Cytidine and guanosine preferentially accumulate over the other rNs. Here we show that human Pol η can incorporate cytidine monophosphate (rCMP) opposite guanine, 8-oxo-7,8-dihydroguanine, 8-methyl-2΄-deoxyguanosine and a cisplatin intrastrand guanine crosslink (cis-PtGG), while it cannot bypass a 3-methylcytidine or an abasic site with rNs as substrates. Pol η is also capable of synthesizing polyribonucleotide chains, and its activity is enhanced by its auxiliary factor DNA Pol δ interacting protein 2 (PolDIP2). Human RNase H2 removes cytidine and guanosine less efficiently than the other rNs and incorporation of rCMP opposite DNA lesions further reduces the efficiency of RNase H2. Experiments with XP-V cell extracts indicate Pol η as the major basis of rCMP incorporation opposite cis-PtGG. These results suggest that translesion synthesis by Pol η can contribute to the accumulation of rCMP in the genome, particularly opposite modified guanines.
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Affiliation(s)
- Elisa Mentegari
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Emmanuele Crespan
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Laura Bavagnoli
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Miroslava Kissova
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Federica Bertoletti
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Barbara van Loon
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Giovanni Maga
- DNA Enzymology & Molecular Virology and Cell Nucleus & DNA replication Units, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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31
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Famiglini V, La Regina G, Coluccia A, Masci D, Brancale A, Badia R, Riveira-Muñoz E, Esté JA, Crespan E, Brambilla A, Maga G, Catalano M, Limatola C, Formica FR, Cirilli R, Novellino E, Silvestri R. Chiral Indolylarylsulfone Non-Nucleoside Reverse Transcriptase Inhibitors as New Potent and Broad Spectrum Anti-HIV-1 Agents. J Med Chem 2017. [DOI: 10.1021/acs.jmedchem.6b01906] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Valeria Famiglini
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Giuseppe La Regina
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Antonio Coluccia
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Domiziana Masci
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
| | - Andrea Brancale
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Roger Badia
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Eva Riveira-Muñoz
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - José A. Esté
- AIDS Research Institute−IrsiCaixa,
Hospitals Germans Trias i Pujol, Universitat Autonóma de Barcelona, 08916 Badalona, Spain
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Alessandro Brambilla
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM−CNR, National Research Council, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Myriam Catalano
- Istituto Pasteur Italia−Fondazione Cenci Bolognetti,
Dipartimento di Fisiologia e Farmacologia “Vittorio Erspamer”, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- IRCCS Neuromed, Via
Atinense 18, I-86077 Pozzilli, Italy
| | - Cristina Limatola
- Istituto Pasteur Italia−Fondazione Cenci Bolognetti,
Dipartimento di Fisiologia e Farmacologia “Vittorio Erspamer”, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
- IRCCS Neuromed, Via
Atinense 18, I-86077 Pozzilli, Italy
| | - Francesca Romana Formica
- Dipartimento del
Farmaco, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Roberto Cirilli
- Dipartimento del
Farmaco, Istituto Superiore di Sanità, Viale Regina Elena 299, I-00161 Roma, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Domenico Montesano 49, I-80131 Napoli, Italy
| | - Romano Silvestri
- Istituto Pasteur
Italia−Fondazione Cenci Bolognetti, Dipartimento di Chimica
e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo
Moro 5, I-00185 Roma, Italy
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32
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Tassini S, Sun L, Lanko K, Crespan E, Langron E, Falchi F, Kissova M, Armijos-Rivera JI, Delang L, Mirabelli C, Neyts J, Pieroni M, Cavalli A, Costantino G, Maga G, Vergani P, Leyssen P, Radi M. Discovery of Multitarget Agents Active as Broad-Spectrum Antivirals and Correctors of Cystic Fibrosis Transmembrane Conductance Regulator for Associated Pulmonary Diseases. J Med Chem 2017; 60:1400-1416. [DOI: 10.1021/acs.jmedchem.6b01521] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sabrina Tassini
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Liang Sun
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Kristina Lanko
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emily Langron
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E
6BT London, U.K
| | - Federico Falchi
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Miroslava Kissova
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | | | - Leen Delang
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Carmen Mirabelli
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Johan Neyts
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Marco Pieroni
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Gabriele Costantino
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Paola Vergani
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E
6BT London, U.K
| | - Pieter Leyssen
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Marco Radi
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
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33
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Musumeci F, Fallacara AL, Brullo C, Grossi G, Botta L, Calandro P, Chiariello M, Kissova M, Crespan E, Maga G, Schenone S. Identification of new pyrrolo[2,3-d]pyrimidines as Src tyrosine kinase inhibitors in vitro active against Glioblastoma. Eur J Med Chem 2016; 127:369-378. [PMID: 28076826 DOI: 10.1016/j.ejmech.2016.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 01/01/2023]
Abstract
In the last few years, several pyrrolo-pyrimidine derivatives have been either approved by the US FDA and in other countries for the treatment of different diseases or are currently in phase I/II clinical trials. Herein we present the synthesis and the characterization of a novel series of pyrrolo[2,3-d]pyrimidines, compounds 8a-j, and their activity against Glioblastoma multiforme (GBM). Docking studies and MM-GBSA analysis revealed the ability of such compounds to efficiently interact with the ATP binding site of Src. Enzymatic assays against a mini-panel of kinases (Src, Fyn, EGFR, Kit, Flt3, Abl, AblT315I) have been performed, showing an unexpected selectivity of our pyrrolo[2,3-d]pyrimidines for Src. Finally, the derivatives were tested for their antiproliferative potency on U87 GBM cell line. Compound 8h showed a considerable cytotoxicity effect against U87 cell line with an IC50 value of 7.1 μM.
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Affiliation(s)
- Francesca Musumeci
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Anna Lucia Fallacara
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Chiara Brullo
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Giancarlo Grossi
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Lorenzo Botta
- Dipartimento di Farmacia, Università"Federico II" di Napoli, Via D. Montesano 49, 80131 Napoli, Italy
| | - Pierpaolo Calandro
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mario Chiariello
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Istituto Toscano Tumori, Core Research Laboratory, Via Fiorentina 1, 53100 Siena, Italy
| | - Miroslava Kissova
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emmanuele Crespan
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Silvia Schenone
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy.
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34
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El-Moghazy SM, George RF, Osman EEA, Elbatrawy AA, Kissova M, Colombo A, Crespan E, Maga G. Novel pyrazolo[3,4- d ]pyrimidines as dual Src-Abl inhibitors active against mutant form of Abl and the leukemia K-562 cell line. Eur J Med Chem 2016; 123:1-13. [DOI: 10.1016/j.ejmech.2016.07.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/14/2016] [Accepted: 07/18/2016] [Indexed: 02/08/2023]
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35
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Mentegari E, Kissova M, Bavagnoli L, Maga G, Crespan E. DNA Polymerases λ and β: The Double-Edged Swords of DNA Repair. Genes (Basel) 2016; 7:genes7090057. [PMID: 27589807 PMCID: PMC5042388 DOI: 10.3390/genes7090057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/30/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022] Open
Abstract
DNA is constantly exposed to both endogenous and exogenous damages. More than 10,000 DNA modifications are induced every day in each cell's genome. Maintenance of the integrity of the genome is accomplished by several DNA repair systems. The core enzymes for these pathways are the DNA polymerases. Out of 17 DNA polymerases present in a mammalian cell, at least 13 are specifically devoted to DNA repair and are often acting in different pathways. DNA polymerases β and λ are involved in base excision repair of modified DNA bases and translesion synthesis past DNA lesions. Polymerase λ also participates in non-homologous end joining of DNA double-strand breaks. However, recent data have revealed that, depending on their relative levels, the cell cycle phase, the ratio between deoxy- and ribo-nucleotide pools and the interaction with particular auxiliary proteins, the repair reactions carried out by these enzymes can be an important source of genetic instability, owing to repair mistakes. This review summarizes the most recent results on the ambivalent properties of these enzymes in limiting or promoting genetic instability in mammalian cells, as well as their potential use as targets for anticancer chemotherapy.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Miroslava Kissova
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Laura Bavagnoli
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Emmanuele Crespan
- Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
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36
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Kissova M, Maga G, Crespan E. The human tyrosine kinase Kit and its gatekeeper mutant T670I, show different kinetic properties: Implications for drug design. Bioorg Med Chem 2016; 24:4555-4562. [PMID: 27527414 DOI: 10.1016/j.bmc.2016.07.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022]
Abstract
The tyrosine kinase Kit, a receptor for Stem Cell Factor, is involved, among others, in processes associated to cell survival, proliferation and migration. Upon physiological conditions, the activity of Kit is tightly regulated. However, primary mutations that lead to its constitutive activation are the causal oncogenic driver of gastrointestinal stromal tumours (GISTs). GISTs are known to be refractory to conventional therapies but the introduction of Imatinib, a selective inhibitor of tyrosine kinases Abl and Kit, significantly ameliorated the treatment options of GISTs patients. However, the acquisition of secondary mutations renders Kit resistant towards all available drugs. Mutation involving gatekeeper residues (such as V654a and T670I) influence both the structure and the catalytic activity of the enzyme. Therefore, detailed knowledge of the enzymatic properties of the mutant forms, in comparison with the wild type enzyme, is an important pre-requisite for the rational development of specific inhibitors. In this paper we report a thorough kinetic analysis of the reaction catalyzed by the Kit kinase and its gatekeeper mutated form T670I. Our results revealed the different mechanisms of action of these two enzymes and may open a new avenue for the future design of specific Kit inhibitors.
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Affiliation(s)
- Miroslava Kissova
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.
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37
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Radi M, Schneider R, Fallacara AL, Botta L, Crespan E, Tintori C, Maga G, Kissova M, Calgani A, Richters A, Musumeci F, Rauh D, Schenone S. A cascade screening approach for the identification of Bcr-Abl myristate pocket binders active against wild type and T315I mutant. Bioorg Med Chem Lett 2016; 26:3436-40. [DOI: 10.1016/j.bmcl.2016.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 01/17/2023]
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38
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De Martino G, La Regina G, Ragno R, Coluccia A, Bergamini A, Ciaprini C, Sinistro A, Maga G, Crespan E, Artico M, Silvestri R. Indolyl Aryl Sulphones as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors: Synthesis, Biological Evaluation and Binding Mode Studies of New Derivatives at Indole-2-carboxamide. ACTA ACUST UNITED AC 2016; 17:59-77. [PMID: 17042328 DOI: 10.1177/095632020601700202] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
New non-nucleoside reverse transcriptase inhibitors (NNRTIs) that are active against the commonly occurring mutations of HIV are urgently needed for the treatment of AIDS. We synthesized new NNRTIs of the indolyl aryl sulphone (IAS) family, which are endowed with high antiviral potency against HIV-1 wt (wild-type), and the Y181C and K103N-Y181C drug resistant mutant strains. Several new compounds were highly active in lymphocytes infected with primary isolates carrying the K103N-V108I-M184V and L100I-V108I mutations. The design of new IASs was based on three-dimensional quantitative structure-activity relationship (3D QSAR) studies and docking simulations. A cross-docking study was also undertaken to gain some insights in to the binding mode of the newly synthesized IASs in the wt and mutated isoforms of reverse transcriptase.
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Affiliation(s)
- Gabriella De Martino
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università di Roma 'La Sapienza', Roma, Italy
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39
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Brai A, Fazi R, Tintori C, Estè J, Badia R, Franco S, Martinez MA, Martinez J, Meyerhans A, Saladini F, Zazzi M, Garbelli A, Botta M, Maga G. Human helicase DDX3 as target for broad-spectrum antivirals against pandemic and emerging viruses. J Virus Erad 2016. [DOI: 10.1016/s2055-6640(20)31180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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40
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Tintori C, Brai A, Dasso Lang MC, Deodato D, Greco AM, Bizzarri BM, Cascone L, Casian A, Zamperini C, Dreassi E, Crespan E, Maga G, Vanham G, Ceresola E, Canducci F, Ariën KK, Botta M. Development and in Vitro Evaluation of a Microbicide Gel Formulation for a Novel Non-Nucleoside Reverse Transcriptase Inhibitor Belonging to the N-Dihydroalkyloxybenzyloxopyrimidines (N-DABOs) Family. J Med Chem 2016; 59:2747-59. [PMID: 26898379 DOI: 10.1021/acs.jmedchem.5b01979] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Preventing HIV transmission by the use of a vaginal microbicide is a topic of considerable interest in the fight against AIDS. Both a potent anti-HIV agent and an efficient formulation are required to develop a successful microbicide. In this regard, molecules able to inhibit the HIV replication before the integration of the viral DNA into the genetic material of the host cells, such as entry inhibitors or reverse transcriptase inhibitors (RTIs), are ideal candidates for prevention purpose. Among RTIs, S- and N-dihydroalkyloxybenzyloxopyrimidines (S-DABOs and N-DABOs) are interesting compounds active at nanomolar concentration against wild type of RT and with a very interesting activity against RT mutations. Herein, novel N-DABOs were synthesized and tested as anti-HIV agents. Furthermore, their mode of binding was studied by molecular modeling. At the same time, a vaginal microbicide gel formulation was developed and tested for one of the most promising candidates.
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Affiliation(s)
- Cristina Tintori
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Davide Deodato
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Antonia Michela Greco
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Bruno Mattia Bizzarri
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorena Cascone
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Alexandru Casian
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Claudio Zamperini
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Guido Vanham
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Elisa Ceresola
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Filippo Canducci
- Department of Biotechnology and Life Sciences, University of Insubria , Dunant 3, 21100, Varese, Italy
| | - Kevin K Ariën
- Virology Unit, Institute of Tropical Medicine , Nationalestraat 155, B-2000 Antwerpen, Belgium
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University , Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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41
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Crespan E, Furrer A, Rösinger M, Bertoletti F, Mentegari E, Chiapparini G, Imhof R, Ziegler N, Sturla SJ, Hübscher U, van Loon B, Maga G. Impact of ribonucleotide incorporation by DNA polymerases β and λ on oxidative base excision repair. Nat Commun 2016; 7:10805. [PMID: 26917111 PMCID: PMC4773436 DOI: 10.1038/ncomms10805] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/22/2016] [Indexed: 12/17/2022] Open
Abstract
Oxidative stress is a very frequent source of DNA damage. Many cellular DNA polymerases (Pols) can incorporate ribonucleotides (rNMPs) during DNA synthesis. However, whether oxidative stress-triggered DNA repair synthesis contributes to genomic rNMPs incorporation is so far not fully understood. Human specialized Pols β and λ are the important enzymes involved in the oxidative stress tolerance, acting both in base excision repair and in translesion synthesis past the very frequent oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxo-G). We found that Pol β, to a greater extent than Pol λ can incorporate rNMPs opposite normal bases or 8-oxo-G, and with a different fidelity. Further, the incorporation of rNMPs opposite 8-oxo-G delays repair by DNA glycosylases. Studies in Pol β- and λ-deficient cell extracts suggest that Pol β levels can greatly affect rNMP incorporation opposite oxidative DNA lesions. Oxidative stress is a common source of DNA damage and is repaired by the base excision repair machinery, including polymerase beta. Here the authors find that polymerase beta, and to a lesser extent lambda, can mistakenly incorporate ribonucleotides during synthesis.
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Affiliation(s)
- Emmanuele Crespan
- DNA Enzymology &Molecular Virology Unit, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Antonia Furrer
- Department of Molecular Mechanisms of Disease, University of Zürich, CH-8057 Zürich, Switzerland
| | - Marcel Rösinger
- Department of Molecular Mechanisms of Disease, University of Zürich, CH-8057 Zürich, Switzerland
| | - Federica Bertoletti
- DNA Enzymology &Molecular Virology Unit, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Elisa Mentegari
- DNA Enzymology &Molecular Virology Unit, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giulia Chiapparini
- DNA Enzymology &Molecular Virology Unit, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zürich, CH-8057 Zürich, Switzerland
| | - Nathalie Ziegler
- Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zürich, Switzerland
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich, CH-8057 Zürich, Switzerland
| | - Barbara van Loon
- Department of Molecular Mechanisms of Disease, University of Zürich, CH-8057 Zürich, Switzerland
| | - Giovanni Maga
- DNA Enzymology &Molecular Virology Unit, Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
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42
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Llona-Minguez S, Höglund A, Jacques SA, Johansson L, Calderón-Montaño JM, Claesson M, Loseva O, Valerie NCK, Lundbäck T, Piedrafita J, Maga G, Crespan E, Meijer L, Morón EB, Baranczewski P, Hagbjörk AL, Svensson R, Wiita E, Almlöf I, Visnes T, Jeppsson F, Sigmundsson K, Jensen AJ, Artursson P, Jemth AS, Stenmark P, Berglund UW, Scobie M, Helleday T. Discovery of the First Potent and Selective Inhibitors of Human dCTP Pyrophosphatase 1. J Med Chem 2016; 59:1140-1148. [PMID: 26771665 DOI: 10.1021/acs.jmedchem.5b01741] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The dCTPase pyrophosphatase 1 (dCTPase) regulates the intracellular nucleotide pool through hydrolytic degradation of canonical and noncanonical nucleotide triphosphates (dNTPs). dCTPase is highly expressed in multiple carcinomas and is associated with cancer cell stemness. Here we report on the development of the first potent and selective dCTPase inhibitors that enhance the cytotoxic effect of cytidine analogues in leukemia cells. Boronate 30 displays a promising in vitro ADME profile, including plasma and mouse microsomal half-lives, aqueous solubility, cell permeability and CYP inhibition, deeming it a suitable compound for in vivo studies.
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Affiliation(s)
- Sabin Llona-Minguez
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Höglund
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sylvain A Jacques
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lars Johansson
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - José Manuel Calderón-Montaño
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden
| | - Olga Loseva
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas C K Valerie
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Lundbäck
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Javier Piedrafita
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121, United States
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Estefanía Burgos Morón
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pawel Baranczewski
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Louise Hagbjörk
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Svensson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisee Wiita
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Almlöf
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Torkild Visnes
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Jeppsson
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristmundur Sigmundsson
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Annika Jenmalm Jensen
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Per Artursson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Sofie Jemth
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Scobie
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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43
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Tassini S, Castagnolo D, Scalacci N, Kissova M, Armijos-Rivera JI, Giagnorio F, Maga G, Costantino G, Crespan E, Radi M. A multicomponent pharmacophore fragment-decoration approach to identify selective LRRK2-targeting probes. Med Chem Commun 2016. [DOI: 10.1039/c5md00462d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein we report the development of a new versatile chemical tool for the rapid identification of LRRK2-targeting probes as potential anti-Parkinson's agents.
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Affiliation(s)
- Sabrina Tassini
- P4T Group, Dipartimento di Farmacia
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Daniele Castagnolo
- Institute of Pharmaceutical Science
- King's College London
- SE1 9NH London
- UK
- Northumbria University Newcastle
| | - Nicolò Scalacci
- Institute of Pharmaceutical Science
- King's College London
- SE1 9NH London
- UK
- Northumbria University Newcastle
| | | | | | - Federica Giagnorio
- P4T Group, Dipartimento di Farmacia
- Università degli Studi di Parma
- 43124 Parma
- Italy
- Northumbria University Newcastle
| | | | - Gabriele Costantino
- P4T Group, Dipartimento di Farmacia
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | | | - Marco Radi
- P4T Group, Dipartimento di Farmacia
- Università degli Studi di Parma
- 43124 Parma
- Italy
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44
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Fazi R, Tintori C, Brai A, Botta L, Selvaraj M, Garbelli A, Maga G, Botta M. Homology Model-Based Virtual Screening for the Identification of Human Helicase DDX3 Inhibitors. J Chem Inf Model 2015; 55:2443-54. [PMID: 26544088 DOI: 10.1021/acs.jcim.5b00419] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Targeting cellular cofactors instead of viral enzymes represents a new strategy to combat infectious diseases, which should help to overcome the problem of viral resistance. Recently, it has been revealed that the cellular ATPase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3) is an essential host factor for the replication of several viruses such as HIV, HCV, JEV, Dengue, and West Nile. Accordingly, a drug targeting DDX3 could theoretically inhibit all viruses that are dependent on this host factor. Herein, for the first time, a model of hDDX3 in its closed conformation, which binds the viral RNA was developed by using the homology module of Prime through the Maestro interface of Schrodinger. Next, a structure-based virtual screening protocol was applied to identify DDX3 small molecule inhibitors targeting the RNA binding pocket. As a result, an impressive hit rate of 40% was obtained with the identification of 10 active compounds out of the 25 tested small molecules. The best poses of the active ligands highlighted the crucial residues to be targeted for the inhibition of the helicase activity of DDX3. The obtained results confirm the reliability of the constructed DDX3/RNA model and the proposed computational strategy for investigating novel DDX3 inhibitors.
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Affiliation(s)
- Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Cristina Tintori
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorenzo Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Manikandan Selvaraj
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University , Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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45
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Bavagnoli L, Cucuzza S, Campanini G, Rovida F, Paolucci S, Baldanti F, Maga G. The novel influenza A virus protein PA-X and its naturally deleted variant show different enzymatic properties in comparison to the viral endonuclease PA. Nucleic Acids Res 2015; 43:9405-17. [PMID: 26384413 PMCID: PMC4627086 DOI: 10.1093/nar/gkv926] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022] Open
Abstract
The PA protein of Influenza A virus (IAV) encoded by segment 3 acts as a specialized RNA endonuclease in the transcription of the viral genome. The same genomic segment encodes for a second shorter protein, termed PA-X, with the first 191 N-terminal aminoacids (aa) identical to PA, but with a completely different C-ter domain of 61 aa, due to a ribosomal frameshifting. In addition, it has been shown that several IAV isolates encode for a naturally truncated PA-X variant, PAXΔC20, missing the last 20 aa. The biochemical properties of PA-X and PAXΔC20 have been poorly investigated so far. Here, we have carried out an enzymatic characterization of PA-X and its naturally deleted form, in comparison with PA from the human IAV strain A/WSN/33 (H1N1). Our results showed, to the best of our knowledge for the first time, that PA-X possesses an endonucleolytic activity. Both PA and PA-X preferentially cut single stranded RNA regions, but with some differences. In addition, we showed that PAXΔC20 has severely reduced nuclease activity. These results point to a previously undetected role of the last C-ter 20 aa for the catalytic activity of PA-X and support distinct roles for these proteins in the viral life cycle.
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Affiliation(s)
- Laura Bavagnoli
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Stefano Cucuzza
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giulia Campanini
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Stefania Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, P.le Golgi 2, 27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
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46
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Vincetti P, Caporuscio F, Kaptein S, Gioiello A, Mancino V, Suzuki Y, Yamamoto N, Crespan E, Lossani A, Maga G, Rastelli G, Castagnolo D, Neyts J, Leyssen P, Costantino G, Radi M. Discovery of Multitarget Antivirals Acting on Both the Dengue Virus NS5-NS3 Interaction and the Host Src/Fyn Kinases. J Med Chem 2015; 58:4964-75. [DOI: 10.1021/acs.jmedchem.5b00108] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Paolo Vincetti
- P4T
Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Fabiana Caporuscio
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Suzanne Kaptein
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical
Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Antimo Gioiello
- Laboratory
of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo 1, I-06123 Perugia, Italy
| | - Valentina Mancino
- Laboratory
of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo 1, I-06123 Perugia, Italy
| | - Youichi Suzuki
- Department
of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Center for Translational Medicine, 14 Medical Drive, 15-02, Level 15, Singapore 117599, Singapore
| | - Naoki Yamamoto
- Department
of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Center for Translational Medicine, 14 Medical Drive, 15-02, Level 15, Singapore 117599, Singapore
| | - Emmanuele Crespan
- Istituto
di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Andrea Lossani
- Istituto
di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Istituto
di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giulio Rastelli
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Daniele Castagnolo
- Department
of Applied Sciences, Northumbria University Newcastle, Ellison Place, NE1 8ST Newcastle upon Tyne, United Kingdom
| | - Johan Neyts
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical
Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Pieter Leyssen
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical
Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Gabriele Costantino
- P4T
Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Marco Radi
- P4T
Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
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47
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Tintori C, La Sala G, Vignaroli G, Botta L, Fallacara AL, Falchi F, Radi M, Zamperini C, Dreassi E, Dello Iacono L, Orioli D, Biamonti G, Garbelli M, Lossani A, Gasparrini F, Tuccinardi T, Laurenzana I, Angelucci A, Maga G, Schenone S, Brullo C, Musumeci F, Desogus A, Crespan E, Botta M. Studies on the ATP Binding Site of Fyn Kinase for the Identification of New Inhibitors and Their Evaluation as Potential Agents against Tauopathies and Tumors. J Med Chem 2015; 58:4590-609. [PMID: 25923950 DOI: 10.1021/acs.jmedchem.5b00140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fyn is a member of the Src-family of nonreceptor protein-tyrosine kinases. Its abnormal activity has been shown to be related to various human cancers as well as to severe pathologies, such as Alzheimer's and Parkinson's diseases. Herein, a structure-based drug design protocol was employed aimed at identifying novel Fyn inhibitors. Two hits from commercial sources (1, 2) were found active against Fyn with K(i) of about 2 μM, while derivative 4a, derived from our internal library, showed a K(i) of 0.9 μM. A hit-to-lead optimization effort was then initiated on derivative 4a to improve its potency. Slightly modifications rapidly determine an increase in the binding affinity, with the best inhibitors 4c and 4d having K(i)s of 70 and 95 nM, respectively. Both compounds were found able to inhibit the phosphorylation of the protein Tau in an Alzheimer's model cell line and showed antiproliferative activities against different cancer cell lines.
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Affiliation(s)
- Cristina Tintori
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Giuseppina La Sala
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Giulia Vignaroli
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorenzo Botta
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Anna Lucia Fallacara
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy.,‡Dipartimento di Chimica e Tecnologie del Farmaco, Università La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Federico Falchi
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Marco Radi
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Claudio Zamperini
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Elena Dreassi
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lucia Dello Iacono
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Donata Orioli
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giuseppe Biamonti
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Mirko Garbelli
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Andrea Lossani
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Francesca Gasparrini
- ‡Dipartimento di Chimica e Tecnologie del Farmaco, Università La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy.,∥Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Tiziano Tuccinardi
- ⊥Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Ilaria Laurenzana
- #Laboratory of Preclinical and Translational Research, IRCCS-Centro di Riferimento Oncologico Basilicata (CROB), Via Padre Pio 1, Rionero in Vulture 85028 Potenza Italy
| | - Adriano Angelucci
- ∇Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università dell'Aquila, Via Vetoio, 67100 Coppito, L'Aquila, Italy
| | - Giovanni Maga
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Silvia Schenone
- ○Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Chiara Brullo
- ○Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Francesca Musumeci
- ○Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Andrea Desogus
- ○Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, I-16132 Genova, Italy
| | - Emmanuele Crespan
- §Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Maurizio Botta
- †Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. De Gasperi 2, I-53100 Siena, Italy.,◆Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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48
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Maga G, Cucuzza S, Bavagnoli L. The Different Substrate Specificities Of Human Influenza Virus PA And PA‐X Endonucleases Support Distinct Roles In The Viral Life Cycle. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.lb157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Giovanni Maga
- DNA Enzymology&Molecular Virology Institute of Molecular Genetics IGM‐CNRPaviaItaly
| | - Stefano Cucuzza
- DNA Enzymology&Molecular Virology Institute of Molecular Genetics IGM‐CNRPaviaItaly
| | - Laura Bavagnoli
- DNA Enzymology&Molecular Virology Institute of Molecular Genetics IGM‐CNRPaviaItaly
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49
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Gemma S, Brogi S, Novellino E, Campiani G, Maga G, Brindisi M, Butini S. HCV-targeted antivirals: current status and future challenges. Curr Pharm Des 2015; 20:3445-64. [PMID: 24001232 DOI: 10.2174/13816128113199990630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022]
Abstract
Hepatitis C virus (HCV) is the major etiological agent of human non-A and non-B hepatitis, affecting more than 170 million people worldwide. While the current standard of care for the treatment of HCV infection is ribavirin in combination with interferon-α (IFN-α), this therapeutic regimen presents several drawbacks, mainly related to important and serious side effects, to resistance issues, and to the lack of efficacy for the treatment of specific viral genotypes. In 2011, the FDA approved two HCV-targeted antivirals, namely boceprevir and telaprevir. These two drugs inhibit the protease activity of the viral enzyme NS3/4A, and in Phase III clinical trials proved to be effective in achieving sustained virological response rate up to 75%. However, problems associated with these therapeutic regimens still exist and need to be addressed. Intense research efforts in the field are aimed at discovering small-molecule inhibitors of HCV enzymes and proteins such as NS5B and NS5A and at developing NS3 protease inhibitors active against resistant viruses expressing mutated NS3 protease. The most recent advances for the rational drug design of such inhibitors are here reviewed.
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Affiliation(s)
| | | | | | | | | | | | - Stefania Butini
- European Research Centre for Drug Discovery and Development (NatSynDrugs), Università di Siena, via Aldo Moro 2, 53100, Siena (Italy).
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50
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Crespan E, Hübscher U, Maga G. Expansion of CAG triplet repeats by human DNA polymerases λ and β in vitro, is regulated by flap endonuclease 1 and DNA ligase 1. DNA Repair (Amst) 2015; 29:101-11. [PMID: 25687118 DOI: 10.1016/j.dnarep.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 11/20/2022]
Abstract
Huntington's disease (HD) is a neurological genetic disorder caused by the expansion of the CAG trinucleotide repeats (TNR) in the N-terminal region of coding sequence of the Huntingtin's (HTT) gene. This results in the addition of a poly-glutamine tract within the Huntingtin protein, resulting in its pathological form. The mechanism by which TRN expansion takes place is not yet fully understood. We have recently shown that DNA polymerase (Pol) β can promote the microhomology-mediated end joining and triplet expansion of a substrate mimicking a double strand break in the TNR region of the HTT gene. Here we show that TNR expansion is dependent on the structure of the DNA substrate, as well as on the two essential Pol β co-factors: flap endonuclease 1 (Fen1) and DNA ligase 1 (Lig1). We found that Fen1 significantly stimulated TNR expansion by Pol β, but not by the related enzyme Pol λ, and subsequent ligation of the DNA products by Lig1. Interestingly, the deletion of N-terminal domains of Pol λ, resulted in an enzyme which displayed properties more similar to Pol β, suggesting a possible evolutionary mechanism. These results may suggest a novel mechanism for somatic TNR expansion in HD.
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Affiliation(s)
- Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, Pavia I-27100, Italy.
| | - Ulrich Hübscher
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Zürich CH-8057, Switzerland
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR, via Abbiategrasso 207, Pavia I-27100, Italy
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