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Article ; Online: High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures.

Dede, Maria / Napolitano, Silvia / Melati, Anna / Pirota, Valentina / Maga, Giovanni / Crespan, Emmanuele

International journal of molecular sciences

2021 Volume 22, Issue 10

Abstract: Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA ... ...

Abstract	Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi-Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences.
MeSH term(s)	Catalysis ; DNA/chemistry ; DNA Replication ; Humans ; Ribonuclease H/chemistry ; Ribonuclease H/metabolism ; Ribonucleotides/chemistry
Chemical Substances	Ribonucleotides ; DNA (9007-49-2) ; Ribonuclease H (EC 3.1.26.4)
Language	English
Publishing date	2021-05-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22105201
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Article ; Online: Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes.

Pirota, Valentina / Lunghi, Enrico / Benassi, Alessandra / Crespan, Emmanuele / Freccero, Mauro / Doria, Filippo

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 16

Abstract: G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against ... ...

Abstract	G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavage and/or modification of G4s by functional-NDIs. This is the case of
MeSH term(s)	Binding Sites ; Coordination Complexes/chemistry ; Copper/chemistry ; DEET/chemistry ; G-Quadruplexes ; Imides/chemistry ; Ligands ; Naphthalenes/chemistry ; Oxidation-Reduction ; Polyethylene Glycols/chemistry ; Structure-Activity Relationship
Chemical Substances	Coordination Complexes ; Imides ; Ligands ; Naphthalenes ; DEET (134-62-3) ; naphthalene (2166IN72UN) ; naphthalenediimide (22291-04-9) ; Polyethylene Glycols (3WJQ0SDW1A) ; Copper (789U1901C5)
Language	English
Publishing date	2021-08-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26165025
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Article ; Online: How to win the HIV-1 drug resistance hurdle race: running faster or jumping higher?

Garbelli, Anna / Riva, Valentina / Crespan, Emmanuele / Maga, Giovanni

The Biochemical journal

2017 Volume 474, Issue 10, Page(s) 1559–1577

Abstract: Infections by the human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), are still totaling an appalling 36.7 millions worldwide, with 1.1 million AIDS deaths/year and a similar number of yearly ...

Abstract	Infections by the human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), are still totaling an appalling 36.7 millions worldwide, with 1.1 million AIDS deaths/year and a similar number of yearly new infections. All this, in spite of the discovery of HIV-1 as the AIDS etiological agent more than 30 years ago and the introduction of an effective combinatorial antiretroviral therapy (cART), able to control disease progression, more than 20 years ago. Although very effective, current cART is plagued by the emergence of drug-resistant viral variants and most of the efforts in the development of novel direct-acting antiviral agents (DAAs) against HIV-1 have been devoted toward the fighting of resistance. In this review, rather than providing a detailed listing of all the drugs and the corresponding resistance mutations, we aim, through relevant examples, at presenting to the general reader the conceptual shift in the approaches that are being taken to overcome the viral resistance hurdle. From the classic 'running faster' strategy, based on the development of novel DAAs active against the mutant viruses selected by the previous drugs and/or presenting to the virus a high genetic barrier toward the development of resilience, to a 'jumping higher' approach, which looks at the cell, rather than the virus, as a source of valuable drug targets, in order to make the cellular environment non-permissive toward the replication of both wild-type and mutated viruses.
MeSH term(s)	Animals ; Anti-HIV Agents/adverse effects ; Anti-HIV Agents/chemistry ; Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Antiretroviral Therapy, Highly Active/adverse effects ; CCR5 Receptor Antagonists/chemistry ; CCR5 Receptor Antagonists/pharmacology ; CCR5 Receptor Antagonists/therapeutic use ; DEAD-box RNA Helicases/antagonists & inhibitors ; DEAD-box RNA Helicases/chemistry ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Drug Design ; Drug Resistance, Multiple, Viral ; Drug Therapy, Combination/adverse effects ; HIV Infections/drug therapy ; HIV Infections/metabolism ; HIV Infections/virology ; HIV Protease Inhibitors/adverse effects ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; HIV Protease Inhibitors/therapeutic use ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/growth & development ; HIV-1/physiology ; Host-Pathogen Interactions/drug effects ; Human Immunodeficiency Virus Proteins/antagonists & inhibitors ; Human Immunodeficiency Virus Proteins/chemistry ; Human Immunodeficiency Virus Proteins/genetics ; Human Immunodeficiency Virus Proteins/metabolism ; Humans ; Models, Biological ; Molecular Structure ; Molecular Targeted Therapy ; Mutation ; Protein Conformation ; Reverse Transcriptase Inhibitors/chemistry ; Reverse Transcriptase Inhibitors/pharmacology ; Reverse Transcriptase Inhibitors/therapeutic use ; Virus Physiological Phenomena/drug effects ; Virus Replication/drug effects
Chemical Substances	Anti-HIV Agents ; CCR5 Receptor Antagonists ; HIV Protease Inhibitors ; Human Immunodeficiency Virus Proteins ; Reverse Transcriptase Inhibitors ; DDX3X protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2017-04-26
Publishing country	England
Document type	Comparative Study ; Journal Article ; Review
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20160772
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Article: Identification and Biological Characterization of the Pyrazolo[3,4-

Contadini, Claudia / Cirotti, Claudia / Carbone, Anna / Norouzi, Mehrdad / Cianciusi, Annarita / Crespan, Emmanuele / Perini, Cecilia / Maga, Giovanni / Barilà, Daniela / Musumeci, Francesca / Schenone, Silvia

Pharmaceuticals (Basel, Switzerland)

2023 Volume 16, Issue 7

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 ... ...

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
Language	English
Publishing date	2023-07-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16070958
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Article: Biological Evaluation and In Vitro Characterization of ADME Profile of In-House Pyrazolo[3,4-

Poggialini, Federica / Vagaggini, Chiara / Brai, Annalaura / Pasqualini, Claudia / Crespan, Emmanuele / Maga, Giovanni / Perini, Cecilia / Cabella, Noemi / Botta, Lorenzo / Musumeci, Francesca / Frosini, Maria / Schenone, Silvia / Dreassi, Elena

Pharmaceutics

2023 Volume 15, Issue 2

Abstract: The therapeutic use of tyrosine kinase inhibitors (TKIs) represents one of the successful strategies for the treatment of glioblastoma (GBM). Pyrazolo[3,4- ...

Abstract	The therapeutic use of tyrosine kinase inhibitors (TKIs) represents one of the successful strategies for the treatment of glioblastoma (GBM). Pyrazolo[3,4-
Language	English
Publishing date	2023-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics15020453
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Article ; Online: The human tyrosine kinase Kit and its gatekeeper mutant T670I, show different kinetic properties: Implications for drug design.

Kissova, Miroslava / Maga, Giovanni / Crespan, Emmanuele

Bioorganic & medicinal chemistry

2016 Volume 24, Issue 19, Page(s) 4555–4562

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 ... ...

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.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Drug Design ; Gastrointestinal Stromal Tumors/drug therapy ; Gastrointestinal Stromal Tumors/enzymology ; Gastrointestinal Stromal Tumors/genetics ; Humans ; Kinetics ; Peptides/metabolism ; Point Mutation ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins c-kit/antagonists & inhibitors ; Proto-Oncogene Proteins c-kit/genetics ; Proto-Oncogene Proteins c-kit/metabolism ; Substrate Specificity
Chemical Substances	Peptides ; Protein Kinase Inhibitors ; Adenosine Triphosphate (8L70Q75FXE) ; Proto-Oncogene Proteins c-kit (EC 2.7.10.1)
Language	English
Publishing date	2016-10-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2016.07.059
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Zs.A 3815: Show issues

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Article ; Online: Towards Innovative Antibacterial Correctors for Cystic Fibrosis Targeting the Lung Microbiome with a Multifunctional Effect.

Martina, Maria Grazia / Sannio, Filomena / Crespan, Emmanuele / Pavone, Marialaura / Simoncini, Alice / Barbieri, Francesca / Perini, Cecilia / Pesce, Emanuela / Maga, Giovanni / Pedemonte, Nicoletta / Docquier, Jean-Denis / Radi, Marco

ChemMedChem

2022 Volume 17, Issue 17, Page(s) e202200277

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 ... ...

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.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Humans ; Lung ; Microbiota ; Mutation
Chemical Substances	Anti-Bacterial Agents ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6)
Language	English
Publishing date	2022-06-23
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2218496-X
ISSN	1860-7187 ; 1860-7179
ISSN (online)	1860-7187
ISSN	1860-7179
DOI	10.1002/cmdc.202200277
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Article ; Online: Synthesis and biological activity evaluation of 3-(hetero) arylideneindolin-2-ones as potential c-Src inhibitors.

Princiotto, Salvatore / Musso, Loana / Manetti, Fabrizio / Marcellini, Valentina / Maga, Giovanni / Crespan, Emmanuele / Perini, Cecilia / Zaffaroni, Nadia / Beretta, Giovanni Luca / Dallavalle, Sabrina

Journal of enzyme inhibition and medicinal chemistry

2022 Volume 37, Issue 1, Page(s) 2382–2394

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 ... ...

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
MeSH term(s)	Antineoplastic Agents/chemistry ; Molecular Docking Simulation ; Oxindoles ; Protein Kinase Inhibitors ; Protein-Tyrosine Kinases ; Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; Oxindoles ; Protein Kinase Inhibitors ; Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2022-09-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2082578-X
ISSN	1475-6374 ; 1475-6366
ISSN (online)	1475-6374
ISSN	1475-6366
DOI	10.1080/14756366.2022.2117317
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Zs.A 3004: Show issues

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Article ; Online: Expansion of CAG triplet repeats by human DNA polymerases λ and β in vitro, is regulated by flap endonuclease 1 and DNA ligase 1.

Crespan, Emmanuele / Hübscher, Ulrich / Maga, Giovanni

DNA repair

2015 Volume 29, Page(s) 101–111

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 ...

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.
MeSH term(s)	DNA/metabolism ; DNA Ligase ATP ; DNA Ligases/metabolism ; DNA Polymerase beta/metabolism ; DNA Replication ; Flap Endonucleases/metabolism ; Humans ; Trinucleotide Repeat Expansion
Chemical Substances	LIG1 protein, human ; DNA (9007-49-2) ; DNA Polymerase beta (EC 2.7.7.-) ; DNA polymerase beta2 (EC 2.7.7.-) ; Flap Endonucleases (EC 3.1.-) ; FEN1 protein, human (EC 3.1.11.-) ; DNA Ligases (EC 6.5.1.-) ; DNA Ligase ATP (EC 6.5.1.1)
Language	English
Publishing date	2015-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2015.01.005
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Article: DNA Polymerases λ and β: The Double-Edged Swords of DNA Repair.

Mentegari, Elisa / Kissova, Miroslava / Bavagnoli, Laura / Maga, Giovanni / Crespan, Emmanuele

Genes

2016 Volume 7, Issue 9

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 ...

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.
Language	English
Publishing date	2016-08-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes7090057
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