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Article ; Online: Interaction of SARS-CoV-2 Nucleocapsid Protein and Human RNA Helicases DDX1 and DDX3X Modulates Their Activities on Double-Stranded RNA

Camilla Lodola / Massimiliano Secchi / Virginia Sinigiani / Antonella De Palma / Rossana Rossi / Davide Perico / Pier Luigi Mauri / Giovanni Maga

International Journal of Molecular Sciences, Vol 24, Iss 5784, p

2023 Volume 5784

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 ... ...

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.
Keywords	SARS-CoV-2 ; dead-box RNA helicase ; RNA binding ; nucleocapsid ; DDX3X ; DDX1 ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors

Flavia Squeglia / Maria Romano / Alessia Ruggiero / Giovanni Maga / Rita Berisio

Frontiers in Chemistry, Vol

A Structural Overview of Their Hijacking Through Multiple Viral Proteins

2020 Volume 8

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- ... ...

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.
Keywords	SARS-CoV-2 ; COVID19 ; protein structure ; viral infection ; DDX helicases ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: A Structural View of SARS-CoV-2 RNA Replication Machinery

Maria Romano / Alessia Ruggiero / Flavia Squeglia / Giovanni Maga / Rita Berisio

Cells ; Volume 9 ; Issue 5

RNA Synthesis, Proofreading and Final Capping

2020

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 ... ...

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.
Keywords	SARS-CoV-2 ; COVID19 ; RNA replication ; protein structure ; infectious disease ; covid19
Language	English
Publishing date	2020-05-20
Publisher	Multidisciplinary Digital Publishing Institute
Publishing country	ch
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Novel Insights into the Biochemical Mechanism of CK1ε and its Functional Interplay with DDX3X

Bartolo Bono / Giulia Franco / Valentina Riva / Anna Garbelli / Giovanni Maga

International Journal of Molecular Sciences, Vol 21, Iss 6449, p

2020 Volume 6449

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 ... ...

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 Km ATP , 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.
Keywords	protein kinase ; CK1ε ; DDX3X ; ATP ; kinetic analysis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Structural View of SARS-CoV-2 RNA Replication Machinery

Maria Romano / Alessia Ruggiero / Flavia Squeglia / Giovanni Maga / Rita Berisio

Cells, Vol 9, Iss 1267, p

RNA Synthesis, Proofreading and Final Capping

2020 Volume 1267

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.
Keywords	SARS-CoV-2 ; COVID19 ; RNA replication ; protein structure ; infectious disease ; Biology (General) ; QH301-705.5 ; covid19
Subject code	612
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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

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

International Journal of Molecular Sciences, Vol 22, Iss 5201, p

2021 Volume 5201

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.
Keywords	RNaseH2 ; misincorporated ribonucleotides ; RER ; non-B DNA ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: DNA Polymerases λ and β

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

Genes, Vol 7, Iss 9, p

The Double-Edged Swords of DNA Repair

2016 Volume 57

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.
Keywords	DNA polymerases ; DNA repair ; translesion synthesis ; cancer chemotherapy ; mutagenesis ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q
Subject code	612
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exploiting the Nucleotide Substrate Specificity of Repair DNA Polymerases To Develop Novel Anticancer Agents

Giovanni Maga / Alessandra Amoroso / Anna Garbelli / Emmanuele Crespan

Molecules, Vol 16, Iss 9, Pp 7994-

2011 Volume 8019

Abstract: The genome is constantly exposed to mutations that can originate during replication or as a result of the action of both endogenous and/or exogenous damaging agents [such as reactive oxygen species (ROS), UV light, genotoxic environmental compounds, etc.] ...

Abstract	The genome is constantly exposed to mutations that can originate during replication or as a result of the action of both endogenous and/or exogenous damaging agents [such as reactive oxygen species (ROS), UV light, genotoxic environmental compounds, etc.]. Cells have developed a set of specialized mechanisms to counteract this mutational burden. Many cancer cells have defects in one or more DNA repair pathways, hence they rely on a narrower set of specialized DNA repair mechanisms than normal cells. Inhibiting one of these pathways in the context of an already DNA repair-deficient genetic background, will be more toxic to cancer cells than to normal cells, a concept recently exploited in cancer chemotherapy by the synthetic lethality approach. Essential to all DNA repair pathways are the DNA pols. Thus, these enzymes are being regarded as attractive targets for the development of specific inhibitors of DNA repair in cancer cells. In this review we examine the current state-of-the-art in the development of nucleotide analogs as inhibitors of repair DNA polymerases.
Keywords	DNA repair ; cancer ; DNA polymerase ; nucleoside analogs ; Organic chemistry ; QD241-441
Subject code	612
Language	English
Publishing date	2011-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Synthesis and antiviral activity of anthracene derivatives of isoxazolino-carbocyclic nucleoside analogues

Memeo, Misal Giuseppe / Francesco Lapolla / Giovanni Maga / Paolo Quadrelli

Tetrahedron letters. 2015 Apr. 08, v. 56, no. 15

2015

Abstract: Isoxazolino-carbocyclic anthracene nor-nucleosides were prepared through nitrosocarbonyl chemistry and tested for their inhibitory activity against some viruses, such as Herpes simplex viruses of type 1 and 2, Zoster virus and Hepatitis B and C. The ... ...

Abstract	Isoxazolino-carbocyclic anthracene nor-nucleosides were prepared through nitrosocarbonyl chemistry and tested for their inhibitory activity against some viruses, such as Herpes simplex viruses of type 1 and 2, Zoster virus and Hepatitis B and C. The activities were almost negligible in most of the cases. A remarkable antiviral activity was found for a specific regioisomer with no cellular toxicity at 1–100μM dose concentration in the case of Human Papilloma virus.
Keywords	anthracenes ; antiviral properties ; chemical reactions ; cytotoxicity ; hepatitis B ; herpes simplex ; nucleosides ; Papillomaviridae ; positional isomers ; viruses
Language	English
Dates of publication	2015-0408
Size	p. 1986-1990.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204287-3
ISSN	1873-3581 ; 0040-4039
ISSN (online)	1873-3581
ISSN	0040-4039
DOI	10.1016/j.tetlet.2015.02.114
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Synthesis and Antiviral Activity of Novel 1,3,4-Thiadiazole Inhibitors of DDX3X

Annalaura Brai / Stefania Ronzini / Valentina Riva / Lorenzo Botta / Claudio Zamperini / Matteo Borgini / Claudia Immacolata Trivisani / Anna Garbelli / Carla Pennisi / Adele Boccuto / Francesco Saladini / Maurizio Zazzi / Giovanni Maga / Maurizio Botta

Molecules, Vol 24, Iss 21, p

2019 Volume 3988

Abstract: The human ATPase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3X) emerged as a novel therapeutic target in the fight against both infectious diseases and cancer. Herein, a new family of DDX3X inhibitors was designed, synthesized, and tested for its ... ...

Abstract	The human ATPase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3X) emerged as a novel therapeutic target in the fight against both infectious diseases and cancer. Herein, a new family of DDX3X inhibitors was designed, synthesized, and tested for its inhibitory action on the ATPase activity of the enzyme. The potential use of the most promising derivatives it has been investigated by evaluating their anti-HIV-1 effects, revealing inhibitory activities in the low micromolar range. A preliminary ADME analysis demonstrated high metabolic stability and good aqueous solubility. The promising biological profile, together with the suitable in vitro pharmacokinetic properties, make these novel compounds a very good starting point for further development.
Keywords	ddx3x ; hiv-1 ; host proteins ; antivirals ; Organic chemistry ; QD241-441
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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