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  1. Article ; Online: Targeting G-quadruplexes to achieve antiviral activity.

    Ruggiero, Emanuela / Richter, Sara N

    Bioorganic & medicinal chemistry letters

    2022  Volume 79, Page(s) 129085

    Abstract: With the emergence of new viruses in the human population and the fast mutation rates of existing viruses, new antiviral targets and compounds are needed. Most existing antiviral drugs are active against proteins of a handful of viruses. Most of these ... ...

    Abstract With the emergence of new viruses in the human population and the fast mutation rates of existing viruses, new antiviral targets and compounds are needed. Most existing antiviral drugs are active against proteins of a handful of viruses. Most of these proteins in the end affect viral nucleic acid processing, but direct nucleic acid targeting is less represented due to the difficulty of selectively acting at the nucleic acid of interest. Recently, nucleic acids have been shown to fold in structures alternative to the classic double helix and Watson and Crick base-pairing. Among these non-canonical structures, G-quadruplexes (G4s) have attracted interest because of their key biological roles that are being discovered. Molecules able to selectively target G4s have been developed and since G4s have been investigated as targets in several human pathologies, including viral infections. Here, after briefly introducing viruses, G4s and the G4-binding molecules with antiviral properties, we comment on the mechanisms at the base of the antiviral activity reported for G4-binding molecules. Understanding how G4-ligands act in infected cells will possibly help designing and developing next-generation antiviral drugs.
    MeSH term(s) Humans ; Antiviral Agents/pharmacology ; G-Quadruplexes/drug effects ; Nucleic Acids/drug effects ; Nucleic Acids/metabolism
    Chemical Substances Antiviral Agents ; Nucleic Acids
    Language English
    Publishing date 2022-11-21
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1063195-1
    ISSN 1464-3405 ; 0960-894X
    ISSN (online) 1464-3405
    ISSN 0960-894X
    DOI 10.1016/j.bmcl.2022.129085
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Production of the anti-G-quadruplex antibody BG4 for efficient genome-wide analyses: From plasmid quality control to antibody validation.

    Maurizio, Ilaria / Tosoni, Beatrice / Gallina, Irene / Ruggiero, Emanuela / Zanin, Irene / Richter, Sara N

    Methods in enzymology

    2024  Volume 695, Page(s) 193–219

    Abstract: G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that can form at guanine-rich sequences of DNA and RNA in every kingdom of life. At the DNA level, G4s can form throughout genomes but they are prevalently found in promoter ... ...

    Abstract G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that can form at guanine-rich sequences of DNA and RNA in every kingdom of life. At the DNA level, G4s can form throughout genomes but they are prevalently found in promoter regions and at telomeres, and they have been attributed functions spanning from transcriptional regulation, to control of DNA replication, to maintenance of chromosome ends. Our understanding of the functions of G4s in cells has greatly improved with the development of specific anti-G4 antibodies, which allow the visualization of G4s by immunofluorescence but also the mapping of these secondary DNA structures genome wide. Whole genome identification of the location and abundance of G4s with techniques such as Chromatin Immunoprecipitation coupled with sequencing (ChIP-Seq) and Cleavage Under Target and Tagmentation (CUT&Tag) has allowed the profiling of G4 distribution across distinct cell types and deepen the understanding of G4 functions, particularly in the regulation of transcription. Crucial for these types of genome-wide studies is the availability of an anti-G4 antibody preparation with high affinity and specificity. Here, we describe a protocol for the expression and purification of the anti-DNA G4 structure antibody (BG4) first developed by the Balasubramanian group, which has been proven to selectively recognize G4 structures both in vitro and within cells, and which has great applicability in high-throughput techniques. We provide a detailed, step-by-step protocol to obtain active BG4 starting from a commercially available expression plasmid. We also describe three different approaches to validate the activity of the BG4 preparation.
    MeSH term(s) DNA/genetics ; DNA/chemistry ; Genome ; G-Quadruplexes ; DNA Replication ; Plasmids/genetics ; Antibodies
    Chemical Substances DNA (9007-49-2) ; Antibodies
    Language English
    Publishing date 2024-02-22
    Publishing country United States
    Document type Journal Article
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.11.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy.

    Ruggiero, Emanuela / Richter, Sara N

    Annual reports in medicinal chemistry

    2020  Volume 54, Page(s) 101–131

    Abstract: Viruses are the most abundant organisms on our planet, affecting all living beings: some of them are responsible for massive epidemics that concern health, national economies and the overall welfare of societies. Although advances in antiviral research ... ...

    Abstract Viruses are the most abundant organisms on our planet, affecting all living beings: some of them are responsible for massive epidemics that concern health, national economies and the overall welfare of societies. Although advances in antiviral research have led to successful therapies against several human viruses, still some of them cannot be eradicated from the host and most of them do not have any treatment available. Consequently, innovative antiviral therapies are urgently needed. In the past few years, research on G-quadruplexes (G4s) in viruses has boomed, providing powerful evidence for the regulatory role of G4s in key viral steps. Comprehensive bioinformatics analyses have traced putative G4-forming sequences in the genome of almost all human viruses, showing that their distribution is statistically significant and their presence highly conserved. Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. Recent studies have demonstrated the formation and function of G4s in pathogens responsible for serious diseases, such as HIV-1, Hepatitis B and C, Ebola viruses, to cite a few. In this chapter, we present the state of the art on the structural and functional characterization of viral G4s in RNA viruses, DNA viruses and retroviruses. We also present the G4 ligands that provide further details on the viral G4 role and which, showing promising antiviral activity, which could be exploited for the development of innovative antiviral agents.
    Keywords covid19
    Language English
    Publishing date 2020-05-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 207988-4
    ISSN 1557-8437 ; 0065-7743
    ISSN (online) 1557-8437
    ISSN 0065-7743
    DOI 10.1016/bs.armc.2020.04.001
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  4. Article ; Online: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy.

    Ruggiero, Emanuela / Richter, Sara N

    Nucleic acids research

    2018  Volume 46, Issue 7, Page(s) 3270–3283

    Abstract: G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in ... ...

    Abstract G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed.
    MeSH term(s) Antiviral Agents/therapeutic use ; Ebolavirus/genetics ; Ebolavirus/pathogenicity ; G-Quadruplexes ; Genome, Human/genetics ; Hemorrhagic Fever, Ebola/genetics ; Hemorrhagic Fever, Ebola/virology ; Humans ; Ligands ; Promoter Regions, Genetic/genetics ; Telomere/genetics ; Virus Latency/genetics ; Virus Replication/genetics ; Zika Virus/genetics ; Zika Virus/pathogenicity ; Zika Virus Infection/genetics ; Zika Virus Infection/virology
    Chemical Substances Antiviral Agents ; Ligands
    Keywords covid19
    Language English
    Publishing date 2018-03-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gky187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: G-Quadruplex Targeting in the Fight against Viruses: An Update.

    Ruggiero, Emanuela / Zanin, Irene / Terreri, Marianna / Richter, Sara N

    International journal of molecular sciences

    2021  Volume 22, Issue 20

    Abstract: G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in ...

    Abstract G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; COVID-19/virology ; DNA, Viral/chemistry ; DNA, Viral/metabolism ; G-Quadruplexes ; Humans ; Ligands ; MicroRNAs/antagonists & inhibitors ; MicroRNAs/metabolism ; RNA, Viral/chemistry ; RNA, Viral/metabolism ; SARS-CoV-2/isolation & purification ; Virus Diseases/drug therapy ; Virus Diseases/pathology
    Chemical Substances Antiviral Agents ; DNA, Viral ; Ligands ; MicroRNAs ; RNA, Viral
    Language English
    Publishing date 2021-10-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222010984
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  6. Article: Preclinical Application of Augmented Reality in Pediatric Craniofacial Surgery: An Accuracy Study.

    Ruggiero, Federica / Cercenelli, Laura / Emiliani, Nicolas / Badiali, Giovanni / Bevini, Mirko / Zucchelli, Mino / Marcelli, Emanuela / Tarsitano, Achille

    Journal of clinical medicine

    2023  Volume 12, Issue 7

    Abstract: Background: Augmented reality (AR) allows the overlapping and integration of virtual information with the real environment. The camera of the AR device reads the object and integrates the virtual data. It has been widely applied to medical and surgical ... ...

    Abstract Background: Augmented reality (AR) allows the overlapping and integration of virtual information with the real environment. The camera of the AR device reads the object and integrates the virtual data. It has been widely applied to medical and surgical sciences in recent years and has the potential to enhance intraoperative navigation.
    Materials and methods: In this study, the authors aim to assess the accuracy of AR guidance when using the commercial HoloLens 2 head-mounted display (HMD) in pediatric craniofacial surgery. The Authors selected fronto-orbital remodeling (FOR) as the procedure to test (specifically, frontal osteotomy and nasal osteotomy were considered). Six people (three surgeons and three engineers) were recruited to perform the osteotomies on a 3D printed stereolithographic model under the guidance of AR. By means of calibrated CAD/CAM cutting guides with different grooves, the authors measured the accuracy of the osteotomies that were performed. We tested accuracy levels of ±1.5 mm, ±1 mm, and ±0.5 mm.
    Results: With the HoloLens 2, the majority of the individuals involved were able to successfully trace the trajectories of the frontal and nasal osteotomies with an accuracy level of ±1.5 mm. Additionally, 80% were able to achieve an accuracy level of ±1 mm when performing a nasal osteotomy, and 52% were able to achieve an accuracy level of ±1 mm when performing a frontal osteotomy, while 61% were able to achieve an accuracy level of ±0.5 mm when performing a nasal osteotomy, and 33% were able to achieve an accuracy level of ±0.5 mm when performing a frontal osteotomy.
    Conclusions: despite this being an in vitro study, the authors reported encouraging results for the prospective use of AR on actual patients.
    Language English
    Publishing date 2023-04-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm12072693
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  7. Article ; Online: Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells.

    Zanin, Irene / Ruggiero, Emanuela / Nicoletto, Giulia / Lago, Sara / Maurizio, Ilaria / Gallina, Irene / Richter, Sara N

    Nucleic acids research

    2023  Volume 51, Issue 16, Page(s) 8309–8321

    Abstract: i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Their formation in cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs ... ...

    Abstract i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Their formation in cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped iMs in two human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters, in open chromatin regions, they overlap with R-loops, and their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs. By simultaneously mapping G-quadruplexes (G4s), which form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent regions; however, when both iMs and G4s are present in the same genomic tract, their formation is enhanced. iMs and G4s were mainly found at genes with low and high transcription rates, respectively. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.
    MeSH term(s) Humans ; Gene Expression Regulation ; G-Quadruplexes ; Regulatory Sequences, Nucleic Acid ; DNA/genetics ; DNA/chemistry ; Genomics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2023-08-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad626
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  8. Article ; Online: Unveiling CD59-Antibody Interactions to Design Paratope-Mimicking Peptides for Complement Modulation.

    Sandomenico, Annamaria / Ruggiero, Alessia / Iaccarino, Emanuela / Oliver, Angela / Squeglia, Flavia / Moreira, Miguel / Esposito, Luciana / Ruvo, Menotti / Berisio, Rita

    International journal of molecular sciences

    2023  Volume 24, Issue 10

    Abstract: CD59 is an abundant immuno-regulatory human protein that protects cells from damage by inhibiting the complement system. CD59 inhibits the assembly of the Membrane Attack Complex (MAC), the bactericidal pore-forming toxin of the innate immune system. In ... ...

    Abstract CD59 is an abundant immuno-regulatory human protein that protects cells from damage by inhibiting the complement system. CD59 inhibits the assembly of the Membrane Attack Complex (MAC), the bactericidal pore-forming toxin of the innate immune system. In addition, several pathogenic viruses, including HIV-1, escape complement-mediated virolysis by incorporating this complement inhibitor in their own viral envelope. This makes human pathogenic viruses, such as HIV-1, not neutralised by the complement in human fluids. CD59 is also overexpressed in several cancer cells to resist the complement attack. Consistent with its importance as a therapeutical target, CD59-targeting antibodies have been proven to be successful in hindering HIV-1 growth and counteracting the effect of complement inhibition by specific cancer cells. In this work, we make use of bioinformatics and computational tools to identify CD59 interactions with blocking antibodies and to describe molecular details of the paratope-epitope interface. Based on this information, we design and produce paratope-mimicking bicyclic peptides able to target CD59. Our results set the basis for the development of antibody-mimicking small molecules targeting CD59 with potential therapeutic interest as complement activators.
    MeSH term(s) Humans ; Binding Sites, Antibody ; Complement System Proteins/metabolism ; CD59 Antigens/metabolism ; Complement Membrane Attack Complex/metabolism ; Complement Inactivating Agents ; HIV-1/physiology
    Chemical Substances Complement System Proteins (9007-36-7) ; CD59 Antigens ; Complement Membrane Attack Complex ; Complement Inactivating Agents ; CD59 protein, human (101754-01-2)
    Language English
    Publishing date 2023-05-10
    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/ijms24108561
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  9. Article ; Online: G-Quadruplex Targeting in the Fight against Viruses

    Emanuela Ruggiero / Irene Zanin / Marianna Terreri / Sara N. Richter

    International Journal of Molecular Sciences, Vol 22, Iss 10984, p

    An Update

    2021  Volume 10984

    Abstract: G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in ...

    Abstract G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
    Keywords G-quadruplexes ; virus ; targeting ; G-quadruplex ligands ; antiviral therapy ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Preclinical Application of Augmented Reality in Pediatric Craniofacial Surgery

    Federica Ruggiero / Laura Cercenelli / Nicolas Emiliani / Giovanni Badiali / Mirko Bevini / Mino Zucchelli / Emanuela Marcelli / Achille Tarsitano

    Journal of Clinical Medicine, Vol 12, Iss 2693, p

    An Accuracy Study

    2023  Volume 2693

    Abstract: Background: Augmented reality (AR) allows the overlapping and integration of virtual information with the real environment. The camera of the AR device reads the object and integrates the virtual data. It has been widely applied to medical and surgical ... ...

    Abstract Background: Augmented reality (AR) allows the overlapping and integration of virtual information with the real environment. The camera of the AR device reads the object and integrates the virtual data. It has been widely applied to medical and surgical sciences in recent years and has the potential to enhance intraoperative navigation. Materials and methods: In this study, the authors aim to assess the accuracy of AR guidance when using the commercial HoloLens 2 head-mounted display (HMD) in pediatric craniofacial surgery. The Authors selected fronto-orbital remodeling (FOR) as the procedure to test (specifically, frontal osteotomy and nasal osteotomy were considered). Six people (three surgeons and three engineers) were recruited to perform the osteotomies on a 3D printed stereolithographic model under the guidance of AR. By means of calibrated CAD/CAM cutting guides with different grooves, the authors measured the accuracy of the osteotomies that were performed. We tested accuracy levels of ±1.5 mm, ±1 mm, and ±0.5 mm. Results: With the HoloLens 2, the majority of the individuals involved were able to successfully trace the trajectories of the frontal and nasal osteotomies with an accuracy level of ±1.5 mm. Additionally, 80% were able to achieve an accuracy level of ±1 mm when performing a nasal osteotomy, and 52% were able to achieve an accuracy level of ±1 mm when performing a frontal osteotomy, while 61% were able to achieve an accuracy level of ±0.5 mm when performing a nasal osteotomy, and 33% were able to achieve an accuracy level of ±0.5 mm when performing a frontal osteotomy. Conclusions: despite this being an in vitro study, the authors reported encouraging results for the prospective use of AR on actual patients.
    Keywords augmented reality ; craniofacial surgery ; head and neck surgery ; computer-assisted surgery ; Medicine ; R
    Subject code 690
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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