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  1. Article ; Online: Traceability of SARS-CoV-2 transmission through quasispecies analysis.

    Messali, Serena / Rondina, Alessandro / Giovanetti, Marta / Bonfanti, Carlo / Ciccozzi, Massimo / Caruso, Arnaldo / Caccuri, Francesca

    Journal of medical virology

    2023  Volume 95, Issue 6, Page(s) e28848

    Abstract: During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of ... ...

    Abstract During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of replicating and closely related viral variants so-called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS-CoV-2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19 ; Quasispecies ; Pandemics ; Genome, Viral
    Language English
    Publishing date 2023-06-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.28848
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Boron Delivery Antibody (BDA) with Boronated Specific Residues: New Perspectives in Boron Neutron Capture Therapy from an In Silico Investigation.

    Rondina, Alessandro / Fossa, Paola / Orro, Alessandro / Milanesi, Luciano / De Palma, Antonella / Perico, Davide / Mauri, Pier Luigi / D'Ursi, Pasqualina

    Cells

    2021  Volume 10, Issue 11

    Abstract: Boron Neutron Capture Therapy (BNCT) is a tumor cell-selective radiotherapy based on a nuclear reaction that occurs when the isotope boron-10 ( ...

    Abstract Boron Neutron Capture Therapy (BNCT) is a tumor cell-selective radiotherapy based on a nuclear reaction that occurs when the isotope boron-10 (
    MeSH term(s) Antibodies, Monoclonal/administration & dosage ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/genetics ; Boron/administration & dosage ; Boron Neutron Capture Therapy ; Boronic Acids/chemistry ; Computer Simulation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutation/genetics
    Chemical Substances Antibodies, Monoclonal ; Boronic Acids ; Boron (N9E3X5056Q)
    Language English
    Publishing date 2021-11-18
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells10113225
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing.

    Fossa, Paola / Uggeri, Matteo / Orro, Alessandro / Urbinati, Chiara / Rondina, Alessandro / Milanesi, Maria / Pedemonte, Nicoletta / Pesce, Emanuela / Padoan, Rita / Ford, Robert C / Meng, Xin / Rusnati, Marco / D'Ursi, Pasqualina

    International journal of molecular sciences

    2022  Volume 23, Issue 20

    Abstract: Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ... ...

    Abstract Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. Cystic fibrosis remains a potentially fatal disease, but it has become treatable as a chronic condition due to some CFTR-rescuing drugs that, when used in combination, increase in their therapeutic effect due to a synergic action. Also, dietary supplementation of natural compounds in combination with approved drugs could represent a promising strategy to further alleviate cystic fibrosis symptoms. On these bases, we screened by in silico drug repositioning 846 small synthetic or natural compounds from the AIFA database to evaluate their capacity to interact with the highly druggable lumacaftor binding site of F508del-CFTR. Among the identified hits, nicotinamide (NAM) was predicted to accommodate into the lumacaftor binding region of F508del-CFTR without competing against the drug but rather stabilizing its binding. The effective capacity of NAM to bind F508del-CFTR in a lumacaftor-uncompetitive manner was then validated experimentally by surface plasmon resonance analysis. Finally, the capacity of NAM to synergize with lumacaftor increasing its CFTR-rescuing activity was demonstrated in cell-based assays. This study suggests the possible identification of natural small molecules devoid of side effects and endowed with the capacity to synergize with drugs currently employed for the treatment of cystic fibrosis, which hopefully will increase the therapeutic efficacy with lower doses.
    MeSH term(s) Humans ; Cystic Fibrosis Transmembrane Conductance Regulator/metabolism ; Cystic Fibrosis/drug therapy ; Cystic Fibrosis/genetics ; Cystic Fibrosis/metabolism ; Drug Repositioning ; Proteasome Endopeptidase Complex/metabolism ; Benzodioxoles/pharmacology ; Benzodioxoles/therapeutic use ; Aminopyridines/pharmacology ; Aminopyridines/therapeutic use ; Niacinamide/therapeutic use ; Ubiquitins/metabolism ; Mutation
    Chemical Substances Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Benzodioxoles ; Aminopyridines ; Niacinamide (25X51I8RD4) ; Ubiquitins ; CFTR protein, human
    Language English
    Publishing date 2022-10-14
    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/ijms232012274
    Database MEDical Literature Analysis and Retrieval System OnLINE

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