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  1. Article ; Online: In Silico Design of New Dual Inhibitors of SARS-CoV-2 M PRO through Ligand- and Structure-Based Methods

    Alessia Bono / Antonino Lauria / Gabriele La Monica / Federica Alamia / Francesco Mingoia / Annamaria Martorana

    International Journal of Molecular Sciences, Vol 24, Iss 8377, p

    2023  Volume 8377

    Abstract: The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating ... ...

    Abstract The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series’ of small molecules with a significant affinity for SARS-CoV-2 M PRO , by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The Biotarget Predictor Tool was used to filter a large in-house structural database and select a set of benzo[ b ]thiophene and benzo[ b ]furan derivatives. ADME properties were investigated, and induced fit docking studies were performed to confirm the DRUDIT prediction. Principal component analysis and docking protocol at the SARS-CoV-2 M PRO dimerization site enable the identification of compounds 1b , c , i , l and 2i , l as promising drug molecules, showing favorable dual binding site affinity on SARS-CoV-2 M PRO .
    Keywords catalytic site ; allosteric site ; SARS-CoV-2 M PRO ; inhibitors ; benzo[ b ]thiophene ; benzo[ b ]furan ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Correction to “Design and Synthesis of Novel Thieno[3,2‑c]quinoline Compounds with Antiproliferative Activity on RET-Dependent Medullary Thyroid Cancer Cells”

    Gabriele La Monica / Giuseppe Pizzolanti / Concetta Baiamonte / Alessia Bono / Federica Alamia / Francesco Mingoia / Antonino Lauria / Annamaria Martorana

    ACS Omega, Vol 8, Iss 50, Pp 48582-

    2023  Volume 48582

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA

    Simone Mulliri / Aatto Laaksonen / Pietro Spanu / Riccardo Farris / Matteo Farci / Francesco Mingoia / Giovanni N. Roviello / Francesca Mocci

    International Journal of Molecular Sciences, Vol 22, Iss 6028, p

    2021  Volume 6028

    Abstract: Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer ... ...

    Abstract Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2–4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (T m s). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the T m s, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.
    Keywords circular dichroism ; docking ; molecular dynamics ; c-myc ; DNA quadruplexes ; anticancer drugs ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 500
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Biochemical and biophysical characterization of water-soluble pectin from Opuntia ficus-indica and its potential cytotoxic activity

    Lefsih, Khalef / Daniela Giacomazza / Donatella Bulone / Francesco Mingoia / Khodir Madani / Maria Assunta Costa / Maria Rosalia Mangione / Pier Luigi San Biagio / Rosa Passantino / Valeria Guarrasi

    Phytochemistry. 2018 Oct., v. 154

    2018  

    Abstract: This work aims to fill the gap in the present knowledge about the structure of pectin from Opuntia ficus-indica. The water-soluble pectin (WSP) fraction, extracted with the Microwave Assisted Extraction (MAE), was further deproteinated (dWSP) and ... ...

    Abstract This work aims to fill the gap in the present knowledge about the structure of pectin from Opuntia ficus-indica. The water-soluble pectin (WSP) fraction, extracted with the Microwave Assisted Extraction (MAE), was further deproteinated (dWSP) and analyzed through several biophysical and biochemical techniques. HPSEC, light scattering and FTIR data showed that dWSP is low methylated high molecular weight pectin. The biochemical structure of dWSP, after methanolysis, silylation, carboxyl reduction showed that dWSP belongs to rhamnogalacturonan I class. Then, dWSP was heat-modified (HM) to obtain small-molecular weight deproteinated fraction (HM-dWSP). Both species, dWSP and HM-dWSP, were tested in LAN5 and NIH 3T3 model cells to study their biological effect. Results indicated that both dWSP and HM-dWSP exerted cytotoxic activity affecting selectively LAN5 cancer cells, without any effect on NIH 3T3 normal cells.
    Keywords cytotoxicity ; Fourier transform infrared spectroscopy ; light scattering ; methanolysis ; microwave treatment ; models ; molecular weight ; neoplasm cells ; Opuntia ficus-indica ; pectins ; silylation ; water solubility
    Language English
    Dates of publication 2018-10
    Size p. 47-55.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 208884-8
    ISSN 1873-3700 ; 0031-9422
    ISSN (online) 1873-3700
    ISSN 0031-9422
    DOI 10.1016/j.phytochem.2018.06.015
    Database NAL-Catalogue (AGRICOLA)

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