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  1. Article ; Online: In Silico Design of New Dual Inhibitors of SARS-CoV-2 M

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

    International journal of molecular sciences

    2023  Volume 24, Issue 9

    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
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; COVID-19 ; Antiviral Agents/chemistry ; Ligands ; Protease Inhibitors/chemistry ; Molecular Docking Simulation ; Molecular Dynamics Simulation
    Chemical Substances Antiviral Agents ; Ligands ; Protease Inhibitors
    Language English
    Publishing date 2023-05-06
    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/ijms24098377
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Correction to "Design and Synthesis of Novel Thieno[3,2-

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

    ACS omega

    2023  Volume 8, Issue 50, Page(s) 48582

    Abstract: This corrects the article DOI: 10.1021/acsomega.3c03578.]. ...

    Abstract [This corrects the article DOI: 10.1021/acsomega.3c03578.].
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Published Erratum
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c08743
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Design of antitumor drugs targeting c-kit receptor by a new mixed ligand-structure based method.

    Martorana, Annamaria / Lauria, Antonino

    Journal of molecular graphics & modelling

    2020  Volume 100, Page(s) 107666

    Abstract: An important challenge, in the medicinal chemistry field, is the research of novel forceful drugs to overcome tumor-acquired resistance. The c-Kit tyrosine kinase receptor (TKR) represents a suitable target for the carcinogenesis control of gastro- ... ...

    Abstract An important challenge, in the medicinal chemistry field, is the research of novel forceful drugs to overcome tumor-acquired resistance. The c-Kit tyrosine kinase receptor (TKR) represents a suitable target for the carcinogenesis control of gastro-intestinal stromal (GIST), leukemia, and mastocytosis tumors; nevertheless, several hotspot mutations of the protein limit the efficacy of a few clinical administered TKRs inhibitors. In this study, a new in silico protocol based on ligand and structure-based combined method is proposed, with the aim to identify a set of new c-Kit inhibitors able to complex c-Kit mutated proteins. A recent and freely available web-server DRUDIT is used for the ligand-based method. The protocol application allows for identifying a new generation of potential TKR inhibitors, which, in silico, complex the V654A and T670I mutated proteins and potentially overcome resistant mutations (D816H). The structure-based analysis is performed by Induced Fit Docking (IFD) studies. The comparison between the explored ligands and well-known drugs highlights the possibility to overcome tumor-acquired resistance. The best-selected structures (630705 and SML1348) provide valuable binding affinities with the mutated c-Kit forms (respectively T670I and V654A).
    MeSH term(s) Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Drug Resistance, Neoplasm ; Gastrointestinal Stromal Tumors/drug therapy ; Humans ; Ligands ; Mutation ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use ; Proto-Oncogene Proteins c-kit/genetics
    Chemical Substances Antineoplastic Agents ; Ligands ; Protein Kinase Inhibitors ; Proto-Oncogene Proteins c-kit (EC 2.7.10.1)
    Language English
    Publishing date 2020-07-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2020.107666
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3491: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives.

    La Monica, Gabriele / Bono, Alessia / Lauria, Antonino / Martorana, Annamaria

    Journal of medicinal chemistry

    2022  Volume 65, Issue 19, Page(s) 12500–12534

    Abstract: The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the ... ...

    Abstract The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Coronavirus 3C Proteases ; Cysteine ; Cysteine Endopeptidases/metabolism ; Humans ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; SARS-CoV-2 ; Structure-Activity Relationship ; Viral Nonstructural Proteins ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Protease Inhibitors ; Viral Nonstructural Proteins ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.2c01005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 151: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MB 1: Show issues

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  5. Article ; Online: Design and Synthesis of Novel Thieno[3,2-

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

    ACS omega

    2023  Volume 8, Issue 38, Page(s) 34640–34649

    Abstract: RET kinase gain-of-function mutations represent the main cause of the high aggressiveness and invasiveness of medullary thyroid cancer (MTC). The selective inhibition of the RET kinase is a suitable strategy for the treatment of this endocrine neoplasia. ...

    Abstract RET kinase gain-of-function mutations represent the main cause of the high aggressiveness and invasiveness of medullary thyroid cancer (MTC). The selective inhibition of the RET kinase is a suitable strategy for the treatment of this endocrine neoplasia. Herein, we performed an innovative ligand-based virtual screening protocol using the DRUDIT
    Language English
    Publishing date 2023-09-11
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c03578
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. 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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  7. 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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  8. Article ; Online: In Silico Mixed Ligand/Structure-Based Design of New CDK-1/PARP-1 Dual Inhibitors as Anti-Breast Cancer Agents.

    Bono, Alessia / La Monica, Gabriele / Alamia, Federica / Mingoia, Francesco / Gentile, Carla / Peri, Daniele / Lauria, Antonino / Martorana, Annamaria

    International journal of molecular sciences

    2023  Volume 24, Issue 18

    Abstract: CDK-1 and PARP-1 play crucial roles in breast cancer progression. Compounds acting as CDK-1 and/or PARP-1 inhibitors can induct cell death in breast cancer with a selective synthetic lethality mechanism. A mixed treatment by means of CDK-1 and PARP-1 ... ...

    Abstract CDK-1 and PARP-1 play crucial roles in breast cancer progression. Compounds acting as CDK-1 and/or PARP-1 inhibitors can induct cell death in breast cancer with a selective synthetic lethality mechanism. A mixed treatment by means of CDK-1 and PARP-1 inhibitors resulted in radical breast cancer cell growth reduction. Inhibitors with a dual target mechanism of action could arrest cancer progression by simultaneously blocking the DNA repair mechanism and cell cycle, resulting in advantageous monotherapy. To this aim, in the present work, we identified compound
    MeSH term(s) Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Ligands ; Antineoplastic Agents/pharmacology ; Mammaplasty ; Cell Cycle ; Neoplasms
    Chemical Substances Poly(ADP-ribose) Polymerase Inhibitors ; Ligands ; Antineoplastic Agents
    Language English
    Publishing date 2023-09-06
    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/ijms241813769
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: In Silico Insights into the SARS CoV-2 Main Protease Suggest NADH Endogenous Defences in the Control of the Pandemic Coronavirus Infection.

    Martorana, Annamaria / Gentile, Carla / Lauria, Antonino

    Viruses

    2020  Volume 12, Issue 8

    Abstract: COVID-19 is a pandemic health emergency faced by the entire world. The clinical treatment of the severe acute respiratory syndrome (SARS) CoV-2 is currently based on the experimental administration of HIV antiviral drugs, such as lopinavir, ritonavir, ... ...

    Abstract COVID-19 is a pandemic health emergency faced by the entire world. The clinical treatment of the severe acute respiratory syndrome (SARS) CoV-2 is currently based on the experimental administration of HIV antiviral drugs, such as lopinavir, ritonavir, and remdesivir (a nucleotide analogue used for Ebola infection). This work proposes a repurposing process using a database containing approximately 8000 known drugs in synergy structure- and ligand-based studies by means of the molecular docking and descriptor-based protocol. The proposed in silico findings identified new potential SARS CoV-2 main protease (M
    MeSH term(s) Aging/metabolism ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Binding Sites ; Computer Simulation ; Coronavirus Infections/drug therapy ; Coronavirus Infections/metabolism ; Coronavirus Infections/virology ; Cysteine Endopeptidases/chemistry ; DNA Damage ; Drug Repositioning ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; Humans ; Models, Molecular ; Molecular Docking Simulation ; NAD/metabolism ; Oxidation-Reduction ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/virology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry
    Chemical Substances Antiviral Agents ; HIV Protease Inhibitors ; Protease Inhibitors ; Viral Nonstructural Proteins ; NAD (0U46U6E8UK) ; 3C-like proteinase, Coronavirus (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-)
    Keywords covid19
    Language English
    Publishing date 2020-07-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v12080805
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors.

    La Monica, Gabriele / Lauria, Antonino / Bono, Alessia / Martorana, Annamaria

    International journal of molecular sciences

    2021  Volume 22, Issue 11

    Abstract: The approval of the first HIV-1 protease inhibitors (HIV-1 PRIs) marked a fundamental step in the control of AIDS, and this class of agents still represents the mainstay therapy for this illness. Despite the undisputed benefits, the necessary lifelong ... ...

    Abstract The approval of the first HIV-1 protease inhibitors (HIV-1 PRIs) marked a fundamental step in the control of AIDS, and this class of agents still represents the mainstay therapy for this illness. Despite the undisputed benefits, the necessary lifelong treatment led to numerous severe side-effects (metabolic syndrome, hepatotoxicity, diabetes, etc.). The HIV-1 PRIs are capable of interacting with "secondary" targets (off-targets) characterized by different biological activities from that of HIV-1 protease. In this scenario, the in-silico techniques undoubtedly contributed to the design of new small molecules with well-fitting selectivity against the main target, analyzing possible undesirable interactions that are already in the early stages of the research process. The present work is focused on a new mixed-hierarchical, ligand-structure-based protocol, which is centered on an on/off-target approach, to identify the new selective inhibitors of HIV-1 PR. The use of the well-established, ligand-based tools available in the DRUDIT web platform, in combination with a conventional, structure-based molecular docking process, permitted to fast screen a large database of active molecules and to select a set of structure with optimal on/off-target profiles. Therefore, the method exposed herein, could represent a reliable help in the research of new selective targeted small molecules, permitting to design new agents without undesirable interactions.
    MeSH term(s) Catalytic Domain ; Computer Simulation ; Drug Design ; Drug Discovery ; HIV Infections/drug therapy ; HIV Infections/enzymology ; HIV Infections/virology ; HIV Protease/chemistry ; HIV Protease Inhibitors/pharmacology ; HIV-1/drug effects ; HIV-1/enzymology ; Humans ; Ligands ; Molecular Docking Simulation ; Molecular Structure ; Protein Conformation ; Structure-Activity Relationship
    Chemical Substances HIV Protease Inhibitors ; Ligands ; HIV Protease (EC 3.4.23.-)
    Language English
    Publishing date 2021-06-04
    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/ijms22116070
    Database MEDical Literature Analysis and Retrieval System OnLINE

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