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  1. Article: SARS-CoV spike proteins can compete for electrolytes in physiological fluids according to structure-based quantum-chemical calculations.

    Margiotta, Enrico / Fonseca Guerra, Célia

    Computational & theoretical chemistry

    2021  , Page(s) 113392

    Abstract: The trimeric spike (S) glycoprotein is the trojan horse and the stronghold of the severe acute respiratory syndrome coronaviruses. Although several structures of the S-protein have been solved, a complete understanding of all its functions is still ... ...

    Abstract The trimeric spike (S) glycoprotein is the trojan horse and the stronghold of the severe acute respiratory syndrome coronaviruses. Although several structures of the S-protein have been solved, a complete understanding of all its functions is still lacking. Our multi-approach study, based on the combination of structural experimental data and quantum-chemical DFT calculations, led to identify a sequestration site for sodium, potassium and chloride ions within the central cavity of both the SARS-CoV-1 and SARS-CoV-2 spike proteins. The same region was found as strictly conserved, even among the sequences of the bat-respective coronaviruses. Due to the prominent role of the main three electrolytes at many levels, and their possible implication in the molecular mechanisms of COVID-19 disease, our study can take the lead in important discoveries related to the SARS-CoV-2 biology, as well as in the design of novel effective therapeutic strategies.
    Language English
    Publishing date 2021-08-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2587365-9
    ISSN 2210-271X
    ISSN 2210-271X
    DOI 10.1016/j.comptc.2021.113392
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification.

    Bian, Yuemin / Kwon, Jason J / Liu, Cong / Margiotta, Enrico / Shekhar, Mrinal / Gould, Alexandra E

    Frontiers in molecular biosciences

    2023  Volume 10, Page(s) 1163536

    Abstract: High-throughput screening (HTS) methods enable the empirical evaluation of a large scale of compounds and can be augmented by virtual screening (VS) techniques to save time and money by using potential active compounds for experimental testing. Structure- ...

    Abstract High-throughput screening (HTS) methods enable the empirical evaluation of a large scale of compounds and can be augmented by virtual screening (VS) techniques to save time and money by using potential active compounds for experimental testing. Structure-based and ligand-based virtual screening approaches have been extensively studied and applied in drug discovery practice with proven outcomes in advancing candidate molecules. However, the experimental data required for VS are expensive, and hit identification in an effective and efficient manner is particularly challenging during early-stage drug discovery for novel protein targets. Herein, we present our TArget-driven Machine learning-Enabled VS (TAME-VS) platform, which leverages existing chemical databases of bioactive molecules to modularly facilitate hit finding. Our methodology enables bespoke hit identification campaigns through a user-defined protein target. The input target ID is used to perform a homology-based target expansion, followed by compound retrieval from a large compilation of molecules with experimentally validated activity. Compounds are subsequently vectorized and adopted for machine learning (ML) model training. These machine learning models are deployed to perform model-based inferential virtual screening, and compounds are nominated based on predicted activity. Our platform was retrospectively validated across ten diverse protein targets and demonstrated clear predictive power. The implemented methodology provides a flexible and efficient approach that is accessible to a wide range of users. The TAME-VS platform is publicly available at https://github.com/bymgood/Target-driven-ML-enabled-VS to facilitate early-stage hit identification.
    Language English
    Publishing date 2023-03-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2023.1163536
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Target-driven machine learning-enabled virtual screening (TAME-VS) platform for early-stage hit identification

    Yuemin Bian / Jason J. Kwon / Cong Liu / Enrico Margiotta / Mrinal Shekhar / Alexandra E. Gould

    Frontiers in Molecular Biosciences, Vol

    2023  Volume 10

    Abstract: High-throughput screening (HTS) methods enable the empirical evaluation of a large scale of compounds and can be augmented by virtual screening (VS) techniques to save time and money by using potential active compounds for experimental testing. Structure- ...

    Abstract High-throughput screening (HTS) methods enable the empirical evaluation of a large scale of compounds and can be augmented by virtual screening (VS) techniques to save time and money by using potential active compounds for experimental testing. Structure-based and ligand-based virtual screening approaches have been extensively studied and applied in drug discovery practice with proven outcomes in advancing candidate molecules. However, the experimental data required for VS are expensive, and hit identification in an effective and efficient manner is particularly challenging during early-stage drug discovery for novel protein targets. Herein, we present our TArget-driven Machine learning-Enabled VS (TAME-VS) platform, which leverages existing chemical databases of bioactive molecules to modularly facilitate hit finding. Our methodology enables bespoke hit identification campaigns through a user-defined protein target. The input target ID is used to perform a homology-based target expansion, followed by compound retrieval from a large compilation of molecules with experimentally validated activity. Compounds are subsequently vectorized and adopted for machine learning (ML) model training. These machine learning models are deployed to perform model-based inferential virtual screening, and compounds are nominated based on predicted activity. Our platform was retrospectively validated across ten diverse protein targets and demonstrated clear predictive power. The implemented methodology provides a flexible and efficient approach that is accessible to a wide range of users. The TAME-VS platform is publicly available at https://github.com/bymgood/Target-driven-ML-enabled-VS to facilitate early-stage hit identification.
    Keywords hit identification ; virtual screening ; machine learning ; drug discovery ; AIDD ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: A Comparison in the Use of the Crystallographic Structure of the Human A 1 or the A 2A Adenosine Receptors as a Template for the Construction of a Homology Model of the A 3 Subtype

    Enrico Margiotta / Stefano Moro

    Applied Sciences, Vol 9, Iss 5, p

    2019  Volume 821

    Abstract: In the last decades, the field of therapeutic application in targeting the human A 3 adenosine receptor has represented a rapidly growing area of research in adenosine field. Both agonists and antagonists have been described to have a potential ... ...

    Abstract In the last decades, the field of therapeutic application in targeting the human A 3 adenosine receptor has represented a rapidly growing area of research in adenosine field. Both agonists and antagonists have been described to have a potential application in the treatment of several diseases, including, for example, glaucoma, cancer, and autoimmune inflammations. To date, the most severe factor limiting the accuracy of the structure-based molecular modeling approaches is the fact that the three-dimensional human A 3 structure has not yet been solved. However, the crystallographic structures of either human A 1 or A 2A subtypes are available as potential templates for the construction of its homology model. In this study, we have compared the propensity of both models to accommodate a series of known potent and selective human A 3 agonists and antagonists. As described, on the basis of the results obtained from this preliminary study, it is possible to affirm that the human A 3 receptor model based on the crystallographic structure of the A 1 subtype can represent a valid alternative to the one conventionally used today, based on the available A 2A structures.
    Keywords G protein-coupled receptor ; adenosine receptors ; A 3 adenosine receptor ; homology modeling ; molecular docking ; structure-activity relationship ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
    Subject code 290
    Language English
    Publishing date 2019-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Potent and selective A

    Federico, Stephanie / Margiotta, Enrico / Moro, Stefano / Kachler, Sonja / Klotz, Karl-Norbert / Spalluto, Giampiero

    RSC medicinal chemistry

    2020  Volume 12, Issue 2, Page(s) 254–262

    Abstract: ... ...

    Abstract A
    Language English
    Publishing date 2020-12-14
    Publishing country England
    Document type Journal Article
    ISSN 2632-8682
    ISSN (online) 2632-8682
    DOI 10.1039/d0md00380h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Molecular determinants of avoidance and inhibition of

    Gervasoni, Silvia / Mehla, Jitender / Bergen, Charles R / Leus, Inga V / Margiotta, Enrico / Malloci, Giuliano / Bosin, Andrea / Vargiu, Attilio V / Lomovskaya, Olga / Rybenkov, Valentin V / Ruggerone, Paolo / Zgurskaya, Helen I

    mBio

    2023  Volume 14, Issue 4, Page(s) e0140323

    Abstract: Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump ... ...

    Abstract Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of
    MeSH term(s) Pseudomonas aeruginosa/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Ligands ; Microbial Sensitivity Tests ; Membrane Transport Proteins/metabolism
    Chemical Substances Bacterial Outer Membrane Proteins ; Ligands ; Membrane Transport Proteins
    Language English
    Publishing date 2023-07-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.01403-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A

    Margiotta, Enrico / Deganutti, Giuseppe / Moro, Stefano

    Journal of computer-aided molecular design

    2018  Volume 32, Issue 12, Page(s) 1337–1346

    Abstract: The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a ... ...

    Abstract The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na
    MeSH term(s) Adenosine A2 Receptor Agonists/chemistry ; Adenosine A2 Receptor Antagonists/chemistry ; Allosteric Site ; Cations, Monovalent/chemistry ; Databases, Protein ; Drug Inverse Agonism ; Humans ; Ligands ; Molecular Docking Simulation/methods ; Protein Binding ; Protein Conformation ; Receptor, Adenosine A2A/metabolism ; Sodium/chemistry
    Chemical Substances Adenosine A2 Receptor Agonists ; Adenosine A2 Receptor Antagonists ; Cations, Monovalent ; Ligands ; Receptor, Adenosine A2A ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2018-10-25
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 808166-9
    ISSN 1573-4951 ; 0920-654X
    ISSN (online) 1573-4951
    ISSN 0920-654X
    DOI 10.1007/s10822-018-0174-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Pyrazolo[4,3-

    Federico, Stephanie / Margiotta, Enrico / Paoletta, Silvia / Kachler, Sonja / Klotz, Karl-Norbert / Jacobson, Kenneth A / Pastorin, Giorgia / Moro, Stefano / Spalluto, Giampiero

    MedChemComm

    2019  Volume 10, Issue 7, Page(s) 1094–1108

    Abstract: A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The ...

    Abstract A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The pyrazolo[4,3-
    Language English
    Publishing date 2019-02-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2545949-1
    ISSN 2040-2511 ; 2040-2503
    ISSN (online) 2040-2511
    ISSN 2040-2503
    DOI 10.1039/c9md00014c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Conjugable A

    Federico, Stephanie / Margiotta, Enrico / Moro, Stefano / Kozma, Eszter / Gao, Zhan-Guo / Jacobson, Kenneth A / Spalluto, Giampiero

    European journal of medicinal chemistry

    2019  Volume 186, Page(s) 111886

    Abstract: Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both ... ...

    Abstract Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both therapeutic and diagnostic applications. The human A
    MeSH term(s) Dose-Response Relationship, Drug ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Fluorescent Dyes/pharmacology ; Humans ; Ligands ; Molecular Dynamics Simulation ; Molecular Structure ; Purinergic P1 Receptor Antagonists/chemical synthesis ; Purinergic P1 Receptor Antagonists/chemistry ; Purinergic P1 Receptor Antagonists/pharmacology ; Receptor, Adenosine A3/metabolism ; Structure-Activity Relationship
    Chemical Substances Fluorescent Dyes ; Ligands ; Purinergic P1 Receptor Antagonists ; Receptor, Adenosine A3
    Language English
    Publishing date 2019-11-22
    Publishing country France
    Document type Journal Article
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2019.111886
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides.

    D'Cunha, Napoleon / Moniruzzaman, Mohammad / Haynes, Keith / Malloci, Giuliano / Cooper, Connor J / Margiotta, Enrico / Vargiu, Attilio V / Uddin, Muhammad R / Leus, Inga V / Cao, Feng / Parks, Jerry M / Rybenkov, Valentin V / Ruggerone, Paolo / Zgurskaya, Helen I / Walker, John K

    ACS infectious diseases

    2021  Volume 7, Issue 9, Page(s) 2650–2665

    Abstract: Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC- ... ...

    Abstract Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB-TolC efflux pump in
    MeSH term(s) Amides/pharmacology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Humans ; Molecular Docking Simulation ; Multidrug Resistance-Associated Proteins/genetics
    Chemical Substances AcrB protein, E coli ; Amides ; Escherichia coli Proteins ; Multidrug Resistance-Associated Proteins
    Language English
    Publishing date 2021-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2373-8227
    ISSN (online) 2373-8227
    DOI 10.1021/acsinfecdis.1c00100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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