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  1. Article ; Online: Targeting hPKM2 in cancer: A bio isosteric approach for ligand design.

    Pipitò, Ludovico / Illingworth, Thomas Arron / Deganutti, Giuseppe

    Computers in biology and medicine

    2023  Volume 158, Page(s) 106852

    Abstract: The term cancer refers to a plethora of diseases characterized by the development of abnormal cells that divide uncontrollably and can infiltrate further proximal or distal body tissues. Each type of cancer can be defined by aggressiveness, localization, ...

    Abstract The term cancer refers to a plethora of diseases characterized by the development of abnormal cells that divide uncontrollably and can infiltrate further proximal or distal body tissues. Each type of cancer can be defined by aggressiveness, localization, metabolism, and response to available treatments. Among the most common hallmarks of cancer is a more acidic intracellular microenvironment. Offset pH values are due to an excess of lactate and an increased hypoxia-inducible factor (HIF) expression, which leads to a hypoxic state and a metabolic shift towards glycolysis to produce adenosine-5'-triphosphate (ATP) necessary for cellular metabolism. Warburg's hypothesis underpins this concept, making glycolysis and its central enzyme pyruvate kinase (hPKM2), an ideal target for drug development. Using molecular docking and extensive molecular dynamics (MD) simulations we investigated the binding mode of phosphoenolpyruvate (PEP) inside the hPKM2 active site, and then evaluated a set of known bio-isosteric inhibitors to understand the differences caused by their substitutions on their binding mode. Ultimately, we propose a new molecular entity to hamper hPKM2, unbalance cellular energy, and possibly trigger autophagic mechanisms.
    MeSH term(s) Humans ; Ligands ; Molecular Docking Simulation ; Neoplasms/metabolism ; Glycolysis ; Adenosine Triphosphate ; Tumor Microenvironment
    Chemical Substances Ligands ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2023-04-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.106852
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 653: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling.

    Majumder, Satyabrata / Deganutti, Giuseppe / Pipitò, Ludovico / Chaudhuri, Dwaipayan / Datta, Joyeeta / Giri, Kalyan

    Journal of chemical information and modeling

    2024  Volume 64, Issue 8, Page(s) 3360–3374

    Abstract: HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the ... ...

    Abstract HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56-77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.
    MeSH term(s) Molecular Dynamics Simulation ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; vpr Gene Products, Human Immunodeficiency Virus/chemistry ; vpr Gene Products, Human Immunodeficiency Virus/metabolism ; Ion Channels/chemistry ; Ion Channels/metabolism ; Protein Conformation ; HIV-1/chemistry
    Chemical Substances Lipid Bilayers ; vpr Gene Products, Human Immunodeficiency Virus ; Ion Channels ; vpr protein, Human immunodeficiency virus 1
    Language English
    Publishing date 2024-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01859
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Is the Stalk of the SARS-CoV-2 Spike Protein Druggable?

    Pipitò, Ludovico / Reynolds, Christopher A / Deganutti, Giuseppe

    Viruses

    2022  Volume 14, Issue 12

    Abstract: The spike protein is key to SARS-CoV-2 high infectivity because it facilitates the receptor binding domain (RBD) encounter with ACE2. As targeting subunit S1 has not yet delivered an ACE2-binding inhibitor, we have assessed the druggability of the ... ...

    Abstract The spike protein is key to SARS-CoV-2 high infectivity because it facilitates the receptor binding domain (RBD) encounter with ACE2. As targeting subunit S1 has not yet delivered an ACE2-binding inhibitor, we have assessed the druggability of the conserved segment of the spike protein stalk within subunit S2 by means of an integrated computational approach that combines the molecular docking of an optimized library of fragments with high-throughput molecular dynamics simulations. The high propensity of the spike protein to mutate in key regions that are responsible for the recognition of the human angiotensin-converting enzyme 2 (hACE2) or for the recognition of antibodies, has made subunit S1 of the spike protein difficult to target. Despite the inherent flexibility of the stalk region, our results suggest two hidden interhelical binding sites, whose accessibility is only partially hampered by glycan residues.
    MeSH term(s) Humans ; COVID-19 ; Spike Glycoprotein, Coronavirus/metabolism ; SARS-CoV-2/metabolism ; Angiotensin-Converting Enzyme 2/metabolism ; Molecular Docking Simulation ; Protein Domains ; Protein Binding ; Molecular Dynamics Simulation
    Chemical Substances spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-12-14
    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/v14122789
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  4. Article ; Online: Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein.

    Pipitò, Ludovico / Rujan, Roxana-Maria / Reynolds, Christopher A / Deganutti, Giuseppe

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2022  Volume 44, Issue 9, Page(s) e2200060

    Abstract: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during ... ...

    Abstract The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.
    MeSH term(s) COVID-19 ; Humans ; Molecular Dynamics Simulation ; Pandemics ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-07-17
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202200060
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2024: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Computer-aided de novo design and optimization of novel potential inhibitors of HIV-1 Nef protein.

    Majumder, Satyabrata / Deganutti, Giuseppe / Pipitò, Ludovico / Chaudhuri, Dwaipayan / Datta, Joyeeta / Giri, Kalyan

    Computational biology and chemistry

    2023  Volume 104, Page(s) 107871

    Abstract: Nef is a small accessory protein pivotal in the HIV-1 viral replication cycle. It is a multifunctional protein and its interactions with kinases in host cells have been well characterized through many in vitro and structural studies. Nef forms a ... ...

    Abstract Nef is a small accessory protein pivotal in the HIV-1 viral replication cycle. It is a multifunctional protein and its interactions with kinases in host cells have been well characterized through many in vitro and structural studies. Nef forms a homodimer to activate the kinases and subsequently the phosphorylation pathways. The disruption of its homodimerization represents a valuable approach in the search for novel classes of antiretroviral. However, this research avenue is still underdeveloped as just a few Nef inhibitors have been reported so far, with very limited structural information about their mechanism of action. To address this issue, we have employed an in silico structure-based drug design strategy that combines de novo ligand design with molecular docking and extensive molecular dynamics simulations. Since the Nef pocket involved in homodimerization has high lipophilicity, the initial de novo-designed structures displayed poor drug-likeness and solubility. Taking information from the hydration sites within the homodimerization pocket, structural modifications in the initial lead compound have been introduced to improve the solubility and drug-likeness, without affecting the binding profile. We propose lead compounds that can be the starting point for further optimizations to deliver long-awaited, rationally designed Nef inhibitors.
    MeSH term(s) Molecular Docking Simulation ; HIV-1 ; Computer-Aided Design ; Gene Products, nef ; Computers
    Chemical Substances Gene Products, nef
    Language English
    Publishing date 2023-04-15
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2023.107871
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  6. Article ; Online: Understanding The Role of Heparinoids on the SARS-CoV-2 Spike Protein through Molecular Dynamics Simulations

    Pipito, Ludovico / Reynolds, Christopher A / Deganutti, Giuseppe

    bioRxiv

    Abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a threat, with an estimated number of deaths exceeding 5 million. SARS-CoV-2 entry into the cell is mediated by its transmembrane spike glycoprotein (S ... ...

    Abstract The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a threat, with an estimated number of deaths exceeding 5 million. SARS-CoV-2 entry into the cell is mediated by its transmembrane spike glycoprotein (S protein), and the angiotensin-converting enzyme 2 (ACE2) receptor on the human cell surface. The extracellular heparan sulphate (ecHS) enhances the S protein binding through a mechanism still unknown. Surprisingly, low molecular weight heparin (LMWH) and HS in the disaccharide form (dHS) hinder the S protein binding to ACE2, despite the similarity with ecHS. We investigated the molecular mechanism behind this inhibition through molecular dynamics (MD) simulations to understand the interaction pattern of the heparinoids with S protein and the ACE2 receptor.
    Keywords covid19
    Language English
    Publishing date 2022-07-06
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.07.05.498807
    Database COVID19

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  7. Article ; Online: Is The Stalk of the SARS-CoV-2 Spike Protein Druggable?

    Pipito, Ludovico / Reynolds, Christopher A. / Deganutti, Giuseppe

    bioRxiv

    Abstract: The SARS-CoV-2 virus spike protein (SP) is the vector of the virus infectivity. The high propensity to mutate in key regions responsible for the recognition of the human angiotensin-converting enzyme 2 (hACE2) or the antibodies produced by the immune ... ...

    Abstract The SARS-CoV-2 virus spike protein (SP) is the vector of the virus infectivity. The high propensity to mutate in key regions responsible for the recognition of the human angiotensin-converting enzyme 2 (hACE2) or the antibodies produced by the immune system following infection or vaccination makes subunit 1 of the SP a difficult to target and, to date, efforts have not delivered any ACE2 binding inhibitor yet. The inherent flexibility of the stalk region, within subunit S2, is key to SARS-CoV-2 high infectivity because it facilitates the receptor binding domain encounter with ACE2. Thus, it could be a valuable therapeutic target. By employing a fragment-based strategy, we computationally studied the druggability of the conserved part of the SP stalk by means of an integrated approach that combines molecular docking with high-throughput molecular dynamics simulations. Our results suggest that the druggability of the stalk is challenging and provide the structural basis for such difficulty.
    Keywords covid19
    Language English
    Publishing date 2022-10-06
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.10.06.511069
    Database COVID19

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  8. Article: Molecular dynamics studies reveal structural and functional features of the SARS‐CoV‐2 spike protein

    Pipitò, Ludovico / Rujan, Roxana‐Maria / Reynolds, Christopher A. / Deganutti, Giuseppe

    BioEssays. 2022 Sept., v. 44, no. 9

    2022  

    Abstract: The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during ... ...

    Abstract The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; drugs ; epitopes ; molecular dynamics ; polysaccharides ; viruses
    Language English
    Dates of publication 2022-09
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202200060
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2009/501: Show issues

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  9. Article ; Online: A Pathway Model to Understand the Evolution of Spike Protein Binding to ACE2 in SARS-CoV-2 Variants.

    Pipitò, Ludovico / Reynolds, Christopher A / Mobarec, Juan Carlos / Vickery, Owen / Deganutti, Giuseppe

    Biomolecules

    2022  Volume 12, Issue 11

    Abstract: After the SARS-CoV-2 Wuhan variant that gave rise to the pandemic, other variants named Delta, Omicron, and Omicron-2 sequentially became prevalent, with mutations spread around the viral genome, including on the spike (S) protein; in order to understand ...

    Abstract After the SARS-CoV-2 Wuhan variant that gave rise to the pandemic, other variants named Delta, Omicron, and Omicron-2 sequentially became prevalent, with mutations spread around the viral genome, including on the spike (S) protein; in order to understand the resultant in gains in infectivity, we interrogated in silico both the equilibrium binding and the binding pathway of the virus' receptor-binding domain (RBD) to the angiotensin-converting enzyme 2 (ACE2) receptor. We interrogated the molecular recognition between the RBD of different variants and ACE2 through supervised molecular dynamics (SuMD) and classic molecular dynamics (MD) simulations to address the effect of mutations on the possible S protein binding pathways. Our results indicate that compensation between binding pathway efficiency and stability of the complex exists for the Omicron BA.1 receptor binding domain, while Omicron BA.2's mutations putatively improved the dynamic recognition of the ACE2 receptor, suggesting an evolutionary advantage over the previous strains.
    MeSH term(s) Humans ; Angiotensin-Converting Enzyme 2/genetics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Protein Binding ; Peptidyl-Dipeptidase A/chemistry ; COVID-19/genetics ; Receptors, Virus/genetics ; Mutation
    Chemical Substances Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; Receptors, Virus
    Language English
    Publishing date 2022-10-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom12111607
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