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  1. Article: Computational Characterizations of the Interactions Between the Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against SARS-CoV-2.

    Munaweera, Rangika / Hu, Ying S

    Frontiers in chemistry

    2021  Volume 8, Page(s) 627340

    Abstract: We report a molecular-docking and virtual-screening-based identification and characterization of interactions of lead molecules with exoribonuclease (ExoN) enzyme in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). From previously identified ...

    Abstract We report a molecular-docking and virtual-screening-based identification and characterization of interactions of lead molecules with exoribonuclease (ExoN) enzyme in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). From previously identified DEDDh/DEEDh subfamily nuclease inhibitors, our results revealed strong binding of pontacyl violet 6R (PV6R) at the catalytic active site of ExoN. The binding was found to be stabilized
    Language English
    Publishing date 2021-01-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2020.627340
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Computational Characterizations of the Interactions Between the Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against SARS-CoV-2

    Rangika Munaweera / Ying S. Hu

    Frontiers in Chemistry, Vol

    2021  Volume 8

    Abstract: We report a molecular-docking and virtual-screening-based identification and characterization of interactions of lead molecules with exoribonuclease (ExoN) enzyme in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). From previously identified ...

    Abstract We report a molecular-docking and virtual-screening-based identification and characterization of interactions of lead molecules with exoribonuclease (ExoN) enzyme in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). From previously identified DEDDh/DEEDh subfamily nuclease inhibitors, our results revealed strong binding of pontacyl violet 6R (PV6R) at the catalytic active site of ExoN. The binding was found to be stabilized via two hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations further confirmed the stability of PV6R at the active site showing a shift in ligand to reach a more stabilized binding. Using PV6R as the lead molecule, we employed virtual screening to identify potential molecular candidates that form strong interactions at the ExoN active site. Our study paves ways for evaluating the ExoN as a novel drug target for antiviral treatment against SARS-CoV-2.
    Keywords exoribonuclease ; SARS-CoV-2 ; pontacyl violet 6R ; DEDDh exonucleases ; RNA-dependent RNA polymerase ; orthocoronavirinae ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Correction to Chaotropic Perturbation of Noncovalent Interactions of the Hemagglutinin Tag Monoclonal Antibody Fragment Enables Superresolution Molecular Census.

    Gunasekara, Hirushi / Munaweera, Rangika / Novotná, Lucie / Lillemeier, Björn F / Hu, Ying S

    ACS nano

    2022  

    Language English
    Publishing date 2022-11-23
    Publishing country United States
    Document type Published Erratum
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.2c10526
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chaotropic Perturbation of Noncovalent Interactions of the Hemagglutinin Tag Monoclonal Antibody Fragment Enables Superresolution Molecular Census.

    Gunasekara, Hirushi / Munaweera, Rangika / Hu, Ying S

    ACS nano

    2021  Volume 16, Issue 1, Page(s) 129–139

    Abstract: Antibody-antigen interactions represent one of the most exploited biomolecular interactions in experimental biology. While numerous techniques harnessed immobilized antibodies for nanoscale fluorescence imaging, few utilized their reversible binding ... ...

    Abstract Antibody-antigen interactions represent one of the most exploited biomolecular interactions in experimental biology. While numerous techniques harnessed immobilized antibodies for nanoscale fluorescence imaging, few utilized their reversible binding kinetics. Here, we investigated noncovalent interactions of the monoclonal hemagglutinin (HA) epitope tag antibody, 12CA5, in the fixed cellular environment. We observed that the use of a chaotropic agent, potassium thiocyanate (KSCN), promoted the dissociation of the 12CA5 antibody fragment (Fab), which already displayed faster dissociation compared to its immunoglobulin G (IgG) counterpart. Molecular dynamic simulations revealed notable root-mean-square deviations and destabilizations in the presence of KSCN, while the hydrogen-bonding network remained primarily unaffected at the antigen-binding site. The reversible interactions enabled us to achieve a superresolution molecular census of local populations of 3xHA tagged microtubule fibers with improved molecular quantification consistency compared to single-molecule localization microscopy (SMLM) techniques utilizing standard immunofluorescence staining for sample labeling. Our technique, termed superresolution census of molecular epitope tags (SR-COMET), highlights the utilization of reversible antibody-antigen interactions for SMLM-based quantitative superresolution imaging.
    MeSH term(s) Hemagglutinins ; Antibodies, Monoclonal ; Immunoglobulin Fragments ; Censuses ; Epitopes/chemistry ; Antigens
    Chemical Substances potassium thiocyanate (TM7213864A) ; Hemagglutinins ; Antibodies, Monoclonal ; Immunoglobulin Fragments ; Epitopes ; Antigens
    Language English
    Publishing date 2021-11-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.1c04237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Main-chain Macromolecular Hydrazone Photoswitches.

    Thai, Linh Duy / Fanelli, Julian / Munaweera, Rangika / O'Mara, Megan L / Barner-Kowollik, Christopher / Mutlu, Hatice

    Angewandte Chemie (International ed. in English)

    2023  Volume 63, Issue 4, Page(s) e202315887

    Abstract: Hydrazones-consisting of a dynamic imine bond and an acidic NH proton-have recently emerged as versatile photoswitches underpinned by their ability to form thermally bistable isomers, (Z) and (E), respectively. Herein, we introduce two photoresponsive ... ...

    Abstract Hydrazones-consisting of a dynamic imine bond and an acidic NH proton-have recently emerged as versatile photoswitches underpinned by their ability to form thermally bistable isomers, (Z) and (E), respectively. Herein, we introduce two photoresponsive homopolymers containing structurally different hydrazones as main-chain repeating units, synthesized via head-to-tail Acyclic Diene METathesis (ADMET) polymerization. Their key difference lies in the hydrazone design, specifically the location of the aliphatic arm connecting the rotor of the hydrazone photoswitch to the aliphatic polymer backbone. Critically, we demonstrate that their main photoresponsive property, i.e., their hydrodynamic volume, changes in opposite directions upon photoisomerization (λ=410 nm) in dilute solution. Further, the polymers-independent of the design of the individual hydrazone monomer-feature a photoswitchable glass transition temperature (T
    Language English
    Publishing date 2023-12-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202315887
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  6. Article ; Online: Rapid statistical discrimination of fluorescence images of T cell receptors on immobilizing surfaces with different coating conditions.

    Saed, Badeia / Munaweera, Rangika / Anderson, Jesse / O'Neill, William D / Hu, Ying S

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 15488

    Abstract: The spatial organization of T cell receptors (TCRs) correlates with membrane-associated signal amplification, dispersion, and regulation during T cell activation. Despite its potential clinical importance, quantitative analysis of the spatial arrangement ...

    Abstract The spatial organization of T cell receptors (TCRs) correlates with membrane-associated signal amplification, dispersion, and regulation during T cell activation. Despite its potential clinical importance, quantitative analysis of the spatial arrangement of TCRs from standard fluorescence images remains difficult. Here, we report Statistical Classification Analyses of Membrane Protein Images or SCAMPI as a technique capable of analyzing the spatial arrangement of TCRs on the plasma membrane of T cells. We leveraged medical image analysis techniques that utilize pixel-based values. We transformed grayscale pixel values from fluorescence images of TCRs into estimated model parameters of partial differential equations. The estimated model parameters enabled an accurate classification using linear discrimination techniques, including Fisher Linear Discriminant (FLD) and Logistic Regression (LR). In a proof-of-principle study, we modeled and discriminated images of fluorescently tagged TCRs from Jurkat T cells on uncoated cover glass surfaces (Null) or coated cover glass surfaces with either positively charged poly-L-lysine (PLL) or TCR cross-linking anti-CD3 antibodies (OKT3). Using 80 training images and 20 test images per class, our statistical technique achieved 85% discrimination accuracy for both OKT3 versus PLL and OKT3 versus Null conditions. The run time of image data download, model construction, and image discrimination was 21.89 s on a laptop computer, comprised of 20.43 s for image data download, 1.30 s on the FLD-SCAMPI analysis, and 0.16 s on the LR-SCAMPI analysis. SCAMPI represents an alternative approach to morphology-based qualifications for discriminating complex patterns of membrane proteins conditioned on a small sample size and fast runtime. The technique paves pathways to characterize various physiological and pathological conditions using the spatial organization of TCRs from patient T cells.
    MeSH term(s) Calcium/metabolism ; Cell Membrane/metabolism ; Cluster Analysis ; Discriminant Analysis ; Humans ; Image Processing, Computer-Assisted/methods ; Jurkat Cells ; Lymphocyte Activation/immunology ; Microscopy, Fluorescence ; Models, Statistical ; Probability ; Receptors, Antigen, T-Cell/physiology ; Regression Analysis ; Statistics as Topic ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
    Chemical Substances Receptors, Antigen, T-Cell ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2021-07-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-94730-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Rapid statistical discrimination of fluorescence images of T cell receptors on immobilizing surfaces with different coating conditions

    Badeia Saed / Rangika Munaweera / Jesse Anderson / William D. O’Neill / Ying S. Hu

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract The spatial organization of T cell receptors (TCRs) correlates with membrane-associated signal amplification, dispersion, and regulation during T cell activation. Despite its potential clinical importance, quantitative analysis of the spatial ... ...

    Abstract Abstract The spatial organization of T cell receptors (TCRs) correlates with membrane-associated signal amplification, dispersion, and regulation during T cell activation. Despite its potential clinical importance, quantitative analysis of the spatial arrangement of TCRs from standard fluorescence images remains difficult. Here, we report Statistical Classification Analyses of Membrane Protein Images or SCAMPI as a technique capable of analyzing the spatial arrangement of TCRs on the plasma membrane of T cells. We leveraged medical image analysis techniques that utilize pixel-based values. We transformed grayscale pixel values from fluorescence images of TCRs into estimated model parameters of partial differential equations. The estimated model parameters enabled an accurate classification using linear discrimination techniques, including Fisher Linear Discriminant (FLD) and Logistic Regression (LR). In a proof-of-principle study, we modeled and discriminated images of fluorescently tagged TCRs from Jurkat T cells on uncoated cover glass surfaces (Null) or coated cover glass surfaces with either positively charged poly-L-lysine (PLL) or TCR cross-linking anti-CD3 antibodies (OKT3). Using 80 training images and 20 test images per class, our statistical technique achieved 85% discrimination accuracy for both OKT3 versus PLL and OKT3 versus Null conditions. The run time of image data download, model construction, and image discrimination was 21.89 s on a laptop computer, comprised of 20.43 s for image data download, 1.30 s on the FLD-SCAMPI analysis, and 0.16 s on the LR-SCAMPI analysis. SCAMPI represents an alternative approach to morphology-based qualifications for discriminating complex patterns of membrane proteins conditioned on a small sample size and fast runtime. The technique paves pathways to characterize various physiological and pathological conditions using the spatial organization of TCRs from patient T cells.
    Keywords Medicine ; R ; Science ; Q
    Subject code 571
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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