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  1. Article ; Online: 501Y.V2 spike protein resists the neutralizing antibody in atomistic simulations.

    Ngo, Son Tung

    Computational biology and chemistry

    2022  Volume 97, Page(s) 107636

    Abstract: SARS-CoV-2 outbreaks worldwide caused COVID-19 pandemic, which is related to several million deaths. In particular, SARS-CoV-2 Spike (S) protein is a major biological target for COVID-19 vaccine design. Unfortunately, recent reports indicated that Spike ( ...

    Abstract SARS-CoV-2 outbreaks worldwide caused COVID-19 pandemic, which is related to several million deaths. In particular, SARS-CoV-2 Spike (S) protein is a major biological target for COVID-19 vaccine design. Unfortunately, recent reports indicated that Spike (S) protein mutations can lead to antibody resistance. However, understanding the process is limited, especially at the atomic scale. The structural change of S protein and neutralizing antibody fragment (FAb) complexes was thus probed using molecular dynamics (MD) simulations. In particular, the backbone RMSD of the 501Y.V2 complex was significantly larger than that of the wild-type one implying a large structural change of the mutation system. Moreover, the mean of R
    MeSH term(s) Antibodies, Neutralizing/genetics ; Antibodies, Neutralizing/metabolism ; COVID-19 ; COVID-19 Vaccines ; Humans ; Mutation ; Pandemics ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Antibodies, Neutralizing ; COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-01-19
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2022.107636
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  2. Article ; Online: Estimating the ligand-binding affinity via λ-dependent umbrella sampling simulations.

    Ngo, Son Tung

    Journal of computational chemistry

    2020  Volume 42, Issue 2, Page(s) 117–123

    Abstract: The umbrella sampling (US) approach has been demonstrated to be a very efficient method for estimating the ligand-binding affinity. However, most of the calculated values overestimate experimental ones that are probably caused by the inaccurate ... ...

    Abstract The umbrella sampling (US) approach has been demonstrated to be a very efficient method for estimating the ligand-binding affinity. However, most of the calculated values overestimate experimental ones that are probably caused by the inaccurate representation of the interaction between the ligand and the surrounding molecules. The issue can be resolved via the implementation aspects of λ-alteration simulation into the US approach, which we call the λ-dependent umbrella sampling (λUS) scheme. In particular, the electrostatic and van der Waals interactions were simultaneously changed by using the coupling parameter λ during λUS simulations. The mean value of obtained results,
    Language English
    Publishing date 2020-10-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.26439
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  3. Article ; Online: Morphology of a Transmembrane Aβ

    Ngo, Son Tung / Nguyen, Trung Hai / Vu, Van V

    Journal of chemical information and modeling

    2023  Volume 63, Issue 14, Page(s) 4376–4382

    Abstract: The folding/misfolding of membrane-permiable Amyloid beta (Aβ) peptides is likely associated with the advancing stage of Alzheimer's disease (AD) by disrupting ... ...

    Abstract The folding/misfolding of membrane-permiable Amyloid beta (Aβ) peptides is likely associated with the advancing stage of Alzheimer's disease (AD) by disrupting Ca
    MeSH term(s) Humans ; Amyloid beta-Peptides/chemistry ; Molecular Dynamics Simulation ; Alzheimer Disease/metabolism ; Protein Structure, Secondary ; Protein Conformation, beta-Strand ; Peptide Fragments/chemistry
    Chemical Substances Amyloid beta-Peptides ; Peptide Fragments
    Language English
    Publishing date 2023-07-06
    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.3c00706
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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)
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  4. Article ; Online: Natural compounds inhibit Monkeypox virus methyltransferase VP39

    Thai, Quynh Mai / Phung, Huong T T / Pham, Ngoc Quynh Anh / Horng, Jim-Tong / Tran, Phuong-Thao / Tung, Nguyen Thanh / Ngo, Son Tung

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–9

    Abstract: VP39, an essential 2'-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role in viral RNA replication and transcription. Inhibition of the enzyme may prevent viral replication. In this context, using a combination of ... ...

    Abstract VP39, an essential 2'-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role in viral RNA replication and transcription. Inhibition of the enzyme may prevent viral replication. In this context, using a combination of molecular docking and molecular dynamics (MDs) simulations, the inhibitory ability of NCI Diversity Set VII natural compounds to VP39 protein was investigated. It should be noted that the computed binding free energy of ligand
    Language English
    Publishing date 2024-02-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2321509
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  5. Article ; Online: Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M

    Ngo, Son Tung / Nguyen, Trung Hai / Tung, Nguyen Thanh / Mai, Binh Khanh

    RSC advances

    2022  Volume 12, Issue 6, Page(s) 3729–3737

    Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the ... ...

    Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to M
    Language English
    Publishing date 2022-01-28
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d1ra08752e
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  6. Article ; Online: Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity.

    Ngo, Son Tung / Pham, Minh Quan

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2385, Page(s) 313–323

    Abstract: Many proteins have a solvent-exposed binding cleft, which permits their inhibitors to bind and unbind without significant protein conformation transforms. The binding/unbinding pathways of these protein-inhibitor complexes can be rather straightforwardly ...

    Abstract Many proteins have a solvent-exposed binding cleft, which permits their inhibitors to bind and unbind without significant protein conformation transforms. The binding/unbinding pathways of these protein-inhibitor complexes can be rather straightforwardly sampled by using umbrella sampling (US) simulation methods. During a US simulation, the C
    MeSH term(s) Ligands ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Proteins/metabolism ; Solvents ; Thermodynamics
    Chemical Substances Ligands ; Proteins ; Solvents
    Language English
    Publishing date 2021-12-09
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1767-0_14
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  7. Article ; Online: Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations.

    Tam, Nguyen Minh / Nguyen, Trung Hai / Pham, Minh Quan / Hong, Nam Dao / Tung, Nguyen Thanh / Vu, Van V / Quang, Duong Tuan / Ngo, Son Tung

    Journal of molecular graphics & modelling

    2023  Volume 124, Page(s) 108535

    Abstract: The first oral drug for the treatment of COVID-19, Paxlovid, has been authorized; however, nirmatrelvir, a major component of the drug, is reported to be associated with some side effects. Moreover, the appearance of many novel variants raises concerns ... ...

    Abstract The first oral drug for the treatment of COVID-19, Paxlovid, has been authorized; however, nirmatrelvir, a major component of the drug, is reported to be associated with some side effects. Moreover, the appearance of many novel variants raises concerns about drug resistance, and designing new potent inhibitors to prevent viral replication is thus urgent. In this context, using a hybrid approach combining machine learning (ML) and free energy simulations, 6 compounds obtained by modifying nirmatrelvir were proposed to bind strongly to SARS-CoV-2 Mpro. The structural modification of nirmatrelvir significantly enhances the electrostatic interaction free energy between the protein and ligand and slightly decreases the vdW term. However, the vdW term is the most important factor in controlling the ligand-binding affinity. In addition, the modified nirmatrelvir might be less toxic to the human body than the original inhibitor.
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19 ; Ligands ; Antiviral Agents/pharmacology
    Chemical Substances nirmatrelvir and ritonavir drug combination ; Ligands ; Antiviral Agents
    Language English
    Publishing date 2023-06-01
    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.2023.108535
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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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  8. Article: Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations.

    Tam, Nguyen Minh / Nguyen, Trung Hai / Ngan, Vu Thi / Tung, Nguyen Thanh / Ngo, Son Tung

    Royal Society open science

    2022  Volume 9, Issue 1, Page(s) 211480

    Abstract: The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear ... ...

    Abstract The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coefficient between US and experiments does not differ from FPL and is slightly smaller than LIE. The root mean square error of US simulations is smaller than that of LIE. Moreover, US is better than FPL and poorer than LIE in classifying SARS-CoV-2 Mpro inhibitors owing to the reciever operating characteristic-area under the curve analysis. Furthermore, the US simulations also provide detailed insights on unbinding pathways of ligands from the binding cleft of SARS-CoV-2 Mpro. The residues
    Language English
    Publishing date 2022-01-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.211480
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  9. Article ; Online: Photofragmentation Patterns of Cobalt Oxide Cations Co

    Mai, Nguyen Thi / Ngo, Son Tung / Lievens, Peter / Janssens, Ewald / Thanh Tung, Nguyen

    The journal of physical chemistry. A

    2020  Volume 124, Issue 37, Page(s) 7333–7339

    Abstract: Cobalt oxide clusters, ... ...

    Abstract Cobalt oxide clusters, Co
    Language English
    Publishing date 2020-07-16
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.0c01545
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Flexible Magnetic Metasurface with Defect Cavity for Wireless Power Transfer System.

    Hiep, Le Thi Hong / Khuyen, Bui Xuan / Tung, Bui Son / Ngo, Quang Minh / Lam, Vu Dinh / Pham, Thanh Son

    Materials (Basel, Switzerland)

    2022  Volume 15, Issue 19

    Abstract: In this paper, we present a flexible magnetic metamaterial structure for enhancing the efficiency of wireless power transfer (WPT) systems operating at 13.56 MHz. The metasurface between transmitter (Tx) and receiver (Rx) coils of the WPT system is ... ...

    Abstract In this paper, we present a flexible magnetic metamaterial structure for enhancing the efficiency of wireless power transfer (WPT) systems operating at 13.56 MHz. The metasurface between transmitter (Tx) and receiver (Rx) coils of the WPT system is constructed of a 3 × 5 metamaterial unit cell array with a total size of 150 × 300 mm
    Language English
    Publishing date 2022-09-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2487261-1
    ISSN 1996-1944
    ISSN 1996-1944
    DOI 10.3390/ma15196583
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