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  1. Article ; Online: Diphenolic boldine, an aporphine alkaloid: inhibitory effect evaluation on α-glucosidase by molecular dynamics integrating enzyme kinetics.

    Si, Yuexiu / Zhu, Jiabo / Xu, Xia / Xu, Yueyuan / Lee, Jinhyuk / Park, Yong-Doo

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–13

    Abstract: Screening α-glucosidase inhibitors with novel structures is an important field in the development of anti-diabetic drugs due to their application in postprandial hyperglycemia control. Boldine is one of the potent natural antioxidants with a wide range ... ...

    Abstract Screening α-glucosidase inhibitors with novel structures is an important field in the development of anti-diabetic drugs due to their application in postprandial hyperglycemia control. Boldine is one of the potent natural antioxidants with a wide range of pharmacological activities. Virtual screening and biochemical inhibition kinetics combined with molecular dynamics simulations were conducted to verify the inactivation function of boldine on α-glucosidase. A series of inhibition kinetics and spectrometry detections were conducted to analyze the α-glucosidase inhibition. Computational simulations of molecular dynamics/docking analyses were conducted to detect boldine docking sites' details and evaluate the key binding residues. Boldine displayed a typical reversible and mixed-type inhibition manner. Measurements of circular dichroism and fluorescence spectrum showed boldine changed the secondary structure and loosened the tertiary conformation of target α-glucosidase. The computational molecular dynamics showed that boldine could block the active pocket site through close interaction with binding key residues, and two phenolic hydroxyl groups of boldine play a core function in α-glucosidase inhibition
    Language English
    Publishing date 2024-01-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2024.2301769
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Improving Geometric Validation Metrics and Ensuring Consistency with Experimental Data through TrioSA: An NMR Refinement Protocol.

    Cho, Youngbeom / Ryu, Hyojung / Lim, Gyutae / Nam, Seungyoon / Lee, Jinhyuk

    International journal of molecular sciences

    2023  Volume 24, Issue 17

    Abstract: Protein model refinement a the crucial step in improving the quality of a predicted protein model. This study presents an NMR refinement protocol called TrioSA (torsion-angle and implicit-solvation-optimized simulated annealing) that improves the ... ...

    Abstract Protein model refinement a the crucial step in improving the quality of a predicted protein model. This study presents an NMR refinement protocol called TrioSA (torsion-angle and implicit-solvation-optimized simulated annealing) that improves the accuracy of backbone/side-chain conformations and the overall structural quality of proteins. TrioSA was applied to a subset of 3752 solution NMR protein structures accompanied by experimental NMR data: distance and dihedral angle restraints. We compared the initial NMR structures with the TrioSA-refined structures and found significant improvements in structural quality. In particular, we observed a reduction in both the maximum and number of NOE (nuclear Overhauser effect) violations, indicating better agreement with experimental NMR data. TrioSA improved geometric validation metrics of NMR protein structure, including backbone accuracy and the secondary structure ratio. We evaluated the contribution of each refinement element and found that the torsional angle potential played a significant role in improving the geometric validation metrics. In addition, we investigated protein-ligand docking to determine if TrioSA can improve biological outcomes. TrioSA structures exhibited better binding prediction compared to the initial NMR structures. This study suggests that further development and research in computational refinement methods could improve biomolecular NMR structural determination.
    MeSH term(s) Benchmarking ; Magnetic Resonance Imaging ; Nuclear Magnetic Resonance, Biomolecular
    Language English
    Publishing date 2023-08-28
    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/ijms241713337
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  3. Article ; Online: Inhibitory effect of acarbose on tyrosinase: application of molecular dynamics integrating inhibition kinetics.

    Xu, Jie-Hao / Lee, Jinhyuk / Yin, Shang-Jun / Wang, Wei / Park, Yong-Doo

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 1, Page(s) 314–325

    Abstract: Due to its clinical and cosmetic applications, investigators have paid attention to tyrosinase (TYR) inhibitor development. In this study, a TYR inhibition study with acarbose was investigated to gain insights into the regulation of the catalytic ... ...

    Abstract Due to its clinical and cosmetic applications, investigators have paid attention to tyrosinase (TYR) inhibitor development. In this study, a TYR inhibition study with acarbose was investigated to gain insights into the regulation of the catalytic function. Biochemical assay results indicated that acarbose was turned to be an inhibitor of TYR in a reversible binding manner and probed as a distinctive mixed-type inhibitor via measurement of double-reciprocal kinetic (
    MeSH term(s) Molecular Dynamics Simulation ; Monophenol Monooxygenase/metabolism ; Acarbose/pharmacology ; Enzyme Inhibitors/chemistry ; Catalytic Domain ; Molecular Docking Simulation ; Kinetics
    Chemical Substances Monophenol Monooxygenase (EC 1.14.18.1) ; Acarbose (T58MSI464G) ; Enzyme Inhibitors
    Language English
    Publishing date 2023-03-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2192800
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Application of Computational Simulation Integrating Inhibition Kinetics for Detecting Tyrosinase Inhibitor: Salsalate Is a New Inhibitor.

    Xu, Jie-Hao / Lee, Jinhyuk / Wang, Wei / Park, Yong-Doo

    Protein and peptide letters

    2022  Volume 29, Issue 9, Page(s) 744–759

    Abstract: Background: Tyrosinase inhibitor developments have been widely attended by investigators for their various applications.: Objective: A combination of virtual screening of docking simulations and biochemical inhibition kinetics was performed to find a ...

    Abstract Background: Tyrosinase inhibitor developments have been widely attended by investigators for their various applications.
    Objective: A combination of virtual screening of docking simulations and biochemical inhibition kinetics was performed to find a new inhibitor of tyrosinase for the clinical application of an antipigment agent.
    Methods: We conducted docking simulations to detect tyrosinase key binding residues and used the detected binding residues to screen the NCBI PubChem database for probing tyrosinase binding compounds. The serial inhibition kinetics and spectrofluorimetry measurements were performed to validate the inhibitory effect on tyrosinase.
    Results: We have detected 200 candidates and categorized them into four clusters. Among them, we successfully confirmed salsalate as a new inhibitor of tyrosinase measured by serial enzyme kinetics. Salsalate was detected as a reversible inhibitor of tyrosinase displaying a typical mixedtype inhibition manner (IC
    Conclusion: Our study suggests that salsalate is a potential anti-pigment drug via inhibition of tyrosinase activity and it might be applicable for dermatologic clinical application. Also, our study enlarges an insight into the salsalate drug application.
    MeSH term(s) Monophenol Monooxygenase/metabolism ; Kinetics ; Computer Simulation ; Salicylates ; Molecular Docking Simulation ; Enzyme Inhibitors/chemistry
    Chemical Substances Monophenol Monooxygenase (EC 1.14.18.1) ; salicylsalicylic acid (V9MO595C9I) ; Salicylates ; Enzyme Inhibitors
    Language English
    Publishing date 2022-08-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1280776-x
    ISSN 1875-5305 ; 0929-8665
    ISSN (online) 1875-5305
    ISSN 0929-8665
    DOI 10.2174/0929866529666220805145244
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Dual BACE1 and Cholinesterase Inhibitory Effects of Phlorotannins from

    Lee, Jinhyuk / Jun, Mira

    Marine drugs

    2019  Volume 17, Issue 2

    Abstract: Alzheimer's disease (AD) is one of the most common neurodegenerative diseases with a multifactorial nature. β-Secretase (BACE1) and acetylcholinesterase (AChE), which are required for the production of neurotoxic β-amyloid (Aβ) and the promotion of Aβ ... ...

    Abstract Alzheimer's disease (AD) is one of the most common neurodegenerative diseases with a multifactorial nature. β-Secretase (BACE1) and acetylcholinesterase (AChE), which are required for the production of neurotoxic β-amyloid (Aβ) and the promotion of Aβ fibril formation, respectively, are considered as prime therapeutic targets for AD. In our efforts towards the development of potent multi-target, directed agents for AD treatment, major phlorotannins such as eckol, dieckol, and 8,8'-bieckol from
    MeSH term(s) ADAM17 Protein/antagonists & inhibitors ; Alzheimer Disease/drug therapy ; Alzheimer Disease/enzymology ; Amyloid Precursor Protein Secretases/antagonists & inhibitors ; Aspartic Acid Endopeptidases/antagonists & inhibitors ; Benzofurans/chemistry ; Benzofurans/pharmacology ; Cholinesterase Inhibitors/pharmacology ; Cholinesterases/chemistry ; Cholinesterases/metabolism ; Dioxins/chemistry ; Dioxins/pharmacology ; Molecular Docking Simulation ; Seaweed/chemistry ; Tannins/chemistry ; Tannins/pharmacology
    Chemical Substances Benzofurans ; Cholinesterase Inhibitors ; Dioxins ; Tannins ; dieckol ; eckol (88798-74-7) ; 8,8'-bieckol (89445-12-5) ; Cholinesterases (EC 3.1.1.8) ; Amyloid Precursor Protein Secretases (EC 3.4.-) ; Aspartic Acid Endopeptidases (EC 3.4.23.-) ; BACE1 protein, human (EC 3.4.23.46) ; ADAM17 Protein (EC 3.4.24.86) ; ADAM17 protein, human (EC 3.4.24.86)
    Language English
    Publishing date 2019-02-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2175190-0
    ISSN 1660-3397 ; 1660-3397
    ISSN (online) 1660-3397
    ISSN 1660-3397
    DOI 10.3390/md17020091
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Development of pluripotent stem cell-derived epidermal organoids that generate effective extracellular vesicles in skin regeneration.

    Kwak, Sojung / Song, Cho Lok / Lee, Jinhyuk / Kim, Sungyeon / Nam, Seungyoon / Park, Young-Jun / Lee, Jungwoon

    Biomaterials

    2024  Volume 307, Page(s) 122522

    Abstract: Cellular skin substitutes such as epidermal constructs have been developed for various applications, including wound healing and skin regeneration. These cellular models are mostly derived from primary cells such as keratinocytes and fibroblasts in a two- ...

    Abstract Cellular skin substitutes such as epidermal constructs have been developed for various applications, including wound healing and skin regeneration. These cellular models are mostly derived from primary cells such as keratinocytes and fibroblasts in a two-dimensional (2D) state, and further development of three-dimensional (3D) cultured organoids is needed to provide insight into the in vivo epidermal phenotype and physiology. Here, we report the development of epidermal organoids (EpiOs) generated from induced pluripotent stem cells (iPSCs) as a novel epidermal construct and its application as a source of secreted biomolecules recovered by extracellular vesicles (EVs) that can be utilized for cell-free therapy of regenerative medicine. Differentiated iPSC-derived epidermal organoids (iEpiOs) are easily cultured and expanded through multiple organoid passages, while retaining molecular and functional features similar to in vivo epidermis. These mature iEpiOs contain epidermal stem cell populations and retain the ability to further differentiate into other skin compartment lineages, such as hair follicle stem cells. By closely recapitulating the epidermal structure, iEpiOs are expected to provide a more relevant microenvironment to influence cellular processes and therapeutic response. Indeed, iEpiOs can generate high-performance EVs containing high levels of the angiogenic growth factor VEGF and miRNAs predicted to regulate cellular processes such as proliferation, migration, differentiation, and angiogenesis. These EVs contribute to target cell proliferation, migration, and angiogenesis, providing a promising therapeutic tool for in vivo wound healing. Overall, the newly developed iEpiOs strategy as an organoid-based approach provides a powerful model for studying basic and translational skin research and may also lead to future therapeutic applications using iEpiOs-secreted EVs.
    MeSH term(s) Epidermis ; Pluripotent Stem Cells ; Cell Differentiation ; Organoids ; Extracellular Vesicles ; Regeneration
    Language English
    Publishing date 2024-02-23
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 603079-8
    ISSN 1878-5905 ; 0142-9612
    ISSN (online) 1878-5905
    ISSN 0142-9612
    DOI 10.1016/j.biomaterials.2024.122522
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  7. Article: Marine invertebrate sialyltransferase of the sea squirt Ciona savignyi sialylated core 1 O-linked glycans

    Kim, Seonghun / Lee, Jinhyuk / Oh, Doo-Byoung / Kwon, Ohsuk

    International journal of biological macromolecules. 2022 Jan. 01, v. 194

    2022  

    Abstract: An invertebrate sialyltransferase, cST3Gal-I, identified from the sea squirt Ciona savignyi, was functionally characterized in vitro using recombinant enzyme expressed in yeast strains. cST3Gal-I was localized to the Golgi membrane when expressed in ... ...

    Abstract An invertebrate sialyltransferase, cST3Gal-I, identified from the sea squirt Ciona savignyi, was functionally characterized in vitro using recombinant enzyme expressed in yeast strains. cST3Gal-I was localized to the Golgi membrane when expressed in Saccharomyces cerevisiae. Enzymatic characterization for substrate specificity and kinetic property indicate that cST3Gal-I prefers O-glycans, rather than N-glycan, of asialoglycoproteins as substrates. Interestingly, C. savignyi sialyltransferase exhibited effectively Neu5Ac transfer to core 1 O-glycan, Gal β(1,3)GalNAc, compared to orthologous human glycosyltransferase. Further, it is shown that cST3Gal-I catalyzes the formation of α(2,3)-linkage, through lectin blot analysis with Maackia amurensis lectin and by linkage-specific sialidase treatments. The putative active sites of cST3Gal-I for putative acid/base catalysts and sialic acid acceptor/donor substrate bindings were also identical to the counterpart residues of a mammalian enzyme, porcine ST3Gal-I, as predicted through homologous structure modeling. These results could imply that an ancestral tunicate ST3Gal-I in C. savignyi would prefer O-glycan onto glycoproteins as its sialic acid acceptor than vertebrate enzymes.
    Keywords Ciona ; Maackia amurensis ; Saccharomyces cerevisiae ; glycoproteins ; glycosyltransferases ; humans ; invertebrates ; lectins ; polysaccharides ; sialic acid ; sialidase ; substrate specificity ; swine ; yeasts
    Language English
    Dates of publication 2022-0101
    Size p. 366-376.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2021.11.078
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  8. Article ; Online: Marine invertebrate sialyltransferase of the sea squirt Ciona savignyi sialylated core 1 O-linked glycans.

    Kim, Seonghun / Lee, Jinhyuk / Oh, Doo-Byoung / Kwon, Ohsuk

    International journal of biological macromolecules

    2021  Volume 194, Page(s) 366–376

    Abstract: An invertebrate sialyltransferase, cST3Gal-I, identified from the sea squirt Ciona savignyi, was functionally characterized in vitro using recombinant enzyme expressed in yeast strains. cST3Gal-I was localized to the Golgi membrane when expressed in ... ...

    Abstract An invertebrate sialyltransferase, cST3Gal-I, identified from the sea squirt Ciona savignyi, was functionally characterized in vitro using recombinant enzyme expressed in yeast strains. cST3Gal-I was localized to the Golgi membrane when expressed in Saccharomyces cerevisiae. Enzymatic characterization for substrate specificity and kinetic property indicate that cST3Gal-I prefers O-glycans, rather than N-glycan, of asialoglycoproteins as substrates. Interestingly, C. savignyi sialyltransferase exhibited effectively Neu5Ac transfer to core 1 O-glycan, Gal β(1,3)GalNAc, compared to orthologous human glycosyltransferase. Further, it is shown that cST3Gal-I catalyzes the formation of α(2,3)-linkage, through lectin blot analysis with Maackia amurensis lectin and by linkage-specific sialidase treatments. The putative active sites of cST3Gal-I for putative acid/base catalysts and sialic acid acceptor/donor substrate bindings were also identical to the counterpart residues of a mammalian enzyme, porcine ST3Gal-I, as predicted through homologous structure modeling. These results could imply that an ancestral tunicate ST3Gal-I in C. savignyi would prefer O-glycan onto glycoproteins as its sialic acid acceptor than vertebrate enzymes.
    MeSH term(s) Animals ; Aquatic Organisms/enzymology ; Ciona/enzymology ; Cloning, Molecular ; Enzyme Activation ; Gene Expression ; Genetic Linkage ; Glycosylation ; Invertebrates ; Phylogeny ; Polysaccharides/chemistry ; Recombinant Proteins ; Sialyltransferases/chemistry ; Sialyltransferases/genetics ; Structure-Activity Relationship
    Chemical Substances Polysaccharides ; Recombinant Proteins ; Sialyltransferases (EC 2.4.99.-)
    Language English
    Publishing date 2021-11-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2021.11.078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Characterization and activity-folding relationship of serine protease from Antarctic krill (

    Yin, Shang-Jun / Lee, Ho-Yeon / Wang, Wei / Lee, Jinhyuk / Park, Yong-Doo

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 11, Page(s) 5138–5151

    Abstract: Euphausia ... ...

    Abstract Euphausia superba
    MeSH term(s) Animals ; Euphausiacea/chemistry ; Serine Proteases ; Serine Endopeptidases ; Antarctic Regions ; Serine
    Chemical Substances Serine Proteases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; Serine (452VLY9402)
    Language English
    Publishing date 2022-05-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2022.2080115
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  10. Article ; Online: BERN2: an advanced neural biomedical named entity recognition and normalization tool.

    Sung, Mujeen / Jeong, Minbyul / Choi, Yonghwa / Kim, Donghyeon / Lee, Jinhyuk / Kang, Jaewoo

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 20, Page(s) 4837–4839

    Abstract: In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. ...

    Abstract In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.
    Availability and implementation: Web service of BERN2 is publicly available at http://bern2.korea.ac.kr. We also provide local installation of BERN2 at https://github.com/dmis-lab/BERN2.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Natural Language Processing ; Neural Networks, Computer ; Software
    Language English
    Publishing date 2022-09-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac598
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