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  1. Article ; Online: Exploring Major Flavonoid Phytochemicals from

    Nutho, Bodee / Tungmunnithum, Duangjai

    International journal of molecular sciences

    2023  Volume 24, Issue 23

    Abstract: ... Nelumbo ... ...

    Abstract Nelumbo nucifera
    MeSH term(s) Flavonoids/pharmacology ; Flavonoids/chemistry ; Plant Extracts/pharmacology ; Plant Extracts/chemistry ; Nelumbo ; Monophenol Monooxygenase ; Molecular Docking Simulation ; Pancreatic Elastase ; Collagenases ; Phytochemicals/pharmacology
    Chemical Substances Flavonoids ; Plant Extracts ; Monophenol Monooxygenase (EC 1.14.18.1) ; Pancreatic Elastase (EC 3.4.21.36) ; Collagenases (EC 3.4.24.-) ; Phytochemicals
    Language English
    Publishing date 2023-11-21
    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/ijms242316571
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Exploring Major Flavonoid Phytochemicals from Nelumbo nucifera Gaertn. as Potential Skin Anti-Aging Agents

    Bodee Nutho / Duangjai Tungmunnithum

    International Journal of Molecular Sciences, Vol 24, Iss 23, p

    In Silico and In Vitro Evaluations

    2023  Volume 16571

    Abstract: Nelumbo nucifera Gaertn., an aquatic medicinal plant (Nelumbonaceae family), has a history of use in traditional medicine across various regions. Our previous study demonstrated the skin anti-aging potential of its stamen ethanolic extract by effectively ...

    Abstract Nelumbo nucifera Gaertn., an aquatic medicinal plant (Nelumbonaceae family), has a history of use in traditional medicine across various regions. Our previous study demonstrated the skin anti-aging potential of its stamen ethanolic extract by effectively inhibiting collagenase and tyrosinase enzymes. While the major constituents of this extract are well documented, there is a lack of research on the individual compounds’ abilities to inhibit skin aging enzymes. Therefore, this study aimed to evaluate the anti-aging potential of the primary flavonoids found in N. nucifera using both in silico and in vitro approaches. Our initial step involved molecular docking to identify compounds with the potential to inhibit collagenase, elastase, and tyrosinase. Among the seven flavonoids studied, kaempferol-3- O -robinobioside (Kae-3-Rob) emerged as the most promising candidate, exhibiting the highest docking scores for three skin aging-related enzymes. Subsequent enzyme-based inhibition assays confirmed that Kae-3-Rob displayed robust inhibitory activity against collagenase (58.24 ± 8.27%), elastase (26.29 ± 7.16%), and tyrosinase (69.84 ± 6.07%). Furthermore, we conducted extensive 200-ns molecular dynamics (MD) simulations, revealing the stability of the complexes formed between Kae-3-Rob and each enzyme along the MD simulation time. MM/PBSA-based binding free energy calculations indicated the considerably stronger binding affinity of Kae-3-Rob for collagenase and tyrosinase compared to elastase, which was related to the greater percentage of hydrogen bond occupations. These computational findings were consistent with the relatively high inhibitory activity of Kae-3-Rob against collagenase and tyrosinase observed in our in vitro experiment. In conclusion, the results obtained from this comprehensive study suggest that Kae-3-Rob, a key flavonoid from N. nucifera , holds significant potential as a source of bioactive compounds for anti-aging cosmeceutical and other phytopharmaceutical application.
    Keywords lotus plant ; skin-aging enzyme inhibition ; molecular docking ; molecular dynamics simulation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 571
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Structural Dynamics of the Precatalytic State of Human Cytochrome c upon T28C, G34C, and A50C Mutations: A Molecular Dynamics Simulation Perspective.

    Nutho, Bodee / Samsri, Sasiprapa / Pornsuwan, Soraya

    ACS omega

    2023  Volume 8, Issue 17, Page(s) 15229–15238

    Abstract: The native structure of ... ...

    Abstract The native structure of cytochrome
    Language English
    Publishing date 2023-04-17
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c00220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Efficiency of membrane fusion inhibitors on different hemagglutinin subtypes: insight from a molecular dynamics simulation perspective.

    Nunthaboot, Nadtanet / Boonma, Thitiya / Rajchakom, Chananya / Nutho, Bodee / Rungrotmongkol, Thanyada

    Journal of biomolecular structure & dynamics

    2024  , Page(s) 1–12

    Abstract: The challenge in vaccine development, along with drug resistance issues, has encouraged the search for new anti-influenza drugs targeting different viral proteins. Hemagglutinin (HA) glycoprotein, crucial in the viral replication cycle, has emerged as a ... ...

    Abstract The challenge in vaccine development, along with drug resistance issues, has encouraged the search for new anti-influenza drugs targeting different viral proteins. Hemagglutinin (HA) glycoprotein, crucial in the viral replication cycle, has emerged as a promising therapeutic target. CBS1117 and JNJ4796 were reported to exhibit similar potencies against infectious group 1 influenza, which included H1 and H5 HAs; however, their potencies were significantly reduced against group 2 HA. This study aims to explore the molecular binding mechanisms and group specificity of these fusion inhibitors against both group 1 (H5) and group 2 (H3) HA influenza viruses using molecular dynamics simulations. CBS1117 and JNJ4796 exhibit stronger interactions with key residues within the H5 HA binding pocket compared to H3-ligand complexes. Hydrogen bonding and hydrophobic interactions involving residues, such as H38
    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 10.1080/07391102.2024.2322629
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  5. Article ; Online: Naturally occurring quercetin and myricetin as potent inhibitors for human ectonucleotide pyrophosphatase/phosphodiesterase 1.

    Duangiad, Peeradon / Nutho, Bodee / Chaijarasphong, Thawatchai / Morales, Noppawan Phumala / Pongtharangkul, Thunyarat / Hamachi, Itaru / Ojida, Akio / Wongkongkatep, Jirarut

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 125

    Abstract: Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto Green, a ... ...

    Abstract Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto Green, a rapid chemical sensor of pyrophosphate, was employed to screen for effective ENPP1 inhibitors among five representative flavonoids (quercetin, myricetin, morin, kaempferol, and quercetin-3-glucoside), five nucleosides (adenosine, guanosine, inosine, uridine, and cytidine), and five deoxynucleosides (2'- and 3'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxyinosine, and 2'-deoxyuridine). Conventional colorimetric, fluorescence, and bioluminescence assays revealed that ENPP1 was effectively inhibited by quercetin (K
    MeSH term(s) Humans ; Quercetin/pharmacology ; Flavonoids/pharmacology ; Flavonoids/chemistry ; Phosphoric Diester Hydrolases/metabolism ; Pyrophosphatases/metabolism
    Chemical Substances myricetin (76XC01FTOJ) ; Quercetin (9IKM0I5T1E) ; Flavonoids ; Phosphoric Diester Hydrolases (EC 3.1.4.-) ; Pyrophosphatases (EC 3.6.1.-)
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-50590-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective.

    Boonma, Thitiya / Soikudrua, Nattharuja / Nutho, Bodee / Rungrotmongkol, Thanyada / Nunthaboot, Nadtanet

    Computational biology and chemistry

    2022  Volume 101, Page(s) 107764

    Abstract: Recently, the H3N2 influenza outbreak has caused serious global public health concern for future control of the next influenza pandemic. Since using current anti-influenza drugs targeting neuraminidase (oseltamivir and zanamivir) and the proton M2 ... ...

    Abstract Recently, the H3N2 influenza outbreak has caused serious global public health concern for future control of the next influenza pandemic. Since using current anti-influenza drugs targeting neuraminidase (oseltamivir and zanamivir) and the proton M2 channel (amantadine and rimantadine) leads to drug resistance, it is essential to seek new anti-viral agents that act on additional viral targets. Hemagglutinin (HA), a glycoprotein embedded in the viral surface and playing a critical role in influenza the viral replication cycle has become an attractive target. This work investigates the molecular binding mechanism of HA H3N2 of influenza virus complexed with the fusion inhibitor, arbidol and its derivative (der-arbidol), by means of molecular dynamics simulation. The result showed that the arbidol derivative could form many and strong hydrogen bonds with the HA surrounding amino acids comprising GLU103
    MeSH term(s) Humans ; Influenza A Virus, H3N2 Subtype ; Hemagglutinins ; Molecular Dynamics Simulation ; Oseltamivir/pharmacology ; Oseltamivir/therapeutic use ; Antiviral Agents/chemistry ; Influenza, Human/drug therapy
    Chemical Substances umifenovir (93M09WW4RU) ; Hemagglutinins ; Oseltamivir (20O93L6F9H) ; Antiviral Agents
    Language English
    Publishing date 2022-08-28
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2022.107764
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species.

    Bhat, Nayana / Nutho, Bodee / Hanpaibool, Chonnikan / Hadsadee, Sarinya / Vangnai, Alisa / Rungrotmongkol, Thanyada

    Proteins

    2023  Volume 92, Issue 1, Page(s) 96–105

    Abstract: Methyl parathion hydrolase (MPH) is an enzyme of the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphates (OPs). Recently, MPH has attracted attention as a promising enzymatic bioremediator. The crystal structure of MPH ... ...

    Abstract Methyl parathion hydrolase (MPH) is an enzyme of the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphates (OPs). Recently, MPH has attracted attention as a promising enzymatic bioremediator. The crystal structure of MPH enzyme shows a dimeric form, with each subunit containing a binuclear metal ion center. MPH also demonstrates metal ion-dependent selectivity patterns. The origins of these patterns remain unclear but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. We aimed to investigate and compare the binding of different OP pesticides to MPH with cobalt(II) metal ions. In this study, MPH was modeled from Ochrobactrum sp. with different OP pesticides bound, including methyl paraoxon and dichlorvos and profenofos. The docked structures for each substrate optimized by DFT calculation were selected and subjected to atomistic molecular dynamics simulations for 500 ns. It was found that alpha metal ions did not coordinate with all the pesticides. Rather, the pesticides coordinated with less buried beta metal ions. It was also observed that the coordination of beta metal ions was perturbed to accommodate the pesticides. The binding free energy calculations and structure-based pharmacophore model revealed that all the three substrates could bind well at the active site. However, profenofos exhibit a stronger binding affinity to MPH in comparison to the other two substrates. Therefore, our findings provide molecular insight on the binding of different OP pesticides which could help us design the enzyme for OP pesticides degradation.
    MeSH term(s) Methyl Parathion/metabolism ; Organophosphates/chemistry ; Organophosphates/metabolism ; Hydrolases ; Ochrobactrum/metabolism ; Phosphoric Monoester Hydrolases/chemistry ; Phosphoric Monoester Hydrolases/metabolism ; Pesticides ; Metals/chemistry ; Ions
    Chemical Substances Methyl Parathion (41BCL2O91D) ; profenofos (7J04O7BS4W) ; Organophosphates ; Hydrolases (EC 3.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2) ; Pesticides ; Metals ; Ions
    Language English
    Publishing date 2023-08-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26579
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Naturally occurring quercetin and myricetin as potent inhibitors for human ectonucleotide pyrophosphatase/phosphodiesterase 1

    Peeradon Duangiad / Bodee Nutho / Thawatchai Chaijarasphong / Noppawan Phumala Morales / Thunyarat Pongtharangkul / Itaru Hamachi / Akio Ojida / Jirarut Wongkongkatep

    Scientific Reports, Vol 14, Iss 1, Pp 1-

    2024  Volume 13

    Abstract: Abstract Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto ... ...

    Abstract Abstract Ecto-nucleotide pyrophosphatases/phosphodiesterases 1 (ENPP1) is a key enzyme in purinergic signaling pathways responsible for cell-to-cell communications and regulation of several fundamental pathophysiological processes. In this study, Kyoto Green, a rapid chemical sensor of pyrophosphate, was employed to screen for effective ENPP1 inhibitors among five representative flavonoids (quercetin, myricetin, morin, kaempferol, and quercetin-3-glucoside), five nucleosides (adenosine, guanosine, inosine, uridine, and cytidine), and five deoxynucleosides (2′- and 3′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxyinosine, and 2′-deoxyuridine). Conventional colorimetric, fluorescence, and bioluminescence assays revealed that ENPP1 was effectively inhibited by quercetin (K i ~ 4 nM) and myricetin (K i ~ 32 nM) when ATP was used as a substrate at pH 7.4. In silico analysis indicated that the presence of a chromone scaffold, particularly one containing a hydroxyl group at the 3′ position on the B ring, may promote binding to the active site pocket of ENPP1 and enhance inhibition. This study demonstrated that the naturally derived quercetin and myricetin could effectively inhibit ENPP1 enzymatic activity and may offer health benefits in arthritis management.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Molecular insights on the conformational dynamics of a P76C mutant of human cytochrome c and the enhancement on its peroxidase activity.

    Samsri, Sasiprapa / Prasertsuk, Possawee / Nutho, Bodee / Pornsuwan, Soraya

    Archives of biochemistry and biophysics

    2021  Volume 716, Page(s) 109112

    Abstract: In apoptotic pathway, the interaction of Cytochrome c (Cytc) with cardiolipin in vivo is a key process to induce peroxidase activity of Cytc and trigger the release of Cytc in the inner mitochondria into cytosol. The peroxidase active form of Cytc occurs ...

    Abstract In apoptotic pathway, the interaction of Cytochrome c (Cytc) with cardiolipin in vivo is a key process to induce peroxidase activity of Cytc and trigger the release of Cytc in the inner mitochondria into cytosol. The peroxidase active form of Cytc occurs due to local conformational changes that support the opening of the heme crevice and the loss of an axial ligand between Met80 and heme Fe. Structural adjustments at the Ω-loop segments of Cytc are required for such process. To study the role of the distal Ω-loop segments comprising residues 71-85 in human Cytc (hCytc), we investigated a cysteine mutation at Pro76, one of the highly conserved residues in this loop. The effect of P76C mutant was explored by the combination of experimental characterizations and molecular dynamics (MD) simulations. The peroxidase activity of the P76C mutant was found to be significantly increased by ∼13 folds relative to the wild type. Experimental data on global denaturation, alkaline transition, heme bleaching, and spin-labeling Electron Spin Resonance were in good agreement with the enhancement of peroxidase activity. The MD results of hCytc in the hexacoordinate form suggest the important changes in P76C mutant occurred due to the unfolding at the central Ω-loop (residues 40-57), and the weakening of H-bond between Tyr67 and Met80. Whereas the experimental data implied that the P76C mutant tend to be in equilibrium between the pentacoordinate and hexacoordinate forms, the MD and experimental information are complementary and were used to support the mechanisms of peroxidase active form of hCytc.
    MeSH term(s) Amino Acid Sequence ; Cardiolipins/metabolism ; Cysteine/chemistry ; Cytochromes c/genetics ; Cytochromes c/metabolism ; Enzyme Activation ; Heme/metabolism ; Humans ; Molecular Dynamics Simulation ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Mutation ; Peroxidases/metabolism ; Protein Conformation ; Structure-Activity Relationship
    Chemical Substances Cardiolipins ; Mutant Proteins ; Heme (42VZT0U6YR) ; Cytochromes c (9007-43-6) ; Peroxidases (EC 1.11.1.-) ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2021-12-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2021.109112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Binding recognition of substrates in NS2B/NS3 serine protease of Zika virus revealed by molecular dynamics simulations.

    Nutho, Bodee / Rungrotmongkol, Thanyada

    Journal of molecular graphics & modelling

    2019  Volume 92, Page(s) 227–235

    Abstract: Zika virus (ZIKV) has become a global public health concern. The recent epidemiological data has revealed a possible association of ZIKV infection with more serious complications, particularly for Guillain-Barré syndrome in adults and microcephaly in ... ...

    Abstract Zika virus (ZIKV) has become a global public health concern. The recent epidemiological data has revealed a possible association of ZIKV infection with more serious complications, particularly for Guillain-Barré syndrome in adults and microcephaly in newborn children. Till now, there is no vaccine or effective drug commercially available to combat with ZIKV infection. An attractive drug target for the ZIKV treatment is the NS2B/NS3 serine protease, which is essential for viral polyprotein processing. Herein, classical molecular dynamics (MD) simulations were performed on the ZIKV NS2B/NS3 serine protease in complex with four peptide substrates to investigate the binding recognition and protein-substrate interactions. The obtained results indicate that the P1 and P2 positions of the substrate play a significant role in binding with the protease enzyme, while the P3 and P4 positions show a minor contribution in binding interaction. Moreover, the binding free energy calculation based on the MM/PBSA method suggests that among the four similar peptide substrates, the peptide Ac-D-RKOR-ACC displays the strongest binding affinity towards the ZIKV protease due to the high energy contribution at the S2 subsite particularly for the NS3 residue D75 with the P2(O) residue of this substrate, which is in line with the experimental data. Thus, the information derived from MD simulations presented here would be useful for the design of potent protease inhibitors.
    MeSH term(s) Binding Sites ; Catalytic Domain ; Humans ; Hydrogen Bonding ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases/chemistry ; Protein Binding ; Protein Conformation ; Substrate Specificity ; Viral Proteins/chemistry ; Zika Virus/enzymology
    Chemical Substances Ligands ; Viral Proteins ; NS3 protein, zika virus (EC 3.4.-) ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2019-08-02
    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.2019.08.001
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