Journal Articles - Natural Science - 2020

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Browsing Journal Articles - Natural Science - 2020 by Author "Bui Thi Phuong Thuy"
  • Publication
    A density functional theory study on silver and bis-silver complexes with lighter tetrylene: are silver and bis-silver carbenes candidates for SARS-CoV-2 inhibition? Insight from molecular docking simulation
    ( 2020)
    Thanh Q. Bui
    ;
    Huynh Thi Phuong Loan
    ;
    Tran Thi Ai My
    ;
    Duong Tuan Quang
    ;
    Bui Thi Phuong Thuy
    ;
    Vo Duy Nhan
    ;
    Phan Tu Quy
    ;
    Pham Van Tat
    ;
    Duy Quang Dao
    ;
    Nguyen Tien Trung
    ;
    Lam K. Huynh
    ;
    Nguyen Thi Ai Nhung
    Ribavirin and remdesivir have been preclinically reported as potential drugs for the treatment of SARS-CoV- 2 infection, while light silver tetrylene complexes (NHEPh–AgCl and (NHEPh–AgCl)2 with E ¼ C, Si, and Ge) have gained significant interest due to their promising applicability on the cytological scale. Firstly, the structures and bonding states of silver–tetrylene complexes (NHE–Ag) and bis-silver–tetrylene complexes (NHE–Ag-bis) were investigated using density functional theory (DFT) at the BP86 level with the def2-SVP and def2-TZVPP basis sets. Secondly, the inhibitory capabilities of the carbene complexes (NHC–Ag and NHC–Ag-bis) and the two potential drugs (ribavirin and remdesivir) on human-protein ACE2 and SARS-CoV-2 protease PDB6LU7 were evaluated using molecular docking simulation. The carbene ligand NHC bonds in a head-on configuration with AgCl and (AgCl)2, whereas, the other NHE (E ¼ Si and Ge) tetrylene ligands bond in a side-on mode to the metal fragments. The bond dissociation energy (BDE) of the NHE–Ag bond in the complex families follows the order of NHC–Ag > NHSi–Ag > NHGe–Ag and NHSi–Ag-bis > NHGe–Ag-bis > NHC–Ag-bis. The natural bond orbital analysis implies that the [NHEPh/AgCl] and [(NHEPh)2/(AgCl)2] donations are derived mainly from the s- and pcontributions of the ligands. The docking results indicate that both the ACE2 and PDB6LU7 proteins are strongly inhibited by silver–carbene NHC–Ag, bis-silver–carbene NHC–Ag-bis, ribavirin, and remdesivir with the docking score energy values varying from 17.5 to 16.5 kcal mol 1 and 16.9 to 16.6 kcal mol 1, respectively. The root-mean-square deviation values were recorded to be less than 2 A in all the calculated systems. Thus, the present study suggests that silver–carbene NHC–Ag and bissilver– carbene NHC–Ag-bis complexes are potential candidates to inhibit ACE2 and PDB6LU7, and thus potentially conducive to prevent infection caused by the SARS-CoV-2 virus.
  • Publication
    A molecular docking simulation study on potent inhibitors against Rhizoctonia solani and Magnaporthe oryzae in rice: silver-tetrylene and bis-silver-tetrylene complexes vs. validamycin and tricyclazole pesticides
    ( 2020)
    Bui Thi Phuong Thuy
    ;
    Tran Thi Ai My
    ;
    Nguyen Thi Thanh Hai
    ;
    Huynh Thi Phuong Loan
    ;
    Le Trung Hieu
    ;
    Tran Thai Hoa
    ;
    Thanh Q. Bui
    ;
    Ho Nhat Tuong
    ;
    Nguyen Thi Thu Thuy
    ;
    Doan Kim Dung
    ;
    Pham Van Tat
    ;
    Phan Tu Quy
    ;
    Nguyen Thi Ai Nhung
    Rice, well known as the most important staple food source worldwide, is highly susceptible to many infectious diseases, especially rice sheath blight caused by fungus Rhizoctonia solani and rice blast caused by fungus Magnaporthe oryzae. The inhibitory ability of silver- and bis-silver-tetrylene complexes, including Ag-E and bis-Ag-E with E = C, Si, Ge, onto protein 4G9M in Rhizoctonia solani and protein 6JBR in Magnaporthe oryzae was theoretically investigated using molecular docking simulation methodology. Two commercial pesticides selected as inhibitory references are validamycin for 4G9M and tricyclazole for 6JBR. The results reveal that bis-silver-tetrylene complexes perform the strongest inhibitory effects towards both proteins. The structures of the complexes exhibit good site–site binding to both proteins given the observations on the hydrogen bond interactions, cation–π bonds, π–π bonds, and ionic interactions, interaction distance between amino acids and ligands, and van der Waals interactions. The inhibitory capacity onto protein 4G9M decreases in the following order: bis-Ag-C > bis-Ag-Si > bis-Ag-Ge > validamycin > Ag-C ≈ Ag-Si ≈ Ag-Ge. The corresponding order observed from the study for protein 6JBR is bis- Ag-C > bis-Ag-Si ≈ bis-Ag-Ge > tricyclazole ≈ Ag-C ≈ Ag-Si ≈ Ag-Ge. The study opens a promising approach to tackle rice blast and rice sheath blight based on a family of silver-tetrylene organometallic chemicals given the theoretical proof of environment-advanced properties and molecule-scaled effectiveness.
  • Publication
    Antioxidant activity of some natural essential oils in Vietnam: Comparison between QSAR simulation and experimental study
    ( 2020)
    Tran Thi Ai My
    ;
    Le Trung Hieu
    ;
    Nguyen Thi Thanh Hai
    ;
    Ton Nu My Phuong
    ;
    Huynh Thi Phuong Loan
    ;
    Bui Thi Phuong Thuy
    ;
    Nguyen Thi Ai Nhung
    Antioxidant activities of essential oils from leaves of Piper betle L. (T) and Cleistocalyx operculatus L. (V), and aerial parts of Ageratum conyzoides L. (H) natively grown in Thua Thien Hue province of Vietnam were investigated. Quantitative structure–activity relationship (QSAR) model was constructed from the 27 compounds including 4-hydroxy-chromene-2H-one and its derivatives. DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity was applied to estimate the antioxidant property of these essential oils through IC50 (μg/mL) values. QSAR model is used to predict the radical scavenging activity IC50 μg/mL of T, V, and H. The results indicate that there is a good agreement between the experimental data and the predicted values using the QSAR model. The three essential oils display the DPPH radical scavenging activities with the IC50 values being in the order of T > H > V of 3.71 μg/mL, 596.44 μg/mL and 637.03 μg/mL, respectively. The essential oil of T exhibits the strong DPPH radical scavenging activity that is close to the reference compound ascorbic acid (IC50 value of 3.03 μg /mL).
  • Publication
    Coordination complexes of slight tetrylene with platinum(II)-8-hydroxyquinolines: Structure and bonding analysis
    ( 2020)
    Huynh Thi Phuong Loan
    ;
    Hoang Van Duc
    ;
    Phan Tu Quy
    ;
    Bui Thi Phuong Thuy
    ;
    Pham Van Tat
    ;
    Duong Tuan Quang
    ;
    Nguyen Thi Ai Nhung
    The structure and bonding situation in platinum complexes containing slight tetrylene ligands [{PtCl-C9H6NO}-NHE] (Pt-NHE) with E = C, Si, Ge were examined by DFT calculations with the levels are BP86/def2-SVP and BP86/def2-TZVPP. The predicted equilibrium structure of the ligands NHE in Pt-NHE are bonded in distorted end-on way to PtCl-8-hydroxyquinolines fragment with the bending angle, , exhibits the biggest value in carbenes systems then slightly decrease from Pt-NHC to Pt-NHGe. Bond dissociation energies (BDEs), De (kcal.mol-1), decrease from the carbene complex to the weaker bonded silylene and germylene manners. The BDE when considering dispersion correction at the BP86-D3(BJ)/def2-TZVPP level confirms that Pt-E bond in Pt-NHE belongs to the effect of the bulky group in slight tetrylene NHE and Pt(II)-group fragment which makes the intrinsic Pt-E bond strength decreases from carbene to germylene complexes. The hybridization of atoms E and Pt have large p characters while the hybridization of atom Pt has greater d character which lead to the Pt-E bond possesses not only NHE→{PtCl-C9H6NO} strong -donation but also a significant contribution π-donation NHE→{PtCl-C9H6NO} and weak π-backdonation metal-ligand NHE←{PtCl-C9H6NO} in complexes Pt-NHE.
  • Publication
    Investigation into SARS-CoV-2 Resistance of Compounds in Garlic Essential Oil
    ( 2020)
    Bui Thi Phuong Thuy
    ;
    Tran Thi Ai My
    ;
    Nguyen Thi Thanh Hai
    ;
    Le Trung Hieu
    ;
    Tran Thai Hoa
    ;
    Huynh Thi Phuong Loan
    ;
    Nguyen Thanh Triet
    ;
    Tran Thi Van Anh
    ;
    Phan Tu Quy
    ;
    Pham Van Tat
    ;
    Nguyen Van Hue
    ;
    Duong Tuan Quang
    ;
    Nguyen Tien Trung
    ;
    Vo Thanh Tung
    ;
    Lam K. Huynh
    ;
    Nguyen Thi Ai Nhung
    Eighteen active substances, including 17 organosulfur compounds found in garlic essential oil (T), were identified by GC−MS analysis. For the first time, using the molecular docking technique, we report the inhibitory effect of the considered compounds on the host receptor angiotensin-converting enzyme 2 (ACE2) protein in the human body that leads to a crucial foundation about coronavirus resistance of individual compounds on the main protease (PDB6LU7) protein of SARS-CoV-2. The results show that the 17 organosulfur compounds, accounting for 99.4% contents of the garlic essential oil, have strong interactions with the amino acids of the ACE2 protein and the main protease PDB6LU7 of SARS-CoV- 2. The strongest anticoronavirus activity is expressed in allyl disulfide and allyl trisulfide, which account for the highest content in the garlic essential oil (51.3%). Interestingly, docking results indicate the synergistic interactions of the 17 substances, which exhibit good inhibition of the ACE2 and PDB6LU7 proteins. The results suggest that the garlic essential oil is a valuable natural antivirus source, which contributes to preventing the invasion of coronavirus into the human body
  • Publication
    Screening for Streptococcus pyogenes antibacterial and Candida albicans antifungal bioactivities of organic compounds in natural essential oils of Piper betle L., Cleistocalyx operculatus L. and Ageratum conyzoides L.
    ( 2020)
    Bui Thi Phuong Thuy
    ;
    Le Trung Hieu
    ;
    Tran Thi Ai My
    ;
    Nguyen Thi Thanh Hai
    ;
    Huynh Thi Phuong Loan
    ;
    Nguyen Thi Thu Thuy
    ;
    Nguyen Thanh Triet
    ;
    Tran Thi Van Anh
    ;
    Nguyen Thi Xuan Dieu
    ;
    Phan Tu Quy
    ;
    Nguyen Van Trung
    ;
    Duong Tuan Quang
    ;
    Lam K. Huynh
    ;
    Nguyen Thi Ai Nhung
    Chemical composition and bioactivities including bacterial and fungal resistance of the essential oils extracted from leaves of Piper betle L. (T) and Cleistocalyx operculatus L. (V) and aerial parts of Ageratum conyzoides L. (H) were investigated. The components presenting in the essential oils of the natural sources were analysized by a gas chromatography–mass spectrometry. Molecular docking simulation was utilised to support an antimicrobial mechanism of the essential oil compounds on Candida albicans fungus and Streptococcus pyogenes bacteria. This was based on the inhibition of the extracted compounds onto the microbial proteins, i.e. 4ESW and P0C0C7, respectively. There are 32 compounds identified in total in the three essential oils. The most effective inhibitors are the following: (i) chavicol acetate (T3), eugenol acetate (T11) and eugenol (T4) found in Piper betle L.; (ii) precocene II (H10) and precocene I (H6) found in Ageratum conyzoides L.; and (iii) caryophyllene oxide (V15) and cis-Lanceol (V19) found in Cleistocalyx operculatus L.. The overall antifungal and antibacterial capability of the investigated essential oils given indirect justification via their average inhabitability towards the two proteins accords with the order Piper betle L. Ageratum conyzoides L. Cleistocalyx operculatus L.. The results suggest these as promising natural sources for antimicrobial remedies.