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

Thuý, Bùi Thị Phương; My, Tran Thi Ai; Hai, Nguyen Thi Thanh; Loan, Huynh Thi Phuong; Hiếu, Lê Trung; Hòa, Trần Thái; Bui, Thanh Q.; Tuong, Ho Nhat; Thủy, Nguyễn Thị Thu; Dung, Doan Thi Kim; Tất, Phạm Văn; Quy, Phan Tu; Nhung, Nguyen Thi Ai

doi:10.1007/s11224-020-01627-4

Cited by 10 publications

(4 citation statements)

References 35 publications

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“…Besides, the significance on the inhibitability is highly justifiable by comparison to other duo-systems already reported in the literature. [45][46][47] Consistently, another work using the docking environment given by Patchdock also predicted the fourth-ranked candidate D5 (aka. Oseltamivir) in this study as a moderate-promising inhibitor towards 6LU7 structure.…”

Section: Protein Inhibitabilitymentioning

confidence: 76%

An in silico study on inhibitability of Baloxavir marboxil, Baricitinib, Galidesivir, Nitazoxanide, and Oseltamivir against SARS‐CoV‐2

Bui,

Hai,

et al. 2022

Vietnam Journal of Chemistry

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Baloxavir marboxil (D1), Baricitinib (D2), Galidesivir (D3), Nitazoxanide (D4), and Oseltamivir (D5) are well‐known performing broad‐spectrum activity against a variety of viruses, thus holding high potentiality towards SARS‐CoV‐2. Quantum properties were examined using density functional theory (DFT). The inhibitability of the drugs towards Angiotensin‐converting enzyme 2 (ACE2) and SARS‐CoV‐2 main protease (6LU7) was evaluated by molecular docking simulation, while their bio‐compatibility was justified by physicochemical properties obtained from QSARIS‐based analysis in reference to Lipinski's rule of five. Quantum analysis suggests that the compounds are highly favourable for intermolecular interaction towards protein structures. Given ligand‐ACE2 systems, the inhibitory effectiveness follows the order D3‐ACE2 > D4‐ACE2 > D2‐ACE2 > D5‐ACE2 > D1‐ACE2; and the corresponding order for ligand‐6LU7 systems is D2‐6LU7 > D4‐6LU7 > D3‐6LU7 > D5‐6LU7 > D1‐6LU7. Galidesivir is predicted as the most effective inhibitor towards both targeted protein structures (DSaverage ‐13.1 kcal.mol‐1) and the most bio‐compatible molecule (Mass 264.9 amu; LogP ‐0.9; Polarisability 26.8 Å3). The theoretical screening suggests all drugs, especially Galidesivir (D3), promising for treatment of SARS‐CoV‐2 infection and encourages in‐related clinical trials.

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Section: Protein Inhibitabilitymentioning

confidence: 76%

An in silico study on inhibitability of Baloxavir marboxil, Baricitinib, Galidesivir, Nitazoxanide, and Oseltamivir against SARS‐CoV‐2

Bui,

Hai,

et al. 2022

Vietnam Journal of Chemistry

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“…Nevertheless, all RSMD values are considered correlating to bio‐conformational rigidness (widely accepted if <2). [38] In reference to either the control drug D‐P98088 (DS ‐10.7 kcal.mol ‐1 ; RMSD 1.89 Å) or the other duo‐systems already reported in the literature, [ 39‐41 ] all the figures indicate the promising intermolecular inhibitability of the ligands towards P98088 structure. Furthermore, F4‐P98088 and F5‐P98088 systems are found to form strong hydrophilic bonding between the ligands and specific amino acid residues of the protein structures, i.e.…”

Section: Resultsmentioning

confidence: 99%

In silico study on inhibitability of flavonoidal derivatives against Helicobacter pylori and their pharmacological potentiality

Quy,

Du,

Triet

et al. 2022

Vietnam Journal of Chemistry

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Flavonoidal derivatives sinensetin (F1), isoorientin (F2), naringenin (F3), morin (F4), daidzein (F5) were experimentally demonstrated with effectiveness against Helicobacter pylori, thus speculated for their inhibitory effects towards structures of mucin‐5AC protein (UniProtKB‐P98088) and urease (PDB‐1E9Z),and subjected for in silico investigations. Their quantum properties were examined using density functional theory (DFT). The ligand‐protein inhibitability was evaluated using molecular docking simulation. Physicochemical properties were obtained from QSARIS‐based analysis in reference to Lipinski's rule of five. Pharmacokinetic parameters were assessed by ADMET‐based analysis. DFT calculations indicate that there are no abnormal bonding constraints observed. NBO analysis suggests F2 and F4 possessing favourable electric configurations for intermolecular inhibition. Regarding ligand‐P98088, the order for static inhibitability is F2‐P98088 > F4‐P98088 > F3‐P98088 > F5‐P98088 > F1‐P98088. Regarding ligand‐1E9Z, the corresponding order follows: F2‐1E9Z ≈ F4‐1E9Z > F5‐1E9Z > F3‐1E9Z ≈ F1‐1E9Z. QSARIS‐based analysis reveals that all the candidates are highly bio‐compatible. ADMET‐based analysis specifies F2 as being safe and suitable for the use as orally administrated drugs. The results encourage further investigations for more in‐depth mechanisms and experimental validations, such as in vitro enzyme assays or clinical trials.

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“…For TPS, compound Lead 25 has good binding affinity to MoTps1 as evaluated in silico; closantel inhibits Tps1 of both C. albicans and Aspergillus fumigatus; silver-tetrylene and bis-silver-tetrylene complexes could be inhibitors of MoTps1 as evaluated with docking; and validoxylamine A and its derivative validoxylamine A 7′-phosphate inhibit the activity of Tps1/OtsA. ,− For TPP, N-(phenylthio)phthalimide has been found to be an inhibitor of nematode TPP . However, all of these compounds target only one enzyme, TPS or TPP.…”

Section: Discussionmentioning

confidence: 99%

Dual-Specificity Inhibitor Targets Enzymes of the Trehalose Biosynthesis Pathway

Chen,

Tang,

Jiang

et al. 2023

J. Agric. Food Chem.

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To reduce the risk of resistance development, a novel fungicide with dual specificity is demanded. Trehalose is absent in animals, and its synthases, trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP), are safe fungicide targets. Here, we report the discovery of a dual-specificity inhibitor of MoTps1 (Magnaporthe oryzae Tps1, TPS) and MoTps2 (M. oryzae Tps2, TPP). The inhibitor, named A1-4, was obtained from a virtual screening and subsequent surface plasmon resonance screening. In in vitro assays, A1-4 interacts with MoTps1 and MoTps2-TPP (MoTps2 TPP domain) and inhibits their enzyme activities. In biological activity assays, A1-4 not only inhibits the virulence of M. oryzae on host but also causes aggregation of conidia cytosol, which is a characteristic phenotype of MoTps2. Furthermore, hydrogen/deuterium exchange mass spectrometry assays support the notion that A1-4 binds to the substrate pockets of TPS and TPP. Collectively, A1-4 is a promising hit compound for the development of safe fungicide with dual-target specificity.

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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

Cited by 10 publications

References 35 publications

An in silico study on inhibitability of Baloxavir marboxil, Baricitinib, Galidesivir, Nitazoxanide, and Oseltamivir against SARS‐CoV‐2

An in silico study on inhibitability of Baloxavir marboxil, Baricitinib, Galidesivir, Nitazoxanide, and Oseltamivir against SARS‐CoV‐2

In silico study on inhibitability of flavonoidal derivatives against Helicobacter pylori and their pharmacological potentiality

Dual-Specificity Inhibitor Targets Enzymes of the Trehalose Biosynthesis Pathway

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