Insights into the binding mechanism of ascorbic acid and violaxanthin with violaxanthin de-epoxidase (VDE) and chlorophycean violaxanthin de-epoxidase (CVDE) enzymes

Biswal, Satyaranjan; Gupta, Parth Sarthi Sen; Panda, Saroj Kumar; Bhat, Haamid Rasool; Rana, Malay Kumar

doi:10.1007/s11120-023-01006-0

Cited by 6 publications

(3 citation statements)

References 80 publications

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“…Hydrogen bond analysis was conducted using the 'gmx hbond' utility in GROMACS, while temperature and potential energy were determined through the 'gmx energy' tool. Furthermore, principal component analysis (PCA) was employed to assess the stability of protein complexes, proving to be highly advantageous [58] , [59] , [60] . The PCA for the MD trajectories obtained was carried out using the Bio3D package facilitated by the Galaxy European server [61] , [62] , [63] .…”

Section: Methodsmentioning

confidence: 99%

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

Uddin,

Meem,

Akter

et al. 2024

MethodsX

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Section: Methodsmentioning

confidence: 99%

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

Uddin,

Meem,

Akter

et al. 2024

MethodsX

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“…Various GROMACS utility tools, including gmx rmsd, gmx gyrate, gmx rmsf, and ‘gmx hbond’, were employed to generate graphs for RMSD, radius of gyration, RMSF, and hydrogen bonds of the ligands at 300 K over the 20 ns period. Furthermore, principal component analysis (PCA) was utilized to assess the stability of protein complexes, proving highly advantageous ( Biswal et al, 2023 ; Panda et al, 2023 ). PCA was carried out for the ligand-protein complexes ( 9 , 11 , 13 , and ofloxacin) at 300 K, as well as for compound 11 at temperature settings of 300 K, 305 K, 310 K, and 320 K, using the Bio3D package of GALAXY Europe server ( Grant et al, 2006 ; Afgan et al, 2018 ; Kumar et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation

Meem,

Yusuf,

Al Abbad

et al. 2024

Front. Chem.

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This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of −7.6, −7.9, −7.5, and −7.8 kcal mol−1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85%. Convergence was confirmed by the eigenvector’s cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.

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“…The "gmx hbond" utility in GROMACS was used for the analysis of hydrogen bonds, and the "gmx energy" tool was used to determine the temperature and potential energy. Furthermore, to evaluate the stability of protein complexes, the utilization of principal component analysis has been included and is found to be highly advantageous [71][72][73]. The principle component analysis (PCA) of the obtained MD trajectories was carried out using the Bio3D package via the Galaxy European server [74][75][76].…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Exploring the potential of fluoro‐flavonoid derivatives as anti‐lung cancer agents: DFT, molecular docking, and molecular dynamics techniques

Esha,

Quayum,

Saif

et al. 2023

Int J of Quantum Chemistry

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The present investigation utilized in silico methodologies to explore the diverse pharmacological activities, toxicity profiles, and chemical reactivity of a series of fluoro‐flavonoid compounds (1–14), which are secondary metabolites of plants known for their broad range of biological effects. A comprehensive strategy is utilized, incorporating methods such as prediction of activity spectra for substances (PASS) prediction, absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessments, and density functional theory (B3LYP) calculations using three basis sets: 6‐31G(d,p), 6‐311G(d,p), and 6‐311++G(d,p). Furthermore, the study employed molecular docking technique to identify target proteins, including HER2 (7JXH), EGFR (4UV7), FPPS (1YQ7), HPGDS (1V40), DCK (1P60), and KEAP1 on Nrf2 (1X2J), for the investigated compounds, with cianidanol and genistein serving as reference drugs for the docking process. The investigated fluoro‐flavonoid compounds exhibited significantly greater binding affinities (ranging from −8.3 to −10.6 kcal mol−1) toward HER2, HPGDS, and KEAP1 compared to the reference drugs, cianidanol and genistein, which displayed binding affinities ranging from −8.4 to −9.4 kcal mol−1. Furthermore, molecular dynamics simulations were conducted to assess the stability of the protein‐ligand interaction, using the root‐mean‐square deviation (RMSD), root‐mean‐square fluctuation (RMSF), Radius of gyration (Rg) parameters and principle component analysis (PCA). Among the tested fluoro‐flavonoid analogs, analog 11 showed a RMSD value of .15 nm with the HER2 protein target, indicating a stable interaction. Based on in silico results, it appears that the fluoro‐flavonoid compound 11 has the potential to serve as a targeted anti‐lung cancer drug. However, additional in vivo and in vitro studies are necessary to confirm this hypothesis.

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Insights into the binding mechanism of ascorbic acid and violaxanthin with violaxanthin de-epoxidase (VDE) and chlorophycean violaxanthin de-epoxidase (CVDE) enzymes

Cited by 6 publications

References 80 publications

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation

Exploring the potential of fluoro‐flavonoid derivatives as anti‐lung cancer agents: DFT, molecular docking, and molecular dynamics techniques

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