Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches

Bendaas, Ridha; Bekkar, Yahia; Messaadia, Lyamine; Bourougaa, Lotfi; Messaoudi, Abdelatif; Kiamouche, Samir; Messaoud, Benamira

doi:10.1007/s00894-024-05866-8

Cited by 3 publications

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Antioxidative Potential of 3‐Methoxyluteolin: Density Functional Theory (DFT), Molecular Docking, and Dynamics—A Combined Experimental and Computational Study

Trang,

Ha,

Son

2024

Chemistry & Biodiversity

View full text Add to dashboard Cite

The flavone 3‐methoxyluteolin (IC50 12.40 µg/mL) was comparable ascorbic acid in antioxidative activity against 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) radicals (IC50 11.38 µg/mL). From DFT (density functional theory) calculations, its principal radical mechanism in gas and lipid was the FHT (formal hydrogen transfer), whereas the SPL‐ET (sequential proton loss‐electron transfer) was the main way in water. Hydroxyl groups, especially at carbon C‐4', were the crucial radical scavenging sites. Kinetic evidence indicated that the reactions between the studied compound with HOO˙ radicals resulted in the koverall (overall rate constant) of 2.5 x 109 and 1.07 x 103 M–1 s–1 in water and pentyl ethanoate, respectively. The studied molecule chelated to Zn metal ion to form Zn(3‐methoxyluteolin)2 complex with the lowest binding energy value of –322.911 kcal/mol. Considering neurodegenerative inhibitory potentials of the studied compound, molecular docking results revealed that 3‐methoxyluteolin interacted with the active sites of both acetylcholinesterase (AChE) and butyrylcholinestease (BChE) with the binding affinities of –9.493 and –8.812 kcal/mol, respectively, which are stronger than the reference compound tacrine. To assess the structural stability and binding interactions with each studied protein, molecular dynamics simulations were conducted. The results indicated that the 3‐methoxyluteolin complexes with AChE and BChE remained stable during a simulation period.

show abstract

Antioxidative Potential of 3‐Methoxyluteolin: Density Functional Theory (DFT), Molecular Docking, and Dynamics—A Combined Experimental and Computational Study

Trang,

Ha,

Son

2024

Chemistry & Biodiversity

View full text Add to dashboard Cite

show abstract

Insight into the structural and dynamic properties of novel HSP90 inhibitors through DFT calculations and molecular dynamics simulations

Saouli,

Abrane,

Bidjou-Haiour

et al. 2024

J Mol Model

View full text Add to dashboard Cite

Insight into the Structural and Dynamic Properties of Novel HSP90 Inhibitors through DFT Calculations and Molecular Dynamics Simulations

Saouli,

Abrane,

Bidjou-Haiour

et al. 2024

Preprint

View full text Add to dashboard Cite

Context: Heat-shock proteins (HSPs), particularly HSP90, are critical molecular chaperones that maintain protein stability, especially in cancer cells. Elevated HSP90 levels in tumors aid in oncogenic protein stabilization. This study focuses on developing potent, selective HSP90 inhibitors to disrupt its chaperone function, targeting cancer cell survival. Using a de novo hybridization approach, we designed novel inhibitors by integrating structural fragments from a known HSP90-binding drug, leading to the creation of hybrid compounds C1, C2, and C3. A 300 ns molecular dynamics simulation of each system revealed that C1, C2, and C3 formed more stable complexes with HSP90 compared to the reference compound, MEY. RMSD, RMSF, Rg, SASA, and MM-PBSA metrics supported these findings. DCCM and FEL analyses confirmed that the inhibitors did not alter HSP90's initial configuration. Further DFT calculations with the B3LYP/6-311++(d,p) basis set assessed frontier molecular orbitals, MEP surfaces, ELF, LOL maps, TDOS and PDOS, affirming their potential as new anti-cancer therapies. Methods Maestro 11.8, Discovery Studio Visualizer, Gromacs-2023, Gaussian 16, and online platforms like SwissADME and ProTox-II were utilized. Fragments generated from eight known HSP90-binding drugs were subjected to SP-docking, leading to 170 fragments. The highest-scoring fragments were merged using the breed panel to create new HSP90 inhibitors. XP-docking and ADMET analyses identified C1, C2, and C3 as the most promising candidates. These compounds were selected for a 300 ns dynamic simulation and subsequent DFT calculations.

show abstract

Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches

Cited by 3 publications

References 52 publications

Antioxidative Potential of 3‐Methoxyluteolin: Density Functional Theory (DFT), Molecular Docking, and Dynamics—A Combined Experimental and Computational Study

Antioxidative Potential of 3‐Methoxyluteolin: Density Functional Theory (DFT), Molecular Docking, and Dynamics—A Combined Experimental and Computational Study

Insight into the structural and dynamic properties of novel HSP90 inhibitors through DFT calculations and molecular dynamics simulations

Insight into the Structural and Dynamic Properties of Novel HSP90 Inhibitors through DFT Calculations and Molecular Dynamics Simulations

Contact Info

Product

Resources

About