Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations

Molecular Dynamics Simulations on Quercetin-3-(6-Malonylglucoside) FromMorus AlbaShows Optimal Inhibition of Bcl-2 with Favorable Anti-Tumor Activities

“…By calculating the free energy difference between different ligand-protein complexes, MM-GBSA can rank and prioritize potential drug candidates based on their predicted binding affinities. This information aids in lead optimization and selecting compounds with the highest likelihood of binding to the target effectively (Wu et al, 2021). The MM-GBSA studies indicated that the compounds are bound favorably to the active site of the target protein, as indicated by the values presented in table 2.…”

Binding selectivity analysis of AURKs inhibitors through molecular dynamics simulation studies

“…With the rapid advancement of simulation and calculation methods [ 22 ], several molecular dynamics (MD) techniques, such as traditional MD [ 23 , 24 ], multiple short molecular dynamics simulations [ 25 , 26 ], accelerated MD (aMD) simulations [ 22 , 27 , 28 ], have been widely used to carry out target conformational evolution, various techniques for predicting binding free energy, including the Poisson Boltzmann surface area (MM-PBSA) method [ 29 , 30 ], thermodynamics integration (TI) [ 31 , 32 ], free energy perturbation (FEP) [ 33 , 34 ], and solvated interaction energy (SIE) methods [ 35 , 36 ], are frequently used to assess ligands’ capacity to bind to targets. Furthermore, techniques for machine learning and deep learning are presented to effectively examine the ligand-target binding process and reveal the underlying molecular causes of ligand-target interactions [ 37 , 38 ].…”

Theoretical exploration of the binding selectivity of inhibitors to BRD7 and BRD9 with multiple short molecular dynamics simulations

“…With fast development of calculation approach and simulation technology, 27–34 various molecular dynamics (MD) methods, including conventional MD, 35–39 multiple molecular dynamics (multiple short molecular dynamics), 40–42 accelerated MD (aMD) simulations, 34,43–51 have been widely utilized to perform conformational evolution of targets. Different methods of binding free energy prediction, involved molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), 52–57 thermodynamics integration (TI), 58,59 free energy perturbation (FEP) 60,61 and solvated interaction energy (SIE) 62–64 methods, are extensively applied to evaluate binding ability of ligands to targets.…”

“…23 Despite extensive experimental researches on interaction mechanism of inhibitors with BRD7 and BRD9 in different works, decoding the conformational changes of these two proteins at atom levels because of inhibitor associations are still highly essential. 25,26 With fast development of calculation approach and simulation technology, [27][28][29][30][31][32][33][34] various molecular dynamics (MD) methods, including conventional MD, [35][36][37][38][39] multiple molecular dynamics (multiple short molecular dynamics), [40][41][42] accelerated MD (aMD) simulations, 34,[43][44][45][46][47][48][49][50][51] have been widely utilized to perform conformational evolution of targets. Different methods of binding free energy prediction, involved molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), [52][53][54][55][56][57] thermodynamics integration (TI), 58,59 free energy perturbation (FEP) 60,61 and solvated interaction energy (SIE) [62][63][64] methods, are extensively applied to evaluate binding ability of ligands to targets.…”