Free energy of solvation from molecular dynamics simulations for low dielectric solvents

In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae

Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.

Molecular dynamics simulation of polystyrene copolymer with octyl short-chain branches in toluene

In this study, dimensional, conformational and dynamic behaviors of a short-chain branched styrene/1-octene copolymer chain with different 1-octene percentages, i.e., 0, 2, 4 and 6%, in toluene are investigated at the temperature of 298.15 K via molecular dynamics simulation. The chain dimensions and flexibility in the solvent are evaluated by calculating the radius of gyration (R_g), end-to-end distance (<r₀>), surface area (A_ch), and volume (V_ch) of the copolymer chain. The mean square displacement (MSD) and diffusivity coefficient for each copolymer chain are measured to determine its dynamic behavior and mobility in aromatic media. To consider the effect of increasing the 1-octene co-monomer percentage on the copolymer chain affinity to the solvent molecules, the interaction energy (E_int) and Flory-Huggins (FH) interaction parameter are calculated for each equilibrated solution model. The simulation results indicate that the co-monomer level increment in the copolymer structure reduces the chain R_g amount and its interaction with the solvent. The <r₀> of the chain increases up to 4% co-monomer content, while further co-monomer content decreases the <r₀> value. Additionally, the viscosity of the equilibrated dilute solutions is calculated via non-equilibrium molecular dynamics simulation (NEMD). Moreover, the steric hindrance of the copolymers and the solvent molecules capturing in the dilute solution is determined via radial distribution function (RDF) analysis. Helmholtz free energy and the system entropy changes are calculated to evaluate the tendency of the copolymer to the solvent molecules and its dilute solution irregularity, respectively. Graphical abstract The figure shows the variations trend of the poly(styrene-co-1-octene) chain dimensions in toluene aromatic solvent by increasing the 1-octene content (x), after the equilibration state. Red and blue colors represent the carbon atoms of the copolymer chain backbone and 1-octene side chains, respectively. The styrene rings and the hydrogen atoms of the chains were removed for better view.

Hybrid QSPR models for the prediction of the free energy of solvation of organic solute/solvent pairs

Due to the importance of the Gibbs free energy of solvation in understanding many physicochemical phenomena, including lipophilicity, phase equilibria and liquid-phase reaction equilibrium and kinetics, there is a need for predictive models that can be applied across large sets of solvents and solutes. In this paper, we propose two quantitative structure property relationships (QSPRs) to predict the Gibbs free energy of solvation, developed using partial least squares (PLS) and multivariate linear regression (MLR) methods for 295 solutes in 210 solvents with total number of data points of 1777. Unlike other QSPR models, the proposed models are not restricted to a specific solvent or solute. Furthermore, while most QSPR models include either experimental or quantum mechanical descriptors, the proposed models combine both, using experimental descriptors to represent the solvent and quantum mechanical descriptors to represent the solute. Up to twelve experimental descriptors and nine quantum mechanical descriptors are considered in the proposed models. Extensive internal and external validation is undertaken to assess model accuracy in predicting the Gibbs free energy of solvation for a large number of solute/solvent pairs. The best MLR model, which includes three solute descriptors and two solvent properties, yields a coefficient of determination (R2) of 0.88 and a root mean squared error (RMSE) of 0.59 kcal mol-1 for the training set. The best PLS model includes six latent variables, and has an R2 value of 0.91 and a RMSE of 0.52 kcal mol-1. The proposed models are compared to selected results based on continuum solvation quantum chemistry calculations. They enable the fast prediction of the Gibbs free energy of solvation of a wide range of solutes in different solvents.

Elucidation of interaction mechanism of ellagic acid to the integrin linked kinase

Integrin-linked kinase (ILK) is a member of Ser/Thr kinase which interacts to the cytoplasmic domain of β-integrins, and thereby induces apoptosis. ILK is considered as potential drug target because it's direct involvement in the tumor progression. Here, we have performed molecular docking followed by 100 ns MD simulation to understand the mechanism of interaction of ILK with the ellagic acid (EA). EA is well known for its antiproliferative and antioxidant properties in cancer cell lines and animal models. We have observed that EA binds to the active site cavity of ILK and causes conformational changes in the ILK structure. The orientation of EA in the active pocket of ILK showed to have least RMSD values and stable. The average binding energy ILK-EA complex calculated during MMPBSA was -191.267 kJ/mol, indicating a relatively strong binding affinity. The actual binding affinity of EA to ILK was measured by fluorescence spectroscopy and K_b and n values were 9.28 μM and 1.9264 (~2), respectively. The IC₅₀ values for EA were 26.22 ± 0.12 μM for MCF-7 and 38.45 ± 2.42 μM for HepG2 cells, estimated by MTT assay. Our findings are helpful to design EA-based novel inhibitors of ILK which have potential to attenuate tumor progression.

Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: acrolein in water

We investigate here the vertical n → π(*) and π → π(*) transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to work with highly correlated electronic wave functions for both the solute ground and excited states and, to study the vertical transitions in the solvent, adopt the commonly used scheme of considering fast and slow dielectric polarization. To perform calculations in a non-equilibrium solvation regime for the solute excited state, we add a correction to the global dielectric polarization charge density, obtained self consistently with the solute ground-state wave function by assuming a linear-response scheme. For the solvent polarization in the field of the solute in the ground state, we use the static dielectric constant while, for the electronic dielectric polarization, we employ the solvent refractive index evaluated at the same frequency of the photon absorbed by the solute for the transition. This choice is shown to be better than adopting the most commonly used value of refractive index measured in the region of visible radiation. Our QMC calculations show that, for standard cavities, the solvatochromic shifts obtained with the PCM are underestimated, even though of the correct sign, for both transitions of acrolein in water. Only by reducing the size of the cavity to values where more than one electron is escaped to the solvent region, we regain the experimental shift for the n → π(*) case and also improve considerably the shift for the π → π(*) transition.

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.