Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors

The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by -substituted indomethacin ethanolamide inhibitors.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Spin interaction with an ideal Fermi gas

We consider the equilibrium dynamics of a system consisting of a spin interacting with an ideal Fermi gas on the lattice , 3. We present two examples: when this system is unitarily equivalent to an ideal Fermi gas or to a spin in an ideal Fermi gas without interaction between them.     

Note on the fractal dimension of hard sphere trajectories

Using Monte Carlo molecular dynamics, a new, careful study is made of the approach of the trajectory of a typical particle in a hard sphere fluid to that of a Brownian particle, discussed before by Powles and Quirke and Rapaport. The apparent fractal dimension of the trajectory, as a function of reduced length scale,(), characterizes the transition from mechanical to Brownian motion and differs markedly from 2 in all present computer simulations.     

Heat conductivity of three periodic Hard Disks via nonequilibrium molecular dynamics

We use a driving field, of the type first suggested by Evans, to generate a steady heat current in the simplest possible system, a two-dimensional periodic fluid of three hard disks. Hard-disk motion equations can be conveniently derived from repulsive constant-force or linear-force potentials by considering the infinitely repulsive limit of these potentials. We show that the isoenergetic and isokinetic forms of the nonequilibrium equations of motion generate steady-state heat conductivities differing by terms of order 1/N, whereN is the number of particles. The resulting conductivities appear to vary as the logarithm of the driving field strength. Even at low fields, the three-body periodic-system results lie well below Enskog's infinite-system prediction.     

Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.     

室温熔盐二(三氟甲基磺酸酰)亚胺锂-尿素体系的分子动力学模拟

应用分子动力学模拟了25 ℃和50 ℃时新型室温熔盐二(三氟甲基磺酸酰)亚胺锂[LiN(SO2CF3)2, LiTFSI]与尿素(摩尔比为1:3.6)体系的结构与动力学性质. 在两个温度下体系的微观结构基本相同, Li+的配位数约为5, 且都是与溶剂和阴离子中的氧原子发生配位. 对TFSI-的研究表明, 每个TFSI-只提供四个氧中的一个与Li+配位; 而且在Li+的配位层中, TFSI-具有顺、反和gauche 等不同的构象, 并且不同构象出现的几率会随着温度的改变而改变.     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).