Jinuk Lee

Critical assessment of the automated AutoDock as a new docking tool for virtual screening

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring function in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and FlexX. These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure‐based virtual screening. Proteins 2006.

Generalization of Wilemski-Fixman-Weiss decoupling approximation to the case involving multiple sinks of different sizes, shapes, and reactivities.

We generalize the Wilemski-Fixman-Weiss decoupling approximation to calculate the transient rate of absorption of point particles into multiple sinks of different sizes, shapes, and reactivities. As an application we consider the case involving two spherical sinks. We obtain a Laplace-transform expression for the transient rate that is in excellent agreement with computer simulations. The long-time steady-state rate has a relatively simple expression, which clearly shows the dependence on the diffusion constant of the particles and on the sizes and reactivities of sinks, and its numerical result is in good agreement with the known exact result that is given in terms of recursion relations.

An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates

We present a molecular dynamics (MD) simulation method for calculating the diffusion-influenced reaction rates in the limit of low reactant concentrations. To calculate the reaction rate coefficient, we use MD trajectories of a nonreactive equilibrium system that are initiated with a pair of reactant molecules in reactive configuration. Hence reaction systems involving complicated reactant molecules with geometrically restricted reactivities can be treated with comparable efficiency as the simple hard-sphere reaction system. Compared to the similar MD method proposed by Van Beijeren, Dong, and Bocquet [J. Chem. Phys. 114, 6265 (2001)], the present method has a couple of advantages. First, reactions involving more general sink functions can be treated. Second, more accurate results can be obtained when the reaction probability upon collision is less than unity. As an application, we investigate the effects of nondiffusive dynamics and hydrodynamic interaction of reactants on the reaction rate.

Theory of intrapolymer excimer-formation kinetics

We generalize the Wilemski–Fixman theory for reversible polymer cyclization to treat the kinetics of intrachain excimer-formation reactions. While most previous theories for intrachain reactions dealt with the end-to-end reaction case, we consider the general situation in which the reacting groups are located at any place on the chain backbone. Various aspects of the reaction kinetics, such as the effect of hydrodynamic interaction and the dependence of reaction rate on the positions of reacting groups as well as on the chain length, are investigated.

Absence of vertical transmission of Helicobacter pylori in an experimental murine model

Helicobacter pylori (H. pylori) infection is acquired mainly in early childhood but the precise transmission routes are unclear. This study examined the maternal H. pylori infection status in order to determine the potential of perinatal transmission. These issues were investigated using an experimental murine model, the Mongolian gerbil, which has been reported to be the most suitable laboratory animal model for studying H. pylori. Pregnant Mongolian gerbils, infected experimentally with H. pylori, were divided into two groups. The stomachs of the mother and litters were isolated and assessed for the transmission of H. pylori at the prenatal period (2 weeks after pregnancy) and at the parturition day. The bacterial culture, polymerase chain reaction (PCR) and rapid urease test were used to examine the presence of the transmitted H. pylori. There was no H. pylori observed in any of the fetuses during pregnancy and in the litters at parturition. This suggests that vertical infection during the prenatal period or delivery procedure is unlikely to be route of mother-to-child transmission of a H. pylori infection.

Experimental peritonitis induced by oral administration of indomethacin in Mongolian gerbils

The possibility of inducing peritoneal inflammation in three murine species (gerbils, rats and mice) via the oral administration of indomethacin was investigated with the overall aim of developing an experimental animal model for human peritonitis. Gerbils given high doses of indomethacin at a rate of 30 mg and 40 mg/kg body weight showed swelling of the abdomen, depression and dyspnea within 4 days after the treatment. The severity of the clinical symptoms increased with time. The animals were confirmed as having developed peritonitis based on the pathological features including inflammation of the peritoneum, and fibrinous adhesion of the abdominal organs in the abdominal cavity. The severity of peritonitis increased with increasing dose of indomethacin, and was not related to the gender of the animal. On the other hand, peritoneal inflammation did not develop in the rats and mice even at high doses. Therefore, the administration of 30 mg/kg body weight of indomethacin is an effective and simple method of inducing peritonitis in 5-week-old Mongolian gerbils. The animal peritonitis model used in this study can be used as an effective tool for examining potential therapeutic compounds for preventing peritoneal damage during peritonitis, and provide insight into the pathophysiology of peritonitis.

Kinetics of collision-induced reactions between hard-sphere reactants

We investigate the reaction kinetics of hard-sphere reactants that undergo reaction upon collision. When the reaction probability at a given collision is unity, the Noyes rate theory provides an exact expression of the rate coefficient. For the general case with the reaction probability less than unity, Noyes assumed that successive recollision times between a tagged pair of reactants are decorrelated. We show that with this renewal assumption, the rate theory of Wilemski and Fixman yields the same rate coefficient expression as the Noyes theory. To evaluate the validity of the renewal assumption, we carry out molecular dynamics simulations. Contrary to the usual expectation, we find that the renewal assumption works better at higher particle densities. The present study shows that the rate coefficient for collision-induced hard-sphere reactions can be estimated with great accuracy by using the first recollision time distribution alone, regardless of the magnitude of the reaction probability at a given collision.