Biomedical subjects

Daniel M Kroll

Publications and source records attributed to Daniel M Kroll.

6 recordsLinked to original sources

PubMed2005

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes, (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational sampling of the complex with constrained metal bonds by force-field-based molecular dynamics (MD), and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of steps 3 and 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds.

Binding Sites↗

PubMed2005

Processing multimode binding situations in simulation-based prediction of ligand-macromolecule affinities.

The linear response (LR) approximation and similar approaches belong to practical methods for estimation of ligand-receptor binding affinities. The approaches correlate experimental binding affinities with the changes upon binding of the ligand electrostatic and van der Waals energies and of solvation characteristics. These attributes are expressed as ensemble averages that are obtained by conformational sampling of the protein-ligand complex and of the free ligand by molecular dynamics or Monte Carlo simulations. We observed that outliers in the LR correlations occasionally exhibit major conformational changes of the complex during sampling. We treated the situation as a multimode binding case, for which the observed association constant is the sum of the partial association constants of individual states/modes. The resulting nonlinear expression for the binding affinities contains all the LR variables for individual modes that are scaled by the same two to four adjustable parameters as in the one-mode LR equation. The multimode method was applied to inhibitors of a matrix metalloproteinase, where this treatment improved the explained variance in experimental activity from 75% for the unimode case to about 85%. The predictive ability scaled accordingly, as verified by extensive cross-validations.

Computer Simulation↗

PubMed2005

A comparison of the binding sites of matrix metalloproteinases and tumor necrosis factor-alpha converting enzyme: implications for selectivity.

MMPs and TACE (ADAM-17) assume independent, parallel, or opposite pathological roles in cancer, arthritis, and several other diseases. For therapeutic purposes, selective inhibition of individual MMPs and TACE is required in most cases due to distinct roles in diseases and the need to preserve activities in normal states. Toward this goal, we compared force-field interaction energies of five ubiquitous inhibitor atoms with flexible binding sites of 24 known human MMPs and TACE. The results indicate that MMPs 1-3, 10, 11, 13, 16, and 17 have at least one subsite very similar to TACE. S3 subsite is the best target for development of specific TACE inhibitors. Specific binding to TACE compared to most MMPs is promoted by placing a negatively charged ligand part at the bottom of S2 subsite, at the entrance of S1' subsite, or the part of S3' subsite that is close to catalytic zinc. Numerous other clues, consistent with available experimental data, are provided for design of selective inhibitors.

ADAM Proteins↗

PubMed2004

Simulation of ordered packed beds in chromatography.

A computer simulation of chromatographic dispersion in an ordered packed bed of spheres is conducted utilizing a detailed fluid flow profile provided by the Lattice Boltzmann technique. The ordered configurations of simple cubic, body-centered cubic, and face-centered cubic are employed in these simulations. It is found that zone broadening is less for the fcc structure than the sc and bcc structures and less than a random packed bed analyzed in a previous study in the low flow velocity region used for experimental chromatography. The factors which contribute to the performance of the ordered pack beds are analyzed in detail and found to be dependent both on the nearest surface to surface distance and on the distribution of velocities found in the various packing geometries. The pressure drops of the four configurations are compared and contrasted with the pressure drop from monolithic columns.

Algorithms↗

PubMed2003

Advanced flicker spectroscopy of fluid membranes.

The bending elasticity of a fluid membrane is characterized by its modulus and spontaneous curvature. We present a new method, advanced flicker spectroscopy of giant nonspherical vesicles, which makes it possible to simultaneously measure both parameters for the first time. Our analysis is based on the generation of a large set of reference data from Monte Carlo simulations of randomly triangulated surfaces. As an example of the potential of the procedure, we monitor thermal trajectories of vesicle shapes and discuss the elastic response of zwitterionic membranes to transmembrane pH gradients. Our technique makes it possible to easily characterize membrane curvature as a function of environmental conditions.

Computer Simulation↗

PubMed2002

Simulation of packed-bed chromatography utilizing high-resolution flow fields: comparison with models.

A computer simulation of a section of the interior region of a liquid chromatographic column is performed. The detailed fluid flow profile is provided from a microscopic calculation of low Reynolds number flow through a random packed bed of nonporous spherical particles. The fluid mechanical calculations are performed on a parallel processor computer utilizing the lattice Boltzmann technique. Convection, diffusion, and retention in this flow field are calculated using a stochastic-based algorithm. This computational scheme provides for the ability to reproduce the essential dynamics of the chromatographic process from the fundamental considerations of particle geometry, particle size, flow velocity, solute diffusion coefficient, and solute retention parameters when retention is utilized. The simulation data are fit to semiempirical models. The best agreement is found for the "coupling" model of Giddings and the four-parameter Knox model. These models are verified over a wide range of particle sizes and flow velocities at both low and high velocity. The simulations appear to capture the essential dynamics of the chromatographic flow process for non-dimensional flow velocities (Péclet number) less than 500. Since the same packing geometry is utilized for different particle size studies, the interpretation of the parameter estimates from these models can be extended to the physical column model. The simulations reported here agree very well with a number of experiments reported previously.

Journal Article↗