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Subcellular Pharmacokinetics aims at a description of the rate and extent of
drug disposition in the body. Most drugs cross the majority of membranes
in the body by passive diffusion through phospholipid bilayers. This
simple process is still not understood to a level allowing accurate and
reliable structure-based predictions.
Trans-bilayer transport and accumulation
are studied in experimental systems like immobilized phospholipid monolayers, liposomes, cells, and tissues
using isothermal titration calorimetry, fluorescence spectroscopy, confocal fluorescence microscopy, and conventional analytical techniques
(HPLC, GC-MS).
The results are analyzed by fitting conceptual models to the experimental data. The obtained transport
(micro)parameters are related to drug and bilayer structures and properties utilizing computational techniques like molecular dynamics at the atomic and coarse-grain levels. Finally, the data characterizing one monolayer or bilayer are used to simulate drug distribution in more complex systems (cells, tissues, and organisms).
The bilayer-based models describe well absorption and, after integration
with protein binding, also distribution. Their combination with
elimination provides the models of Subcellular Pharmacokinetics -
comprehensive kinetic descriptions of drug fates in the body.
Prediction of Distribution Volume is based
on the in vitro measurement and prediction of binding to the
preponderant body constituents: phospholipids, triglycerides, albumin,
extracellular matrix, and actin. Binding to proteins cannot be
approximated by physicochemical properties of chemicals and 3D-QSAR
models are necessary. |
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Drug-Receptor Interactions are the key steps in drug action and
need to be estimated as precisely as possible. We use and develop both ligand-based and structure-based computational
approaches.
The lab pioneered the conceptual use of multiple bound ligand
orientations or conformations (binding modes) in receptor site modeling.
The classical approaches suffer from the need to define one active mode, in which
all studied molecules are to be aligned. Multi-mode approach allows the
user to input several modes and the procedure objectively select the
best mode(s). The used approach allowed for a straightforward treatment
of multiple drug species, such as protomers and tautomers, interacting with
the receptor. The multi-species, multi-mode approach is being
implemented in Comparative Molecular Field Analysis
(CoMFA) that represents the most frequently used ligand-based (3D-QSAR)
method.
The energies of binding to receptors of known structures are computationally estimated using molecular dynamics-based methods.
We improved Linear Response method by replacing the ensemble averages of
van der Waals and electrostatic interactions by the QM/MM energy of
time-averaged structures from the simulations..
The drug-receptor interactions are also
studied experimentally, using state-of-the-art spectroscopic and calorimetric techniques.
We are focusing on matrix metalloproteinases (MMPs) and other metzincins
because they are implicated in diseases like cancer metastasis,
arthritis, and neurological disorders. The inhibitors, which are used to
treat aberrant activities of these enzymes, frequently need up to
several hours to exert full, steady-state effects. This period can be
prohibitively long for many inhibitors because they are rapidly
eliminated. We analyze the slow metzincin inhibition and strive to
identify the rate-limiting step. |
