Variation in predicted internal concentrations in relation to PBPK model complexity for rainbow trout.

The present study is motivated by the increasing demand to consider internal partitioning into tissues instead of exposure concentrations for the environmental toxicity assessment. To this end, physiologically based pharmacokinetic (PBPK) models can be applied. We evaluated the variation in accuracy of PBPK model outcomes depending on tissue constituents modeled as sorptive phases and chemical distribution tendencies addressed by molecular descriptors. The model performance was examined using data from 150 experiments for 28 chemicals collected from US EPA databases. The simplest PBPK model is based on the "Kow-lipid content" approach as being traditional for environmental toxicology. The most elaborated one considers five biological sorptive phases (polar and non-polar lipids, water, albumin and the remaining proteins) and makes use of LSER (linear solvation energy relationship) parameters to describe the compound partitioning behavior. The "Kow-lipid content"-based PBPK model shows more than one order of magnitude difference in predicted and measured values for 37% of the studied exposure experiments while for the most elaborated model this happens only for 7%. It is shown that further improvements could be achieved by introducing corrections for metabolic biotransformation and compound transmission hindrance through a cellular membrane. The analysis of the interface distribution tendencies shows that polar tissue constituents, namely water, polar lipids and proteins, play an important role in the accumulation behavior of polar compounds with H-bond donating functional groups. For compounds without H-bond donating fragments preferable accumulation phases are storage lipids and water depending on compound polarity.

Mutations in fd phage major coat protein modulate affinity of the displayed peptide.

Multibillion-clone libraries of phages displaying guest peptides fused to the major coat protein pVIII (landscape libraries) are a rich source of probes for proteinaceous and non-proteinaceous targets. As opposed to the pIII-type fusion phages, which display peptides as independent structural domains, the guest peptides in the pVIII-fusion phages can be structurally and functionally influenced by contiguous subunits. To decipher the impact of the locale of a guest peptide on its affinity characteristics, we constructed a library of phages carrying beta-galactosidase-binding peptide ADTFAKSMQ at the N-terminus of the pVIII protein surrounded by random amino acids. It was found that mutagenesis of amino acids 12-19 (domain C) has polar effects on target binding affinity of the displayed peptide. The phages with highest affinity are characterized by: (i) a net electrostatic charge around -1 of domain C of the mutated phages at pH 7.0; (ii) a lower radius of cylinder coaxial to alpha-helix formed by domain C; (iii) a lower higher occupied molecular orbital (HOMO) of domain C leading to a decreased formation of hydrogen bonds and (iv) positively charged surface and torsion energy of domain C, which may require a conformational transition of N-terminal peptide ADTFAKSMQ for its binding with beta-galactosidase. Influence of the guest peptide on the diversity of mutations in the neighboring landscape area was also observed.

[A study of conformational states of substrates of cytochrome P450 3A4].

A multiconformational study of substrates of cytochrome P450 3A4 has been carried out within the BiS/MC algorithm. The method allowed one to create a pseudoatomic model of the cytochrome and to find the substrate conformers responsible for the interaction with the cytochrome. It has been found that, in most cases, the geometry of the acting conformer is much different from the geometry of the global minimum conformer. It has been shown that the mirror conformational antipodes ("enantioconformers") are characterized as a rule by different Michaelis constants. A quantitative relationship between the Michaelis constants and the parameters of interactions in "model 3A4 isoform-substrate" complexes has been determined. The relationship describes the experimental value of Michaelis constant with the squared cross-validation correlation coefficient of 0.88.

New type of phase transformation in gas hydrate forming system at high pressures. Some experimental and computational investigations of clathrate hydrates formed in the SF6-H2O system.

In this work, we present a new, previously unknown type of structure transformation in the high-pressure gas hydrates, which is related to the existence of two different isostructural phases of the sulfur hexafluoride clathrate hydrates. Each of these phases has its own stability field on the phase diagram. The difference between these hydrates consists of partial filling of small D cages by SF(6) molecules in the high-pressure phase; at 900 MPa, about half of small cages are occupied. Our calculations indicate that the increase of population of small cavities is improbable, therefore, at any pressure value, a part of the cavities remains vacant and the packing density is relatively low. This fact allowed us to suppose the existence of the upper pressure limit of hydrate formation in this system; the experimental results obtained confirm this assumption.

Molecular and crystal properties of ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate from experimental and theoretical electron densities.

The electron density and electronic energy densities in ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate have been studied from accurate X-ray diffraction measurements at 110 K and theoretical single-molecule and periodic crystal calculations. The Quantum Theory of Atoms in Molecules and Crystals (QTAMC) was applied to analyze the electron-density and electronic energy-density features to estimate their reproducibility in molecules and crystals. It was found that the local electron-density values at the bond critical points derived by different methods are in reasonable agreement, while the Laplacian of the electron density computed from wavefunctions, and electron densities derived from experimental or theoretical structure factors in terms of the Hansen-Coppens multipole model differ significantly. This disagreement results from insufficient flexibility of the multipole model to describe the longitudinal electron-density curvature in the case of shared atomic interactions. This deficiency runs through all the existing QTAMC bonding descriptors which contain the Laplacian term. The integrated atomic characteristics, however, suffer noticeably less from the aforementioned shortcoming. We conclude that the electron-density and electronic energy QTAMC characteristics derived from wavefunctions, especially the integrated quantities, are nowadays the most suitable candidates for analysis of the transferability of atoms and atomic groups in similar compounds.

[The incidence and primary multiplicity of colon cancer].

Analysis of Moscow cancer register demonstrates a steady growth of colon cancer (CC) incidence and mortality in Moscow, also noted in all large industrial cities of economically developed countries. In Moscow between 1996 and 2001, the incidence of CC had grown 1.5 times (from 19.6 up to 30% per 100,000), and the CC-related mortality had grown twice (from 9.1 up to 19.5% per 100,000). The incidence of CC among women is 1.5 to 2 times higher than that among men. The burst of CC incidence is noted after age 55, and the peak incidence is noted at age 65. Not rare (2.9% of cases) are tumors that develop simultaneously in different divisions of the colon, which are diagnosed during the surgery or are omitted even then. Such synchronous large bowel tumors are found mostly in patients over 60. The analysis show that metachronous tumors (3.4% of cases) usually develop in the colon 8 to 10 years after the first surgery for CC, or some other cancer, and are found mostly in patients over 70. Unlike foreign statistics on multicentric CC cancer, according to which primary-multiple (synchronous and metachronous) cancers occur in 1.24 to 14% of cases, Moscow statistics demonstrate a lower likelihood of such a pathology in Muscovites. To sum up, patients who underwent treatment for CC or any other cancer should keep being under an oncologist's observation due to the likelihood of the development of a metachronous colon tumor 8 to 10 years later.

[The modeling of interactions of the CYP2E1 isoform of human cytochrome P450 with substrates].

The interactions between the substrates of the 2E1 isoform of the human cytochrome P450 and receptor were simulated. It was found that the CP4 isoform of the cytochrome of the bacterial cell is highly homologous to the 2E1 isoform of the human cytochrome P450. The orientation of the substrates of the 2E1 isoform in the CP4 isoform of the bacterial cell cytochrome was performed. A cavity in the receptor was found that is responsible for the binding of the substrate. Amino acid residues Phe87, Pro89, Val119, Thr185, Leu244, Leu245, Leu246, Val247, Gly248, Gly249, Thr252, Val295, Asp297, Cys357, Ile395, and Val396, the heme, and water molecules are involved in the formation of the cavity. The mode of the interactions of the substrate molecule with cytochrome was analyzed. Active sites of the receptor, and a part of the substrate molecule responsible for the binding to cytochrome were found. Equations for the dependence of the Michaelis constant on the structural parameters of complexes of substrates with cytochrome were derived.