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Accurate, wide-range, automated, high-performance liquid chromatographic method for the estimation of octanol/water partition coefficients II: Equilibrium in partition coefficient measurements, additivity of substituent constants, and correlation of biological data.

Occasionally, results from the highly reproducible automated log P(o/w) measurement (ALPM) differ from those determined by shake-flask methods. Several specific examples affording different values are presented. One source of these differences may be curvilinearity in plots of log (t - t0) versus percent methanol, which complicate accurate intercept determinations and, thus, estimates of log P(o/w). Other sources of these differences are presented and discussed, although their cause remains unclear. Equilibrium ALPM log P(o/w) measurements of various phenyl-, methyl-, fluoro-, chloro-, and bromobenzenes, suggest substituent constants are not strictly additive. Moreover, the higher values indicate that calculated values may not be accurate for those compounds having multiple substituents or high log P(o/w) values. ALPM gives better predictability of the in vivo concentration process of 8 or 12 toxicants in fish than the shake-flask method, another HPLC method, or even calculated log P(o/w) values. However, it equally correlates the binding to bovine serum albumin by 34 chemicals as predicted by a combination of shake-flask and calculated log P(o/w) values reported elsewhere.

Chemical Phenomena↗

A computer program for the graphical and iterative fitting of probability density functions to biological data.

A tutorially-assisted, interactive program, written for a Digital Equipment Corporation LAB-11 minicomputer (PDP-11/20, is described which allows a user to fit (with or without automatic estimation of initial parameter values), by a method of nonlinear least squres, any one of seven different types of probability density functions (p.d.f.'s) to an empirical frequency distribution; the latter of which may be input to the program or formed by the program whenever it is furnished a series of times between events. The iteratively-obtained, "best fit" p.d.f. is displayed on a two color, point-plot display against the background of a point-plot histogram. By selecting any one of nine output modes, the user is allowed: (1) to view histograms successively on the point-plot display, (2) to generate selected p.d.f.'s (3) to "force" p.d.f.'s having known parameters through the histogram data, (4) to obtain Chi-square (x2) and Kolmogorov-Smionov estimates of the goodness of fit to the data, and (5) to apply a special test [Williams and Kloot, 1953] in order to determine whether the least squares estimates of two candidate models are statistically different. The resident driver program and the four overlayable program segments are written in standard FORTRAN IV; except for two plot routines, which are written in PDP-11 assembly language.

Computers↗

Multidimensional curve fitting program for biological data.

A program written for use with the IBM-PC can be used to find least squares solutions to linearized multidimensional equations. The program is 'user-friendly' by requiring little from the user except to make decisions; most responses can be entered by a single keystroke. Once data are entered by the user, they can be repeatedly manipulated, graphed, and correlated. Many models relating data variables can be tried relatively easily, and best fit results found. Examples using respiratory mechanical data illustrate the ease of model comparisons.

Biometry↗

AVG--A signal averager for biological data.

A paper presents a versatile computer program for averaging evoked responses. The program, called AVG is set up interactively on a DEC-PDP-12 computer, equipped with 12 kbytes memory. A protocol, recording the experimental conditions, as well as messages and prompters are displayed on the screen to inform the operator and indicate which action must be taken. AVG is written in assembly program LAP-6. The program has been useful for averaging cortical visual evoked responses.

Analog-Digital Conversion↗

DATAC: a multipurpose biological data analysis program based on a mathematical interpreter.

The use of a mathematical command interpreter combined with the structural facility of the C-language allowed us to design a data treatment program having considerable flexibility and being able to handle any types of data (electrophysiological, biochemical and theoretical data). Ensembles of data are treated by the interpreter as if they were simple variables so that an elaborate computation can be performed on the spot by simply writing the appropriate equation on the terminal. These facilities combined with the ability of editing macrocommands at run time provide the user with data treatment possibilities that extend far beyond the possibilities actually implemented in the program. The originality of this program is that the user can easily implement the commands he most often needs, writing them in a language that most scientists will know, algebra.

Biometry↗

Non-linear fitting program for biological data.

A simple microcomputer program written in Microsoft Basic estimates pharmacokinetic parameters using the coordinate search technique to minimize the sum of squared errors. The program developed for portable computers combines a plot of data and curve fitting so as to find rapidly the initial parameters with the subsequent optimization of the parameter estimate.

Computers↗

[Hodgkin disease: recent histological and biological data].

Recent histologic, immunophenotypic and genotypic data have restricted the concept of Hodgkin's disease (HD) to the type 2 and 3 of Rye classification. This classification should be revised since the lymphocyte-predominance type has been shown to include the nodular paragranuloma which is a B-cell lymphoma, cases which have been confused with T-cell-rich large B-cell non Hodgkin's lymphoma (NHL) and cases which should be reclassified among the mixed cellularity group. Further more, most types 4 are now regarded as anaplastic large cell NHL. Immunophenotypic and genotypic studies support the heterogeneous nature of Reed-Sternberg and Hodgkin's (RSH) cells since they could be derived from B, T or null lymphocytes. In 50% of cases, RSH cells harbour the Epstein-Barr virus genome and express a viral protein, the latent membrane protein, which could play an oncogenic role in HD. Finally, RSH cells produce a wide range of cytokines that could stimulate their proliferation and explain the marked cellular reaction that is observed in HD.

Cytokines↗

Application of biological data in cancer risk estimations of chlordane and heptachlor.

Regulatory agencies traditionally use doses associated with ambient concentrations of contaminants in environmental media to estimate lifetime excess cancer risks. This approach is, however, limited by the errors inherent in making several default assumptions such as daily water and food intakes and organ absorption factors. A methodology was developed in this study to estimate daily human doses of chlordane and heptachlor from measured metabolites in adipose tissue. Human biomonitoring data, pharmacodynamic and pharmacokinetic parameters in humans and animals, and selected dose-response data from animal carcinogenicity studies were utilized in this procedure for cancer risk assessment in man. Conversion factors, based on body surface area, were used for animal-to-man extrapolation. Conservative estimates from the Global 82 linearized multistage mathematical model (95% upper confidence limit) associate a 1 x 10(-5) risk probability level to chlordane and heptachlor doses of 1.1 x 10(-4) and 4.0 x 10(-5) mg/kg-day, respectively, via all potential routes of exposure. The unit cancer risks associated with "internal" dose estimates from human adipose tissue concentrations were calculated and compared with U.S. Environmental Protection Agency (1986a, Carcinogenicity Assessment of Chlordane and Heptachlor/Heptachlor Epoxide, EPA-600/6-87-004) unit risks in air and water. The implications and uncertainties associated with the risk estimates were also discussed.

Animals↗

Rodenticide-humic acid adsorption mechanisms and role of humic acid on their toxicity on human keratinocytes: chromatographic approach to support the biological data.

Humic substances are the most important soil components affecting the behaviour and performances of herbicides in the soil-water-organism system. In this paper, a chromatographic approach was used for analysis of anticoagulant rodenticide-humic acid adsorption mechanisms. Using an equilibrium perturbation method, it was clearly shown that: (i) humic acid can be adsorbed on the C18 stationary phase, and (ii) all the rodenticides can be adsorbed on the humic acid adsorbed on the C18 stationary phase. This approach allowed the determination of the adsorption constant values between the anticoagulant rodenticides and humic acid as well as the corresponding thermodynamic data of this adsorption mechanism. The role of humic acid on the toxicity of these rodenticides on human keratinocytes was also clearly described in relation to these physico-chemical data.

Adsorption↗

Association mechanism between a series of rodenticide and humic acid: a frontal analysis to support the biological data.

The binding constants (K) of a series of anticoagulant rodenticides with the main soil organic component, humic acid (HA), were determined using frontal analysis approach. The order of the binding constants was identical as the one obtained in a previous paper [J. Chromatogr. B 813 (2004) 295], i.e. bromadiolone>brodifacoum>difenacoum>chlorophacinone>diphacinone, confirming the power of this frontal analysis approach for the determination of binding constants. Moreover, and for the first time, the concentration of unbound rodenticide to HAs could be determined. Thanks this approach, we could clearly demonstrate that HA acid protected the human hepatoma cell line HepG2 against the cytotoxicity of all the rodenticides tested and that the toxicity of rodenticides was directly linked to the free rodenticide fraction in the medium (i.e. unbound rodenticide to HA).

Animals↗

Structure-function inferences based on molecular modeling, sequence-based methods and biological data analysis of snake venom lectins.

Lectins are a structurally and functionally diverse group of proteins from different sources, capable to recognize and bind specifically carbohydrates. Several snake venoms contain calcium-dependent true lectins (SVLs) that recognize galactose. Herein, in order to enlighten some of the structure-function relationships of snake venom lectins (SVLs), we constructed theoretical models for 10 SVLs based on the Crotalus atrox lectin (CaL), the only SVL crystal structure available, and compared with other animal and plant lectins, and C-type lectin-like proteins (CLPs) that do not bind carbohydrates. Although these are theoretical structures, we could identify some SVL features, including: (i) a singular intrachain disulfide bond (Cys(38)-Cys(133)) that is not present in CLPs; (ii) a significant reorientation (39-41A) of the 80's loop position that folds back to the globular domain, assists the carbohydrate recognition domain (CRD), and orients the dimer formation, even in BfL-1 and BfL-2, which did not present the Cys(86) interchain; (iii) a CRD presenting a negative and concave surface that allows the interaction with the specific saccharide hydroxyl groups and calcium ion; (iv) the role of water molecules in some interchain interactions, similar to other animal and plant lectins; and (v) the inability of forming oligomers in contrast to CaL and some CLPs, such as convulxin.

Amino Acid Sequence↗

Molecular dynamics simulations of the NGF-TrkA domain 5 complex and comparison with biological data.

The nerve growth factor (NGF) is an important pharmacological target for Alzheimer's and other neurodegenerative diseases. Its action derives partly from its binding to the tyrosine kinase A receptor (TrkA). Here we study energetics and dynamics of the NGF-TrkA complex by carrying out multinanosecond molecular dynamics simulations, accompanied by electrostatic calculations based on the Poisson-Boltzmann equation. Our calculations, which are based on the x-ray structure of the complex, suggest that some of the mutations affecting dramatically the affinity of the complex involve residues that form highly favorable, direct or water-mediated hydrogen bond interactions at the ligand-receptor interface and, in some cases, that also critically participate to the large-scale motions of the complex. Furthermore, our calculations offer a rationale for the small effect on binding affinity observed upon specific mutations involving large changes in electrostatics (i.e., the charged-to-neutral mutations). Finally, these calculations, used along with the mutagenesis data, provide a basis for designing new peptides that mimic NGF in TrkA binding function.

Binding Sites↗