Biological activity quantitation

B. Testa, Inhibition of monoamine oxidase-B by 5H-indeno[1,2-c]pyridazines Biological activities, quantitative structure-activity relationships (QSARs) and 3D-QSARs, J. Med. Chem. 38 (1995) 3874-3883. 

Lewis, D.F.V. (1999) Frontier orbitals in chemical and biological activity quantitative relationships and mechanistic implications. Drug Metab. Rev., 31 (3), 755-816. 

Dearden, J. C., ed.. Quantitative Approaches to Drug Design (Proceedings of the 4" European Symposium on Chemical Structure — Biological Activity Quantitative Approaches, Bath, 1982), Pharmacochem. Lihr. 6, Elsevier, Amsterdam, 1983... 

In chemoinformatics, chirality is taken into account by many structural representation schemes, in order that a specific enantiomer can be imambiguously specified. A challenging task is the automatic detection of chirality in a molecular structure, which was solved for the case of chiral atoms, but not for chirality arising from other stereogenic units. Beyond labeling, quantitative descriptors of molecular chirahty are required for the prediction of chiral properties such as biological activity or enantioselectivity in chemical reactions) from the molecular structure. These descriptors, and how chemoinformatics can be used to automatically detect, specify, and represent molecular chirality, are described in more detail in Chapter 8. 

The fundamental assumption of SAR and QSAR (Structure-Activity Relationships and Quantitative Structure-Activity Relationships) is that the activity of a compound is related to its structural and/or physicochemical properties. In a classic article Corwin Hansch formulated Eq. (15) as a linear frcc-cncrgy related model for the biological activity (e.g.. toxicity) of a group of congeneric chemicals [37, in which the inverse of C, the concentration effect of the toxicant, is related to a hy-drophobidty term, FI, an electronic term, a (the Hammett substituent constant). Stcric terms can be added to this equation (typically Taft s steric parameter, E,). 

The objective of this study is to show how data sets of compounds for which dif-ferent biological activities have been determined can be studied. It will be shown how the use of a counter-propagation neural networb can lead to new insights [46]. The cmpha.si.s in this example is placed on the comparison of different network architectures and not on quantitative results. 

Rather than making this statement, one should consider first whether the representation of the Y-variablc is appropriate. What wc did here was to take categorical information as a quantitative value. So if wc have, for instance, a vector of class 1 and one of c lass 9 falling into the same neuron, the weights of the output layer will be adapted to a value between 1 and 9, which docs not make much sense. Thus, it is necessary to choose another representation with one layer for each biological activity. The architecture of such a counter-propagation network is shown in Figure 10.1 -11. Each of the nine layers in the output block corresponds to a different MOA. 

When the property being described is a physical property, such as the boiling point, this is referred to as a quantitative structure-property relationship (QSPR). When the property being described is a type of biological activity, such as drug activity, this is referred to as a quantitative structure-activity relationship (QSAR). Our discussion will first address QSPR. All the points covered in the QSPR section are also applicable to QSAR, which is discussed next. 

PW91 (Perdew, Wang 1991) a gradient corrected DFT method QCI (quadratic conhguration interaction) a correlated ah initio method QMC (quantum Monte Carlo) an explicitly correlated ah initio method QM/MM a technique in which orbital-based calculations and molecular mechanics calculations are combined into one calculation QSAR (quantitative structure-activity relationship) a technique for computing chemical properties, particularly as applied to biological activity QSPR (quantitative structure-property relationship) a technique for computing chemical properties... 

Quantitative Structure—Activity Relationships (QSAR). Quantitative Stmcture—Activity Relationships (QSAR) is the name given to a broad spectmm of modeling methods which attempt to relate the biological activities of molecules to specific stmctural features, and do so in a quantitative manner (see Enzyme INHIBITORS). The method has been extensively appHed. The concepts involved in QSAR studies and a brief overview of the methodology and appHcations are given here. 

The alkyl and alkoxy substituents of phosphate or phosphonate esters also affect the phosphorylating abiUty of the compound through steric and inductive effects. A satisfactory correlation has been developed between the quantitative measure of these effects, Tafts s O, and anticholinesterase activity as well as toxicity (33). Thus long-chain and highly branched alkyl and alkoxy groups attached to phosphoms promote high stabiUty and low biological activity. 

Present research is devoted to investigation of application of luminol reactions in heterogeneous systems. Systems of rapid consecutive reactions usable for the determination of biologically active, toxic anions have been studied. Anions were quantitatively converted into chemiluminescing solid or gaseous products detectable on solid / liquid or gas / liquid interface. Methodology developed made it possible to combine concentration of microcomponents with chemiluminescence detection and to achieve high sensitivity of determination. 

Many different approaches to QSAR have been developed since Hansch s seminal work. These include both two-dimensional (2D) and 3D QSAR methods. The major differences among these methods can be analyzed from two viewpoints (1) the strucmral parameters that are used to characterize molecular identities and (2) the mathematical procedure that is employed to obtain the quantitative relationship between a biological activity and the structural parameters. 

Side chain fluonnaied aryl isocyanates are an important group of substances used in the manufacture of biologically active compounds The synthetic routes to the meta- and para trifluoromethylphenyl isocyanates permit the chlorine-fluonne exchange with hydrogen fluoride to proceed under moderate conditions and in a virtually quantitative manner (equation 22)... 

These pharmacophore techniques are different in format from the traditional pharmacophore definitions. They can not be easily visualized and mapped to the molecular structures rather, they are encoded as keys or topological/topographical descriptors. Nonetheless, they capture the same idea as the classic pharmacophore concept. Furthermore, this formalism is quite useful in building quantitative predictive models that can be used to classify and predict biological activities. 

In general, the described techniques provide an effective, flexible, and relatively fast solution for library design based on analysis of bioscreening data. The quantitative relationships, based on the assessment of contribution values of various molecular descriptors, not only permit the estimation of potential biological activity of candidate compounds before synthesis but also provide information concerning the modification of the structural features necessary for this activity. Usually these techniques are applied in the form of computational filters for constraining the size of virtual combinatorial libraries and... 

The attempt to classify biological activities upon the basis of their velocities as affected by temperature involves for a number of cases the adjustment of curves to data inevitably subject to several sources of variation. One of these arises from the fact that the measurements may be secured with different individuals at each of several temperatures. The latitude of variation in series of data obtained in this way may be large, and unless great numbers of observations are available interpretation may be difficult. Indication already obtained as to the theoretical significance of the exact quantitative relationship between velocity of a vital process and temperatme make it desirable to demonstrate the limits of variation in material which is as nearly as possible biologically homogeneous. 

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