Handbook Chemoinformatics

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A variety of different methods for the prediction of relevant physico-chemical properties, like log P , p K a and aqueous solubility, of organic compounds are available, and in general these methods perform satisfactorily considering the data available. In the case of the aqueous solubility, a large number of methods have been developed, and there is continued interest in this property.

The effect of the pH value of the solution on solubility needs to be studied in much greater detail. Concerning ADMET properties, a number of in silico models have been proposed for intestinal absorption and BBB penetration, some models for metabolism and toxicity and only very few models for distribution and excretion.

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The total amount of data available for a certain end point often limits the possibility of developing improved predictive models for ADMET properties. Permeability of the BBB is such a case, where measured values are only available for a little more than compounds. The lack of structural diversity within these compounds is another limiting factor. Properties like metabolism, oral bioavailability, etc. Due to lack of reliable data, combined with a very complex mode of action of the processes involved, the present methods often fail.

In some cases where a method yields promising results for a set of compounds, the transferability of the method to another series or class of compounds may be questionable. Within this area there is much need for developing better and more robust predictive methods, but there is also a need for determining and collecting larger amount of experimental data for the individual processes. Oral bioavailability is a particularly difficult property to model as it involves a huge number of processes within the human organism, and depends on all the ADMET and physico-chemical properties discussed above.

The molecule has to dissolve, be adsorbed into the bloodstream, transported to the target, and not metabolized on its way. Thus for an orally administrated drug to reach its final destination, a whole range of properties need to be within acceptable limits, and thus a model which defines such limits would be very useful. Dynamic modeling of processes within a living cell with systems biology methods is growing rapidly, and is expected to have a huge impact on future drug design, in particular on the modeling of the oral bioavailability.

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As discussed by Parsons et al. Such methods could thus be very useful for identifying the mechanism of action and cellular targets of bioactive compounds. Improved understanding of how different drugs affect one another within the human organism is also of great importance, and thus much interest is presently devoted to studies of drug—drug interactions. An extremely exciting perspective is of course also to use pharmacogenomic methods for examining how individual patients respond to specific drugs, and how that depends on their genetic makeup.

Computational chemistry in drug discovery

Although more data, better data and an improved understanding of the interplay between the different processes in the human organism are required, the present level of available data has already made chemoinformatics an effective tool in the drug discovery and development process. Protein—protein interaction databases. VolSurf version 3.

Learning outcomes

Some of the databases and programs are represented by an ordinary reference, and are not included in this list. Number of compounds varies from one database to another, see text for details.


Handbook of Computational Chemistry

Overview of relevant experimental physico-chemical and ADMET properties provided in small molecule databases. The SMILES string and the 2D drawing contain information about which atoms are bound to one another, and the 3D representation shows how the atoms are located geometrically in relation to one another. The atomic coordinates used are shown behind the 3D picture. This figure can be viewed in colour on Bioinformatics online.

Comparison of various methods for prediction of drug-likeness of molecules, including neural networks, functional group filters, quantitative structure-activity relationships and decision trees. Chemoinformatics integrates information on ADMET properties in the relationship between chemistry space, biological targets and diseases. The information about the databases are mostly found on the internet pages provided by the suppliers.

Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Article Navigation. Close mobile search navigation Article Navigation. Volume Article Contents. Oxford Academic. Google Scholar. Cite Citation. Permissions Icon Permissions.

Handbook of Chemoinformatics: From Data to Knowledge - Google книги

Abstract Motivation: To gather information about available databases and chemoinformatics methods for prediction of properties relevant to the drug discovery and optimization process. Contact: svava cbs. Redundancy in this context means that the compounds in their vectors, component for component, are similar. Similarity of the chemical compounds within a data set can lead to over-fitting of a model, such that predictions for compounds similar to those used in the training set are excellent, but for different compounds the predictions are not accurate to the same level.

There are several examples of compound clustering techniques, where the Tanimoto coefficient Patterson et al. Open in new tab Download slide. Table 1. Overview of small molecule databases and key informations provided in those. Open in new tab. Table 2. Table 3. Agoram, B. Ajay, B. Anzali, S. Avdeef, A. Bader, G.

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Bajorath, J. Baldi, P. Bioinformatics: The Machine Learning Approach. Adaptive Computation and Machine Learning. Beresford, A. Blake, J. Bodor, N. Virtual Screening for Bioactive Molecules.

Chemical Information Sources/SIRCh/Cheminformatics/Introductory Resources

Boobis, A. Browne, L. Burkert, U. Buttom, W. Clark, D.

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