Computational library design molecular descriptors

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

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... 

Computational models relating molecular structure and/or properties to biological activity are required for the design of both target-focused and target class combinatorial libraries based on known active ligands. These models are developed from descriptors, which encode information about molecular properties... 

In this chapter, we will give a brief introduction to the basic concepts of chemoinformatics and their relevance to chemical library design. In Section 2, we will describe chemical representation, molecular data, and molecular data mining in computer we will introduce some of the chemoinformatics concepts such as molecular descriptors, chemical space, dimension reduction, similarity and diversity and we will review the most useful methods and applications of chemoinformatics, the quantitative structure-activity relationship (QSAR), the quantitative structure-property relationship (QSPR), multiobjective optimization, and virtual screening. In Section 3, we will outline some of the elements of library design and connect chemoinformatics tools, such as molecular similarity, molecular diversity, and multiple objective optimizations, with designing optimal libraries. Finally, we will put library design into perspective in Section 4. 

Tounge, B.A., Pfahler, L.B. and Reynolds, C.H. (2002) Chemical information based scaling of molecular descriptors a universal chemical scale for library design and analysis./. Chem. Inf. Comput. Sci., 42, 879-884. 

Hence, one may consider construction of new molecular descriptors of very high discriminatory power specifically designed for screening combinatorial libraries one unsolved problem in this area. Observe that Lahana and coworkers used available molecular descriptors, most of which have limited discrimination powers and have been intended for use in MRA. There have been few molecular descriptors of very high discrimination power available, such as the molecular ID numbers [2,3-5], but they may not be suitable for screening combinatorial libraries because they are computationally intensive. 

While many computational chemistry teams in the pharmaceutical industry have developed proprietary software for analyzing the diversity of libraries, many of them have done so using tools supplied by commercial vendors of computational chemistry software (e.g, Barnard Chemical Information, Chemical Design, Daylight Chemical Information Systems, MDL Information Systems, Molecular Simulations, and Tripos). Some vendors emphasize the importance of 3D descriptors, although 2D descriptors seem to work surprisingly well for certain applications. In the future, key issues are likely to... 

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