Combinatorial libraries virtual screens

Topliss tree and Craig plot Factorial, central composite and D-optimal designs Principal properties of substituents Drug-like properties Combinatorial libraries Virtual screens IV Determining relationships between chemical and biological data A Overview... 

Research projects in pharmaceutical industry that are in an early phase need bioactive chemotypes as potential lead structures for optimization. Hits with a medium or even weak activity can serve as leads if the overall profile looks attractive. HTS of the in-house compound libraries is the most common source of these lead structures. If information about the 3D structure of the target and/or about bioactive ligand(s) is available, virtual screening can be used to add further active chemotypes either from the existing compounds, for example, from vendor catalogues, or from the virtual chemical space, for example, from virtual combinatorial libraries. Virtual screening can also be used to select a subset from the in-house screening collection if a full HTS is not possible due to cost or time limitations. 

HTS data as well as virtual screening can guide and direct the design of combinatorial libraries. A genetic algorithm (GA) can be applied to the generation of combinatorial libraries [18. The number of compounds accessible by combinatorial synthesis often exceeds the number of compounds which can be syiithcsii ed... 

Another example for the use of hydrogen as reductant is observed in the reduction of imine [5b]. New imine reductase activity has been discovered in the anaerobic bacterium Acetobacterium woodii by screening a dynamic combinatorial library of virtual imine substrates, using a biphasic water-tetradecane solvent system. 

Closely related to the use of PSA in virtual screening is its application in the design of combinatorial libraries with optimal properties. These applications are reviewed further in Refs. [46, 47], for example. 

As stated above, an advantage of virtual screening is that any compound, real or virtual, can be screened and the user is not restricted to those compounds available in corporate or external collections. The technology can also be used to screen proposed libraries and even select monomers for a combinatorial library based on 3D fit to the target structure. 

The next vague of tools will be around computational or in silico ADME approaches. These will allow to include ADME into the design of combinatorial libraries, the evaluation of virtual libraries, as well as in selecting the most promising compounds to go through a battery of in vitro screens, possibly even replacing some of these experimental screens. Several of these computational tools are currently under development as will be discussed in this volume. 

Software tools for virtual screening can be best classified by the input data available for screening. On the one side, there is always a collection of compounds to be screened, which differs in size (from a few tens to several millions) and in structure (from structurally unrelated compounds via combinatorial libraries to chemistry spaces). On the other side, there is the data that is used to create the screening query, which can be a protein structure, a known active compound or a pharmacophore created from several known actives (see Figure 4.1). In summary, we are ending up with four classes of screening tools ... 

Fig. 4.1 Virtual screening tools can be categorized by the compound data to be screened (compound collection, combinatorial library, chemistry space) and the query type (structure-based, ligand-based, descriptor-based, pharmacophore-based). The output is always a list of compounds together with a score quantifying the fit to the query.

The integration of combinatorial chemistry, structure-based library design and virtual screening [268, 269] also resulted in successful applications [270, 271]. It ultimately should result in broader SAR information about directionality and physicochemical requirements of acceptable building blocks. This concept is based on feasible scaffolds for exploring protein subsites using parallel or combinatorial synthesis. 

In general, reagent-based selection is much faster and more convenient to execute in the laboratory as compared with the product-based selection. On the other hand, the latter strategy usually provides more accurate results. There exists a potential to combine both approaches to achieve more optimal results, particularly in the case of large exploratory virtual combinatorial libraries, for which mass random synthesis and screening are not economically feasible. In this article, we demonstrated the usefulness of property-based approach for selection of optimal GPCR ligands. 

Virtual screening on a 2-D basis is far more efficient in terms of computing time, although the information content of the resulting virtual hits is far less sophisticated than for a 3-D pharmacophore search. It is in this setting that combinatorial chemistry approaches are applied most effectively. The many interactions possible with a compound library based on virtual hits compensates for the inherent fuzziness of any prediction tool. Examples have been described where the 2-D structure of a... 

The concepts of molecular similarity (1-3) and molecular diversity (4,5) play important roles in modern approaches to computer-aided molecular design. Molecular similarity provides the simplest, and most widely used, method for virtual screening and underlies the use of clustering methods on chemical databases. Molecular diversity analysis provides a range of tools for exploring the extent to which a set of molecules spans structural space, and underlies many approaches to compound selection and to the design of combinatorial libraries. Many different similarity and diversity methods have been described in the literature, and new methods continue to appear. This raises the question of how one can compare different methods, so as to identify the most appropriate method(s) for some particular application this chapter provides an overview of the ways in which this can be carried out, illustrating such comparisons by,... 

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