3D-Pharmacophore

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

The Web-based graphical user interface permits a choice from numerous criteria and the performance of rapid searches. This service, based on the chemistry information toolkit CACTVS, provides complex Boolean searches. Flexible substructure searches have also been implemented. Users can conduct 3D pharmacophore queries in up to 25 conformations pre-calculated for each compound. Numerous output formats as well as 2D and 3D visuaHzation options are supplied. It is possible to export search results in various forms and with choices for data contents in the exported files, for structure sets ranging in size from a single compound to the entire database. Additional information and down-loadable files (in various formats) can be obtained from this service. 

The 3D pharmacophore search with C(5)ROL in the Biochemical Pathways database provided 13 different molecules as hits. To further limit the number of hits, the additional restriction was imposed that the hits should have only two hydrogen... 

There are two problems to consider when calculating 3D pharmacophores. First, unless the molecules are all completely rigid, one must take account of their conformational properties The second problem is to determine which combinations of pharmacophoric groups are common to the molecules and can be positioned in a similar orientation in space. More than one pharmacophore may be possible indeed, some algorithms can generate hundreds of possible pharmacophores, which must then be evaluated to determine which best fits the data. It is important to realise that all of these approaches to finding 3D pharmacophores assume that all of the molecules bind in a common manner to the macromolecule. 

Incorporating Additional Geometric Features Into a 3D Pharmacophore... 

Finally, 3D pharmacophores can be used to provide a naturally partitioned space. By com bining the pharmacophore keys of a set of molecules one can determine how many of th potential 3- or 4- point pharmacophores are accessible to the set and easily identify thos which are not represented. This use of pharmacophores is the basis of a method namei Pharmacophore-Derived Queries (PDQ) [Pickett et al. 1996]. One feature of this particula method is that most molecules will occupy more than one cell (as nearly all molecules wil contain more than one 3-point pharmacophore due to the functionality present an( conformational flexibility). This contrasts with the usual situation, wherein each molecul occupies just one cell. 

Pickett S D, J S Mason and IM McLay 1996. Diversity Profiling and Design Using 3D Pharmacophore Pharmacophore-Derived Queries (PDQ). Journal of Chemical Information and Computer Scien 36 1214-1223. 

S Pickett, IS Mason, IM McLay. Diversity profiling and design using 3D pharmacophores Pharmacophore-derived queries (PDQ). I Chem Inf Comput Sci 36 1214-1223, 1996. 

This method represents the most common and traditional application of computational tools to rational drug design. From a list of molecules of known activity, one can establish a 3D-pharmacophore hypothesis that is then transformed into a 3D-search query. This query is then used to search a 3D database for structures that fit the hypothesis within a certain tolerance. If the yield of active molecules is significant, then the query can be used to predict activities on novel compounds. In our situation, the enantiophore is built from the superposition of a list of sample molecules, which are all well separated on a given CSR Hence, the common features of this series of molecules can become a good enantiophore hypothesis for the enantiores-olution on this CSR... 

Beno BR, Mason JS. The design of combinatorial libraries using properties and 3D pharmacophore fingerprints. Drug Discov Today 2001 6(5) 251-8. 

Historically, ligand structure-based design has been the most widely used approach to the design of target-directed chemical libraries. Methods that start from hits or leads are among the most diverse, ranging from 2D substructure search and similarity-based techniques to analysis of 3D pharmacophores and molecular interaction fields (Fig. 15.2). 

Mason JS, Good AC, Martin EJ. 3D pharmacophores in drug discovery. Curr Pharm Des 2001 7 567-97. 

An improved 3D pharmacophore, considering all results obtained so far, and a new 3D search in the Aventis compound collection with the program... 

A 3D model of the fibrinogen-derived (very late antigen-4, VLA-4) inhibitor 4-[N -(2-methylphenyl)ureido]phenylacetyl-Leu-Asp-Val was derived from the X-ray structure of the related integrin-binding region of the vascular cell adhesion molecule-1 (VCAM-1). A 3D pharmacophore was generated with the program Catalyst, and a 3D search was performed in 8624 molecules from... 

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