Three-dimensional pharmacophoric patterns

Gund P. Three-dimensional pharmacophoric pattern searching. Prog Mol Subcell Biol 1977 5 117-43. 

Gund P. Three-dimensional pharmacophore pattern searching. In Hahn FE, editor, Progress in molecular and subcellular biology. Berlin Springer-Verlag, 1977. p.117-43. 

Gund conceived the first prototypic program designed to search for molecules that match three-dimensional pharmacophoric patterns (201,202). This program, MOLPAT, performed atom-by-atom searches to verify comparable interatomic distances between... 

Three-dimensional pharmacophore patterns Target interaction sites (hydrogen bonds, electrostatic or lipophilic interactions, etc.). Similarities between different chemical classes and scaffolds can be recognized. 10 to 10 s... 

Gund, P. Three-dimensional Pharmacophoric Pattern Searching . Prog. Mol. Subcell. Biol. 1977, 5, 117-43. 

Databases and Searching of Multiple Three-Dimensional Pharmacophoric Patterns... 

P. Gund, in Progress in Molecular and Subcellular Biology. F. E. Hahn, Ed., Vol. 5, Springer-Verlag, Berlin, 1977, pp. 117-143. Three-Dimensional Pharmacophoric Pattern Searching. 

T. Esaki, unpublished report, 1983. Approach to Lead Generation by Three-Dimensional Pharmacophoric Pattern Searching Development of a Graphic Module for Prediction of Pharmacological Features of Drugs. 

Activity versus Affinity. Given a consistent model of either type, a limitation is that one can only ask whether the compound under consideration can present the three-dimensional electronic pattern (pharmacophore) that is the current candidate. In other words, one is limited to predicting the presence or absence of activity, a binary choice. Even the presence of the appropriate pattern is insufficient to ensure biological activity. For example, competition with the receptor for occupied space by other parts of the molecule can inhibit binding and preclude activity. We can thus postulate the following conditions for activity ... 

Clark DE, Willett P, Kenny PW. Pharmacophoric pattern matching in files of three-dimensional chemical structures use of smoothed bounded-distance matrices for the representation and searching of conformationally-fiexible molecules. J Mol Graph 1992 10 194-204. 

Catalyst [67] was launched 1992 by BioCAD (now Accelrys) as a tool for automated pharmacophore pattern recognition in a collection of compounds based on chemical features correlated with three-dimensional structure and biological activity data. 

Pharmacophore Models. It is often useful to assume that the receptor site is rigid and that structurally different drugs bind in conformations that present a similar steric and electronic pattern, the pharmacophore. Most drugs, because of inherent conformational freedom, are capable of presenting a multitude of three-dimensional patterns to a receptor. The pharmacophoric assumption led to a problem statement that logically is composed of two processes. F irst is the determina-... 

Clark, D.E., Willett, P. and Kenny, P. (1992). Pharmacophoric Pattern Matching in Files of Three-Dimensional Chemical Structures Use of Smoothed-Bounded Distance Matrices for the Representation and Searching of Conformationally-Flexible Molecules. J.MoLGraphics, 10,194-204. 

Complementary groups on the protein target recognize key features of the ligand. The three-dimensional arrangement of these features is commonly referred to as a pharmacophore. The Medicinal Chemistry Section of lUPAC has published a glossary of terms used in medicinal chemistry that includes an entry for the concept pharmacophore or pharmacophoric pattern. ... 

Willett, P., Searching for Pharmacophoric Patterns in Databases of Three-Dimensional Chemical Structures, J. Mol. Recogn., 8, 290, 1995. 

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