Drug design pharmacophores

Guner O F (Editor) 2000. Pharmacophore Perception, Development, and Use in Drug Design. International University Line Biotechnology Series, 2. 

Since the summation in Eq. (12) may be on any subset of atoms, it can be fine-tuned to best suit the problem at hand. The summation may be over the whole molecule, but it is very common to calculate conformational distances based only on non-hydrogen heavy atoms or, in the case of proteins, even based on only the backbone Ca atoms. Alternatively, in a study related to drug design one may consider, for example, focusing only on atoms that make up the pharmacophore region or that are otherwise known to be functionally important. 

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... 

Guner OF. Preface. In Guner OF, editor, Pharmacophore perception, development, and use in drug design. La Jolla International University Line, 2000. 

Guner, O.F. (2002) History and evolution of the pharmacophore concept in computer-aided drug design. Current Topics in Medicinal Chemistry, 2, 1321-1332. 

It is well known that the identification of the pharmacophoric moiety (i.e. the essential atoms and molecular fragments of the bioactive compound, which selectively recognize the receptor eliciting the observed specific pharmacological effect) constitutes an important aspect of drug design procedures and SAR studies [84—86]. 

Clement, O.O. and Mehl, A.T. (2000) HipHop pharmacophores based on multiple common-feature alignments, in Pharmacophore Perception, Development, and Use in Drug Design (ed. O.F. Giiner), International University Line, La Jolla, CA, pp.69-84. 

Bures, M.G. Recent techniques and applications in pharmacophore mapping. In Practical Application of Computer-Aided Drug Design,... 

Guner, O.E. Pharmacophore Perception, Use and Development in Drug Design, lUL Biotechnologies Series, USA, 2000. 

Mother Nature still continues to be a resource of novel chemotypes and pharmacophores, and an impressive number of modem drugs have been isolated from natural sources, many based on their uses in traditional medicine systems. " To a large extent, the use of natural products in drug design represents the natural evolution of this old tradition. It has been extensively documented that the traditional medicine systems of many cultures worldwide are based on plants,for example in countries like China and India where plants have formed the basis for traditional systems of medicines. According to Kim and Park, natural... 

Giiner, O. F. and Henry, D. R. (2000) Metric for analyzing hit lists and pharmacophores. In Pharmacophore perception, development and use in drug design, Giiner, O. (ed.), International University Line, La Jolla, CA, pp.193-212... 

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