Pharmacophores determination

Demeter, D.A., Weintraub, H.J.R. and Knittel, J.J. (1998). The Local Minima Method (LMM) of Pharmacophore Determination A Protocol for Predicting the Bioactive Conformation of Small, Conformationally Flexible Molecules. J.Chem.lnf.Comput.Sci.,38,1125-1136. 

The ultimate test of the objectivity of the process of pharmacophore discovery is that these results should conform to the physical reality of the receptor, as determined by independent biophysical experimentation. For example, the standard pharmacophore determined by DANTE for most GPCRs contains a basic amine separated by 5-7 A from an aromatic ring. These groups interact with the conserved Asp on helix III and conserved aromatic residues on helices VI and VII in most protein models of GPCRs. 

Demeter DA, Weintraub HJR, Knittel JJ. The local minima method of pharmacophore determination a protocol for predicting the bioactive conformation of small, con-formationally flexible molecules. J Chem Inf Comput Sci 1998 38 1125-1136. 

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. 

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. 

Similar conformational analyses were performed for inactive compounds, and inactive compounds in pharmacophoric conformations were superimposed with the active compounds to determine steric limitations in the active site. Where appropriate, the geometry of each inactive molecule was obtained by modifying the chemical strucmre of the relevant active analogs followed by the energy minimization of the resulting structure. 

Compounds with cis double bonds in the side chain were in general found to be more potent and efficacious than their triple-bond congeners, both in in vivo and in in vitro functional assays [98, 106, 107]. QSAR models have been generated for the compounds with unsaturated [108] and l, l -dimethyl [96] side chains to determine more precisely the pharmacophoric requirements of the receptor. It is postulated that for optimum potency, the side chain must be of a suitable length and flexibility to have the ability to loop back so that its terminus is in proximity to the phenolic ring. The widely used, potency enhancing 1 - and 2 -methyl substituents would be expected to increase the tendency of the side chain to adopt a looped back, rather than an extended conformation. 

In many respects the fragment approach is ideally suited to projects which have X-ray crystal structures available. The fragments are small and relatively weak binders, but they often only possess one pharmacophoric element that binds to a specific feature on the target. If this interaction is identified by X-ray structure determination, then project teams can propose specific plans which maintain that critical interaction, and ideally optimize binding through other vectors in their fragments. 

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