The handbook of medicinal chemistry : principles and by Davis, Andrew M.; Ward, Simon Edward

By Davis, Andrew M.; Ward, Simon Edward

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Hydrogen bond counts are, however, widely used, and in particular the number of hydrogen bond donors appears to be a very important compound quality metric, as the number of hydrogen bond donors appears to have a large impact on permeability. The number of hydrogen bond acceptors has a wider tolerated range and is the primary means of manipulating log P. The topological polar surface area (PSA or TPSA) descriptor is a means of quantifying the overall number of polar hydrogen bonding groups contained in the molecule.

But pKas can also be calculated using physics-based approaches of computational chemistry. 4 Hydrogen Bonding Hydrogen bonds are key drug-receptor interactions driving enthalpic binding, but also a key means of manipulating bulk physicochemical properties. Different functional groups have intrinsic different hydrogen bonding abilities, and various hydrogen bonding scales have been derived. But so far these have found few applications in drug projects. 15 Maybe one of the reasons why the intrinsic hydrogen bonding ability may be less important is that we are often exchanging hydrogen bonds (between solvent and a protein active site for example), and so increasing the hydrogen binding ability may favour the formation of the new bond but disfavour the breaking of another.

Lipophilicity represents the affinity of a molecule for a lipophilic environment. For many years the standard system in which to measure lipophilicity has been the n-octanol/ water partition system. The equilibrium of a neutral compound between n-octanol and water is measured, normally at 20 1C and the partition coefficient reported on a log10 scale.  log P ¼ log10 ½drugŠn-octanol ½drugŠwater  The solvent n-octanol became the standard lipophilic phase for the partition experiment, as it is almost non-water miscible, UV-transparent, and due to its hydroxyl group, many drug molecules can dissolve in it, unlike more hydrophobic alkane phases.

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