Molecular Polar Surface Area PSA |
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Molecular polar surface area (PSA) is a very useful parameter for prediction of drug transport properties. Polar surface area is defined as a sum of surfaces of polar atoms (usually oxygens, nitrogens and attached hydrogens) in a molecule. This parameter has been shown to correlate very well with the human intestinal absorption, Caco-2 monolayers permeability, and blood-brain barrier penetration.
The calculation of PSA in a classical way, however, is rather time consuming, because of the necessity to generate a reasonable 3D molecular geometry and the determine the surface itself. Additionally, calculations require specialized software to generate the 3D molecular structures and to determine the surface.
In today's era of drug development shaped by high-throughput screening and combinatorial chemistry, fast bioavailability screening of virtual libraries consisting of hundreds of thousands, even millions of molecules is required. That is the reason why in our molecular property prediction toolkit so called topological polar surface area - TPSA is implemented.
The methodology for the calculation of TPSA is described in details in [1]. Briefly, the procedure is based on the summation of tabulated surface contributions of polar fragments (atoms regarding also their environment). These fragment contributions were determined by least squares fitting to the single conformer 3D PSA for 34,810 drugs from the World Drug Index. Topological polar surface area provides results of practically the same quality as the classical 3D PSA, the calculations, however, are two to three orders of magnitude faster.
[1] Ertl, P., Rohde, B., Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000, 43: 3714-3717.
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