Prediction of molecular polar surface area and bioabsorption

A method of estimating the molecular polar surface area of a molecule comprising performing counts of pre-defined atom types and/or atom cluster types present in said molecule and estimating said molecular polar surface area using said counts weighted by coefficients and summed together, without reference to an energy minimized three-dimensional molecular structure of said molecule.

A method of predicting the propensity of a molecule for membrane permeability comprising:

• computing a polar surface area for said molecule without reference to an energy minimized three dimensional structure of said molecule;
• and
• using said computed polar surface area to predict said propensity.

A method of drug discovery comprising:

• computing polar surface areas for a plurality of molecules without reference to an energy minimized three dimensional structure for at least some of said molecules;
• and
• using said computed polar surface area in a membrane permeability prediction model so as to select one or more of said molecules for further analysis.

A computer readable medium having instructions stored thereon which cause a general purpose computer to perform a method of molecular PSA estimation, said method comprising:

• making separate counts of the number of atoms or atom clusters in a molecule which fall within the definition of each of each of a plurality of atomic classes;
• retrieving a plurality of coefficients;
• multiplying said separate counts by selected ones of said plurality of coefficients and summing the products thereof.

A computer implemented drug discovery system comprising:

• an estimation module for estimating a numerical measure of molecular polar quality without reference to three dimensional molecular structures;
• an estimation module for estimating a numerical measure of molecular lipophilicity without reference to three dimensional molecular structures;
• a molecule selection module for categorizing molecules based on the results of said estimations.

A system for drug discovery comprising:

• a database storing information regarding the atomic constituents and interatomic bonds for a plurality of molecules;
• and
• means for estimating the PSA for each of said plurality of molecules without reference to an energy minimized three dimensional structure for any of said plurality of molecules