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Method for Searching Compound Databases Using Topomeric Shape Descriptors and Pharmacophoric Features Identified by a Comparative Molecular Field Analysis (CoMFA) Utilizing Topomeric Alignment of Molecular Fragments

  • US 20090228463A1
  • Filed: 03/10/2008
  • Published: 09/10/2009
  • Est. Priority Date: 03/10/2008
  • Status: Abandoned Application
First Claim
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1. A computer implemented method for identifying fragments from a heterogeneous compound database which are likely to share the same type of activity as fragments derived from molecules identified as sharing that activity, comprising the steps of:

  • (a) fragmenting the molecules in the series according to a consistent procedure;

    (b) topomerically aligning each fragment according to a defined set of rules;

    (c) calculating steric and electrostatic field descriptor values for the topomerically aligned fragments;

    (d) entering the field descriptor values in a CoMFA table wherein the field descriptors for each fragment are associated with the unique parameter value for the molecule from which the fragment was derived;

    (e) analyzing the table with the CoMFA methodology to derive a 3D CoMFA QSAR model generating coefficients of each field descriptor value in the 3D CoMFA QSAR table;

    (f) using the steric field values of the fragments in the CoMFA table, searching a heterogeneous compound database for fragments, the database compounds similarly fragmented and the fragments topomerically aligned and characterised by steric and electrosatic field descriptors, to identify those fragments having shapes similar to the fragments used to generate the 3D CoMFA QSAR; and

    (g) determining the likely activity of fragments identified as being similar in shape by determining the likely activity for each fragment by multiplying the steric and electrostatic field values for each fragment by the 3D CoMFA QSAR coefficients of the similarly positioned fragments derived from molecules in the initial activity series.

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