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Comparative Molecular
Field Analysis (CoMFA)
      Pinky Sheetal V
        1801110004
   M.Tech Bioinformatics
Introduction
• CoMFA (Comparative Molecular Field Analysis) is a 3D QSAR technique based on
  data from known active molecules.
• The aim of CoMFA is to derive a correlation between the biological activity of a set
  of molecules and their 3D shape, electrostatic and hydrogen bonding
  characteristics.
Methodology

1.       A set of molecules is first selected which will be included in the analysis.
            As a most important precondition, all molecules have to interact with the same kind of
            receptor (or enzyme, ion channel, transporter) in the same manner, i.e., with identical
            binding sites in the same relative geometry.

2.       A certain subgroup of molecules is selected which constitutes a training set to
         derive the CoMFA model.

3.       Atomic partial charges are calculated and (several) low energy conformations are
         generated.

4.       A pharmacophore hypothesis is derived to orient the superposition of all
         individual molecules and to afford a rational and consistent alignment.

5.       A sufficiently large box is positioned around the molecules and a grid distance is
         defined.

6.       Different atomic probes, e.g., a carbon atom, a positively or negatively charged
         atom, a hydrogen bond donor or acceptor, or a lipophilic probe, are used to
         calculate field values in each grid point, i.e., the energy values which the probe
         would experience in the corresponding position of the regular 3D lattice.
7.    PLS analysis is the most appropriate method for this purpose .

8.    The result of the analysis corresponds to a regression equation with thousands of
      coefficients.
        Most often it is presented as a set of contour maps. These contour maps
         show favorable and unfavorable steric regions around the molecules as well
         as favorable and unfavorable regions for electropositive or electronegative
         substituents in certain positions

9.    Predictions for the test set (the compounds not included in the analysis) and for
      other compounds can be made, either by a qualitative inspection of these
      contour maps or, in a quantitative manner, by calculating the fields of these
      molecules and by inserting the grid values into the PLS model.
Summary of the alignment procedure used for sulfotransferase substrates in CoMFA. Vyas
Sharma, Michael W. Duffel, 2005
On a rectangular bounding grid measure interaction energies
of each ligand with probe atoms placed successively at each
grid point
The color coding's indicate
                                regions where
                                electronegative
                                substituents enhance
                                (blue) or reduce (red) the
                                binding affinity.




Regions where substitution
enhances (green) or reduces
(yellow) the binding affinity
Applications

• Predict the properties and activities of untested molecules
• Compare different QSAR models statistically and visually
• Optimize the properties of a lead compound
• Validate models of receptor binding sites
• Generate hypotheses about the characteristics of a receptor binding
  site
• Prioritize compounds for synthesis or screening

• There are now a few hundred practical applications of CoMFA in drug
  design. Most applications are in the field of

    – Ligand protein interactions
    – Describing affinity or inhibition constants
    – Correlate steric and electronic parameters
Problems in CoMFA

•   The force field functions do not model all interaction types
•   Show singularities at the atomic positions
•   Deliberately defined cut-off values needed
•   Contour plots often not contiguously connected



 New approach: CoMSIA (Comparative Molecular Similarity Indices)
• Does not calculate interaction energies but distance-dependent
  similarity indices (similarity of probe to molecule atoms) resulting in
  smooth contour plot
Contour Plot

blue: negative correlation with binding affinity
red: positive correlation with binding affinity
References

• http://www.cmbi.ru.nl/edu/bioinf4/comfa-Prac/comfa.shtml
• Comparative Molecular Field Analysis (CoMFA), Hugo Kubinyi, BASF
  AG, D-67056 Ludwigshafen, Germany
• Vyas Sharma, Michael W. Duffel, A Comparative Molecular Field
  Analysis‐Based Approach to Prediction of Sulfotransferase Catalytic
  Specificity, Methods in Enzymology,2005
• http://tripos.com/index.php?family=modules,SimplePage,,,&page=Q
  SAR_CoMFA
• http://bioptrain.org/uploads/3/33/Comfa_ASAPseminar.pdf
Thank you

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CoMFA CoMFA Comparative Molecular Field Analysis)

  • 1. Comparative Molecular Field Analysis (CoMFA) Pinky Sheetal V 1801110004 M.Tech Bioinformatics
  • 2. Introduction • CoMFA (Comparative Molecular Field Analysis) is a 3D QSAR technique based on data from known active molecules. • The aim of CoMFA is to derive a correlation between the biological activity of a set of molecules and their 3D shape, electrostatic and hydrogen bonding characteristics.
  • 3. Methodology 1. A set of molecules is first selected which will be included in the analysis.  As a most important precondition, all molecules have to interact with the same kind of receptor (or enzyme, ion channel, transporter) in the same manner, i.e., with identical binding sites in the same relative geometry. 2. A certain subgroup of molecules is selected which constitutes a training set to derive the CoMFA model. 3. Atomic partial charges are calculated and (several) low energy conformations are generated. 4. A pharmacophore hypothesis is derived to orient the superposition of all individual molecules and to afford a rational and consistent alignment. 5. A sufficiently large box is positioned around the molecules and a grid distance is defined. 6. Different atomic probes, e.g., a carbon atom, a positively or negatively charged atom, a hydrogen bond donor or acceptor, or a lipophilic probe, are used to calculate field values in each grid point, i.e., the energy values which the probe would experience in the corresponding position of the regular 3D lattice.
  • 4. 7. PLS analysis is the most appropriate method for this purpose . 8. The result of the analysis corresponds to a regression equation with thousands of coefficients.  Most often it is presented as a set of contour maps. These contour maps show favorable and unfavorable steric regions around the molecules as well as favorable and unfavorable regions for electropositive or electronegative substituents in certain positions 9. Predictions for the test set (the compounds not included in the analysis) and for other compounds can be made, either by a qualitative inspection of these contour maps or, in a quantitative manner, by calculating the fields of these molecules and by inserting the grid values into the PLS model.
  • 5. Summary of the alignment procedure used for sulfotransferase substrates in CoMFA. Vyas Sharma, Michael W. Duffel, 2005
  • 6. On a rectangular bounding grid measure interaction energies of each ligand with probe atoms placed successively at each grid point
  • 7. The color coding's indicate regions where electronegative substituents enhance (blue) or reduce (red) the binding affinity. Regions where substitution enhances (green) or reduces (yellow) the binding affinity
  • 8. Applications • Predict the properties and activities of untested molecules • Compare different QSAR models statistically and visually • Optimize the properties of a lead compound • Validate models of receptor binding sites • Generate hypotheses about the characteristics of a receptor binding site • Prioritize compounds for synthesis or screening • There are now a few hundred practical applications of CoMFA in drug design. Most applications are in the field of – Ligand protein interactions – Describing affinity or inhibition constants – Correlate steric and electronic parameters
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  • 10. Problems in CoMFA • The force field functions do not model all interaction types • Show singularities at the atomic positions • Deliberately defined cut-off values needed • Contour plots often not contiguously connected New approach: CoMSIA (Comparative Molecular Similarity Indices) • Does not calculate interaction energies but distance-dependent similarity indices (similarity of probe to molecule atoms) resulting in smooth contour plot
  • 11. Contour Plot blue: negative correlation with binding affinity red: positive correlation with binding affinity
  • 12. References • http://www.cmbi.ru.nl/edu/bioinf4/comfa-Prac/comfa.shtml • Comparative Molecular Field Analysis (CoMFA), Hugo Kubinyi, BASF AG, D-67056 Ludwigshafen, Germany • Vyas Sharma, Michael W. Duffel, A Comparative Molecular Field Analysis‐Based Approach to Prediction of Sulfotransferase Catalytic Specificity, Methods in Enzymology,2005 • http://tripos.com/index.php?family=modules,SimplePage,,,&page=Q SAR_CoMFA • http://bioptrain.org/uploads/3/33/Comfa_ASAPseminar.pdf