• Alex Kentsis

  • Nov 10, 2013

Working Paper: Activity Correlation Proteomics

The identification of biologically and therapeutically relevant targets of small molecule drugs is challenging. This is particularly true for small molecules that bind to diverse proteins in cells and for those with low binding affinities, necessitating analyses under relatively high concentrations that lead to heterogeneous binding. Pleiotropy is a property of all drugs, which are rendered specific only by the extent of pleiotropic effects within empiric therapeutic windows.

One approach to optimize desired biologic activities is to identify distinct molecular targets responsible for particular biologic effects. To do this, we assume a monotonic relationship between apparent binding affinities of a series of structurally related drugs and their biologic activities. For protein targets, this can be accomplished using ligand affinity chromatography and quantitative mass spectrometry. To eliminate the need for synthesis of more than one ligand affinity capture probe, we analyze proteome binding as captured by a single capture probe in the presence of varying free competitor drugs.

Qualitatively, the relationship between protein binding and activity is reflected by the enhanced competition and reduced apparent binding of biologically relevant protein targets in the presence of competitor drugs with higher biologic activity. This structure-activity relationship can be linearly approximated by:

A = a + bB

where A  is a vector of biological activities of structurally related competitor drugs (strong to weak), as represented by the inverse of their half-maximal effective concentration needed to elicit observed biologic activity (1 / EC50),  B is a vector of their binding affinities (high to low), as measured by the ratio of the observed intensities of heavy and light isotope labeled proteins bound to the capture probe after competition with the vehicle control and competitor drug, and a and b are offset constants.

We calculate the strength of the relationship between biologic activity  and binding to any given protein  for any given drug series using the Pearson correlation coefficient, where value of 1 represents a perfect correlation between target binding and observed biologic activity, value of 0 represents lack of association between target binding and biologic activity, and value of -1 indicates decreasing biologic activity with increased target binding (antagonism).

Termed activity correlation proteomics, this formalism relates the binding of molecular targets of drugs to their biologic activities, enabling the identification of specific targets responsible for distinct activities.