If all analyses are taken together, the selectivity entropy avoids many pitfalls of the other methods, shows consistent compound ranking, and is among the most Binimetinib robust methods across profiling datasets. For this reason, we propose the entropy method as the best metric for gen eral selectivity. Defining average selectivity Quantification of selectivity helps to define when a com pound is selective or promiscuous. Because of its consis tency, the entropy method is ideally suited for benchmarking selectivity values. In the 290 kinase pro filing dataset, the entropies are monomodally distribu ted, with an average of 1. 8 and a standard deviation of 1. 0. Based on the correlation in Figure 2, it is expected that these statistics will be conserved in other profiling sets.

Therefore, in general, a kinase compound with an entropy less than about 2 can be called selective, and more than 2 promis cuous. This provides a first quantitative definition of kinase selectivity. Selectivity of allosteric inhibitors It is generally thought that allosteric kinase inhibitors are more selective. The selectivity entropy now allows quantitative testing of this idea. We identified, from literature, which inhibitors in the profiling datasets are type II and III, based on X ray structures. Sorafenib induces the kinase DFG out conformation in B RAF, nilotinib and gleevec in Abl, GW 2580 in Fms and BIRB 796 in p38a. Lapatinib induces a C helix shift in EGFR. PD 0325901 and AZD 6244 induce a C helix shift in MEK1. All other kinase inhibitors in the profile were labelled type I.

Comparing the entropy distributions in both samples shows that type II III inhibitors have significantly lower entropies. Although other factors, such as the time at which a compound was developed, could influence the entropy differences, the correlation between low entropy and allostery strongly supports the focus on allostery for developing specific inhibitors. Among the specific inhibitors in the type I category, 3D structures of PI 103, CI 1033 and VX 745 bound to their targets have not been determined. Therefore, potentially, these inhibitors could also derive their speci ficity from a form of undiscovered induced fit. Indeed, VX 745 related compounds induce a peptide flip near Met109 Gly110 in P38a.

Of the five most selective compounds in Table 1, only gefitinib so far is undoubt edly a type I inhibitor, making this EGFR inhibitor an interesting model for the structural biology of non allosteric specificity. Use of selectivity measures in nuclear receptor profiling Selectivity profiling is most advanced in the kinase field, but is Cilengitide emerging in other fields. To illustrate that selec tivity metrics such as the entropy can also be used with other target families, we investigated a long standing question in the nuclear receptor field are non steroidal ligands more selective than steroidals.