Method for the Identification of Allosteric Drug Binding Sites

Reference Number: 1695

Background

Conventional methods for protein-targeted drug design are very heavily biased towards exploiting those sites on the protein targets where other molecules are already known to bind. In the case of enzymes, this usually means seeking ligands that are capable of binding tightly to the catalytic sites in place of the substrate. The discovery of such “competitive” inhibitors may achieve the goal of stopping the enzyme working, but common problems are:

• The necessary selectivity to avoid toxicity may not be achieved (catalytic sites strongly resemble each other structurally throughout enzyme families)
• The action terminates the enzyme action rather than controlling it

In nature, selectivity for particular enzymes and “time and place” control of enzyme function is predominantly achieved via allosteric inhibitors and activators that bind some distance from the catalytic sites. Allosteric sites are in areas of the enzyme that have more structural variation from one family member to another. This increases the possibility of achieving selectivity within that enzyme family. Natural allosteric effectors are very difficult to identify because of the complexity of cell metabolism, the practice of assaying enzymes in purified forms away from their natural context, and a general lack of success in predicting the locations of potential binding sites. However, the prediction problem has been tackled at Strathclyde by development of the Simple Intrasequence Difference (SID) screening service.

Technology

The Simple Intrasequence Difference (SID) screening service identifies allosteric binding sites and protein-protein interaction sites in a client’s chosen target. When provided with structural data on the target, SID will generate co-ordinates for these sites and conduct a kinetic evaluation to determine the likelihood of a drug interaction at the site. These results can be used for the identification of novel hit compounds.

Key Benefits

• Identification of novel allosteric binding sites offering modulatory, rather than all-or-nothing control of the target
• Virtual screening of allosteric binding sites will reveal compounds likely to offer greater selectivity than compounds binding at conventional sites
• Allosteric binding sites offer greater IP potential, even for well-validated targets

Markets and Applications

SID is applicable to any protein target implicated in disease for which crystal structure information is available.

Accessing the Service

SID researchers will identify potential allosteric binding site co-ordinates and subject the target to a molecular dynamics simulation in order to confirm druggability. Co-ordinates will be provided to the client on a fee-for-service basis.

For further information, please contact Research & Knowledge Exchange Services:
e: rkes@strath.ac.uk t: 0141 548 3707 f: 0141 552 4409