Molecular Recognition in Protein-Small Molecule Interactions

Lee Makowski
Biosciences Division
Argonne National Laboratory
9700 S. Cass Avenue
Argonne, Illinois 60439

As observed in crystal structures of proteins with bound 
small molecule ligands, the interaction of a protein and a 
small molecule involves contacts between the small 
molecule and multiple short peptide fragments within the 
context of the larger protein structure.  Nevertheless, short 
peptide consensus sequences have been identified that are 
predictive for the binding of small molecules to proteins.  
For instance, the p-loop motif is predictive for nucleotide 
tri-phosphate binding in proteins.  Unfortunately, very few 
small molecule consensus binding sequences have been 
identified.  We have explored the use of phage-displayed 
peptide libraries for the generation of consensus sequences 
that could be predictive for small molecule binding on 
proteins.  The method involves statistical analysis of an 
affinity-selected set of peptides obtained by screening of 
libraries of random, phage-displayed peptides against small 
molecules attached to solid surfaces.  A random sample of  
the selected peptides is sequenced and used as input for a 
similarity analysis that calculates cumulative similarity 
scores along the length of the putative receptor.  Regions of 
the protein sequence exhibiting the highest similarity with 
the selected peptides proved to have a high probability of 
being involved in ligand binding. This technique has been 
successfully employed to map the contact residues in 
multiple known targets of the anticancer drugs paclitaxel 
(Taxol TM), docetaxel (Taxotere TM) and 2-methoxyestradiol 
and the glycosaminoglycan hyaluronan, and to identify a 
novel paclitaxel receptor [1].  These data corroborate the 
observation that the binding properties of peptides 
displayed on the surface of phage particles can mimic the 
binding properties of peptides in naturally occurring 
proteins.  It follows  that structural context is relatively 
unimportant for determining the binding properties of these 
peptides.  This technique represents a novel, rapid, high 
resolution method for identifying potential ligand binding 
sites in the absence of three-dimensional information and 
has the potential to greatly enhance the speed of 
development of novel small molecule pharmaceuticals.