Searching for heparin binding partners

Heparin modulates diverse key physiological processes, from coagulation to angiogenesis, also contributing to the host-pathogen recognition process. New potential roles are still emerging, such as the inhibition of amyloidogenesis. To fully understand heparin function, and eventually modulate its action, we must first find out who are the travel companions. The chapter presents an overview on the heparin binding proteins known up to date. Following, the review offers useful tools to assist the discovering of new binding molecules, and identify the structural determinants involved in the interaction. Heparin complexes can be studied by experimental and in silico approaches, including docking and molecular dynamics simulations. Next, protein-ligand interfaces can be further analyzed by chemical-based computational tools to redesign even discontinuous binding epitopes in order to develop new active drugs. New in silico developed leads can be efficiently synthesized by high-throughput and combinatorial chemical synthesis allowing the screening of thousands of compounds. Thenceforth, they can be tested by experimental screening analysis to refine the leads designed, which once validated can undergo first clinical trials. © 2012 by Nova Science Publishers, Inc. All rights reserved.