AbstractThe first and rate‐limiting step of the kynurenine pathway, in which tryptophan (Trp) is converted to N‐formylkynurenine is catalyzed by two heme‐containing proteins, Indoleamine 2,3‐dioxygenase (IDO), and Tryptophan 2,3‐dioxygenase (TDO). In mammals, TDO is found exclusively in liver tissue, IDO is found ubiquitously in all tissues. IDO has become increasingly popular in pharmaceutical research as it was found to be involved in many physiological situations, including immune escape of cancer. More importantly, small‐molecule inhibitors of IDO are currently utilized in cancer therapy. One of the main concerns for the design of human IDO (hIDO) inhibitors is that they should be selective enough to avoid inhibition of TDO. In this work, we have used a combination of classical molecular dynamics (MD) and hybrid quantum‐classical (QM/MM) methodologies to establish the structural basis that determine the differences in (a) the interactions of TDO and IDO with small ligands (CO/O2) and (b) the substrate stereo‐specificity in hIDO and TDO. Our results indicate that the differences in small ligand bound structures of IDO and TDO arise from slight differences in the structure of the bound substrate complex. The results also show that substrate stereo‐specificity of TDO is achieved by the perfect fit of L‐Trp, but not D‐Trp, which exhibits weaker interactions with the protein matrix. For hIDO, the presence of multiple stable binding conformations for L/D‐Trp reveal the existence of a large and dynamic active site. Taken together, our data allow determination of key interactions useful for the future design of more potent hIDO‐selective inhibitors. Proteins 2010; © 2010 Wiley‐Liss, Inc.