Modeling study of the structure of the macromolecular antitumor antibiotic neocarzinostatin. Origin of the stabilization of the chromophore

A three-dimensional structure of the apoprotein of neocarzinostatin (NCS) was built by using the actinoxanthin (AXN) crystal structure as template, and the subsequent favored-site search for the binding of the fragments of the chromophore of NCS at the binding cleft led to a reasonable complex structure of apo-NCS and the chromophore, after refinement of the molecular mechanics program AMBER. The refined three-dimensional structure model of NCS shows the "Y"-shaped cleft of the binding site in which the bicyclic epoxy dienediyne part 4 and its substituents, the naphthoate 3, the amino sugar 2, and cyclic carbonate 1 moieties are nicely fitted. Contacts of the chromophore with the specific amino acid residues in the cleft indicate their contribution to the specific and high affinity binding through ionic interaction, hydrogen bonding, aromatic stacking, and van der Waals contact. Stabilization of the labile chromophore is likely due to the steric hindrance toward the reactive sites such as the C12 position as well as the epoxide, and, more interestingly, the stabilization interaction between the disulfide group (Cys37 and Cys47) and the acetylenic bond is also suggested.