Structure-based design of potent inhibitors of scytalone dehydratase: Displacement of a water molecule from the active site

Scytalone dehydratase (SD) is a molecular target of inhibitor design effort s aimed at protecting rice plants from the fungal disease caused by Magnapo rthe grisea, As determined from X-ray diffraction data of an SD-inhibitor c omplex [Lundqvist et al. (1994) Structure (London) 2, 937-944], there is an extended hydrogen-bonding network between protein side chains, the inhibit or, and two bound water molecules. From models of SD complexed to quinazoli ne and benztriazine inhibitors, a new class of potent SD inhibitors involvi ng the displacement of an active-site water molecule were designed. We were able to increase inhibitory potency by synthesizing compounds with a nitri le functionality displayed into the space occupied by one of the crystallog raphic water molecules. Sixteen inhibitors are compared. The net conversion of potent quinazoline and benztriazine inhibitors to cyanoquinolines and c yanocinnolines increased binding potency 2-20-fold. Replacement of the nitr ile with a hydrogen atom lowered binding affinity 100-30000-fold. X-ray cry stallographic data at 1.65 Angstrom resolution on a SD-inhibitor complex co nfirmed that the nitrile functionality displaced the water molecule as inte nded and that a favorable orientation was created with tyrosines 30 and 50 which had been part of the hydrogen-bonding network with the water molecule . Additional data on inhibitors presented herein reveals the importance of two hydrogen-bonding networks toward inhibitory potency: one between Asn131 and an appropriately positioned inhibitor heteroatom and one between a bou nd water molecule and a second inhibitor heteroatom.