Discovery of a novel warhead against beta-secretase through fragment-based lead generation.

Fragment-based lead generation was applied to find novel small-molecule inhibitors of beta-secretase (BACE-1), a key target for the treatment of Alzheimer's disease. Fragment hits coming from a 1D NMR screen were characterized by BIAcore, and the most promising compounds were soaked into protein crystals to help the rational design of more potent hit analogues. Problems arising due to our inability to grow BACE-1 crystals at the biologically relevant pH at which the screen was run were overcome by using endothiapepsin as a surrogate aspartyl protease. Among others, we identified 6-substituted isocytosines as a novel warhead against BACE-1, and the accompanying paper in this journal describes how these were optimized to a lead series of nanomolar inhibitors.1.

A critical interplay between Ca2+ inhibition and activation by Mg2+ of AC5 revealed by mutants and chimeric constructs.

Adenylyl cyclase type 5 (AC5) is sensitive to both high and low affinity inhibition by Ca(2+). This property provides a sensitive feedback mechanism of the Ca(2+) entry that is potentiated by cAMP in sources where AC5 is commonly expressed (e.g. myocardium). Remarkably little is known about the molecular mechanism whereby Ca(2+) inhibits AC5. Because previous studies had showed that Ca(2+) antagonized the activation of adenylyl cyclase brought about by Mg(2+), we have now evaluated the Mg(2+)-binding domain in the catalytic site as the potential site of the interaction, using a number of mutations of AC5 with impaired Mg(2+) activation. Mg(2+) activation exerted contrasting effects on the high and low affinity Ca(2+) inhibition. In both wild type and mutants, activation by Mg(2+) decreased the absolute amount of high affinity inhibition without affecting the K(i) value, whereas the K(i) value for low affinity inhibition was decreased. These effects were directly proportional to the sensitivity of the mutants to Mg(2+). Parallel changes were noted in the efficacies of Ca(2+), Sr(2+), and Ba(2+) in the mutant species, suggesting a simple mutation in a shared domain. Strikingly, forskolin, which activates by a mechanism different from Mg(2+), did not modify inhibition by Ca(2+). Deletion of the N terminus and the C1b domain of AC5 and a chimera formed with AC2 confirmed that the catalytic domain alone was responsible for high affinity inhibition. We therefore conclude that both low and high affinity inhibition by Ca(2+) are exerted on different conformations of the Mg(2+)-binding sites in the catalytic domain of AC5.

Insights into specific DNA recognition during the assembly of a viral genome packaging machine.

Terminase enzymes mediate genome "packaging" during the reproduction of DNA viruses. In lambda, the gpNu1 subunit guides site-specific assembly of terminase onto DNA. The structure of the dimeric DNA binding domain of gpNu1 was solved using nuclear magnetic resonance spectroscopy. Its fold contains a unique winged helix-turn-helix (wHTH) motif within a novel scaffold. Surprisingly, a predicted P loop ATP binding motif is in fact the wing of the DNA binding motif. Structural and genetic analysis has identified determinants of DNA recognition specificity within the wHTH motif and the DNA recognition sequence. The structure reveals an unexpected DNA binding mode and provides a mechanistic basis for the concerted action of gpNu1 and Escherichia coli integration host factor during assembly of the packaging machinery.