Fragments vs BACE1: Amgen’s story

Some targets that have proven recalcitrant to standard screening approaches seem to be particularly amenable to fragment-based approaches. Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) is one such example: Practical Fragments has previously discussed programs from both Evotec and Schering/Merck, the latter of which has resulted in more than one clinical candidate. In a recent issue of J. Med. Chem., researchers at Amgen describe their adventures with this Alzheimer’s disease target.

The researchers started by using SPR to screen a library of about 4000 fragments (which had MW < 300, polar surface area < 30 Ų, and ≤ 2 hydrogen bond donors). This led to 106 hits with 10 mM or better potency, of which 8 confirmed in an orthogonal assay with potency better than 1 mM. Among these was fragment 1, which was also discovered as a BACE1 binder by researchers at Astex using crystallographic screening.

Astex’s crystallographic structure showed compound 1 packed pretty tightly into BACE1, but surprisingly, the Amgen team found that walking a bromine atom around the phenyl ring produced gains in potency at all four positions. In fact, adding an aromatic group off the 6-position, as in compound 34, led to a dramatic increase in potency, and crystallography revealed that the protein undergoes a conformational change to accommodate the extra bulk and form an edge-face interaction between a phenylalanine side chain and the added aromatic group.

Putting substituents off the 3-position, as in compound 44, led to molecules that could access either the P1 pocket or the P2’ pocket of the enzyme, but adding the ortho-tolyl group from compound 34 to give compound 43 locked the binding mode down to the P2’ pocket and gave a satisfying boost in potency such that standard enzymatic assays could be used instead of SPR. Further medicinal chemistry led to picomolar binders such as compound 57 as well as compounds less active in the biochemical assay but with better permeability and lower efflux, such as compound 59. This compound also showed in vivo activity in a rat model, though it is rapidly metabolized.

Although crystallography was clearly enabling throughout the process, this paper is a warning not to be too slavish in adherence to structure, as the initial break (compound 1 to compound 34) would not have been predicted to be active based on the co-crystal structure of compound 1 with BACE1.

This is also another nice example of starting with a rather generic fragment (heck, one published by another group!) and advancing it to a potent, proprietary series.