In fragment-based drug discovery, the binding mode of the initial fragment often remains constant during the course of optimization (see AT9283 and AT7519 from Astex). But this isn't always true. An intriguing counterexample has recently been published in J. Med. Chem.
Ruth Brenk and colleagues at the University of Dundee were interested in pteridine reductase 1 (PTR1), an enzyme from Trypanosoma brucei, the protozoan that causes sleeping sickness. They used the program DOCK 3.5.54 (which has been successfully used for fragment-docking) to screen 26,084 commercially available fragments against the crystal structure of PTR1. After a variety of computational and manual filters were applied, the researchers purchased and tested 45 compounds in an enzymatic assay. Of these, 10 fragments inhibited PTR1 at least 30% at 100 micromolar concentration, the most potent of which was compound 4 (below).
Removing the chlorine atom to generate compound 5 resulted in a dramatic loss in activity, while adding the dichlorobenzyl moiety caused a similarly large boost in activity (compound 9). The researchers were able to characterize the binding mode of each of these molecules crystallographically, and it turns out that, despite sharing a common aminobenzimidazole core, they all bind in very different fashions.
The initial compound 4 binds in two orientations, one of which closely resembles the binding mode predicted from the computational screen, with hydrogen bonds between the fragment and the enzyme cofactor NADP+. Compound 5 makes indirect (water-mediated) hydrogen bonds with the cofactor, while compound 9 binds in a completely different manner some distance from the cofactor.
Brenk and colleagues observed a hydrophobic pocket near compound 9 which they exploited to generate the low nanomolar compound 12; crystallography confirmed this binds in a similar fashion to compound 9. This molecule also displayed impressive selectivity against the potential off-target dihydrofolate reductase. Unfortunately, despite the promising biochemical activity of compound 12, it displays only modest activity against T. brucei in cell culture.
This study illustrates two important points. First, it can be hazardous to assume that even very closely related molecules, such as 4 and 5, bind in the same manner. Second, because of this, one should not adhere too slavishly to models, even those based on crystal structures. The binding modes of compounds 4 and 5 would not accommodate the dichlorobenzyl moiety, and yet this addition provided a sizable boost in potency. Sometimes it pays to make substitutions even where you wouldn’t expect them to make sense, especially where the changes are easy to make.