Richard Silverman, the discoverer of pregabalin, has published a trifecta of papers describing the use of his “fragment hopping”strategy to discover selective, potent, and pharmacologically active inhibitors of neuronal nitric oxide synthase (nNOS).
nNOS is itself part of a triad of closely related enzymes: nNOS, iNOS, and eNOS. All synthesize the radical signaling molecule NO from arginine, but their tissue localizations and functions differ considerably. Both nNOS and iNOS have been pursued as drug targets, with nNOS implicated in a variety of diseases of the central nervous system. However, as eNOS is involved in maintaining blood pressure, identifying inhibitors selective for the desired NOS is essential. Doing so is difficult because all three enzymes share very similar active sites: of the 18 amino acids close to the substrate binding site, 16 are identical, and one of the two residues that vary has its side chain facing away from the substrate binding site.
The Silverman group has been working on selective nNOS inhibitors for over a decade, and succeeded in generating remarkably selective inhibitors, such as the compound shown on the left. But with its peptidic nature and dramatic CLogP, this compound is a long way from a drug. Enter “fragment hopping.” First, a known inhibitor is computationally deconstructed into its minimal pharmacophores; these can be as rudimentary as a positive charge or a hydrophobic spot. Next these virtual fragments are rebuilt into new virtual molecules; further computation weeds out molecules that are likely to be metabolically unstable or toxic. Finally, the best molecules are synthesized and tested. The process is computationally intensive, and I’m simplifying it greatly here, but the results, first published in J. Am. Chem. Soc. last year, are impressive: the dipeptide was transformed into a smaller, more drug-like molecule (center in figure), with increased ligand efficiency. It also retained selectivity over iNOS and eNOS.
In the latest issue of J. Med. Chem., Silverman and colleagues report using the technique again, this time to not only improve potency, but to improve the drug-like properties as well. The resulting molecule (right in figure) still maintains good selectivity, but now also boasts a respectable CLogP. Consistent with this, the molecule shows efficacy in a rabbit model of cerebral palsy. For a great review summarizing the long march to these compounds, check out this just released Acc. Chem. Res. paper.
What I really like about this work is that the researchers use fragment-based methods to actually improve the pharmaceutical properties of their molecules. Much of the focus of FBDD has been in discovery of early leads; these papers show that the approach can be useful downstream as well.
And finally, we can’t let today pass without sending out a Happy 200th Birthday to Charles Darwin (as well as Abraham Lincoln). As Teddy noted in an earlier post, “it’s evolution baby.”