Fragments vs Pharma

As the year winds down I’ve been catching up on some reading, and finally got to the study that Paul Leeson and Stephen St-Gallay published a couple months ago in Nature Reviews Drug Discovery. They analyzed compounds disclosed in patent applications from 18 large companies (mostly pharmaceutical companies, but also Amgen and Vertex) between 2000 and 2010. Even controlling for different targets, the companies differed considerably in the drug-likeness of their compounds, with some companies producing compounds that are considerably larger and more lipophilic than other companies. In the Pipeline has an excellent summary of the paper overall.

But what caught my eye as being of special interest to readers here is a small part of the main paper. In addition to analyzing large companies, Leeson and St-Gallay dug into the patent applications of a fragment-focused company, Astex Therapeutics (now Astex Pharmaceuticals). A dozen of the kinase targets pursued by Astex were also pursued by one or more of the large companies, and by analyzing the inhibitors from each organization, the authors could compare leads derived from fragments with leads derived using conventional approaches. The results were striking:

With the exception of chirality and sp³ measures, molecular properties are more drug-like in the compounds patented by Astex Therapeutics. This specific application of fragment-based drug design is perhaps the most compelling realization to date of the principle of lead-like chemical starting points that was first proposed more than a decade ago.

This does not mean that FBDD is a panacea: as noted previously, it is all too easy to take a perfectly good fragment and turn it into an obese grease-ball. But an attractive fragment, combined with adept medicinal chemistry and intolerance for unnecessary lipophilicity, can be a powerful combination.

And with that, Practical Fragments says goodbye to 2011. Thanks to all of you for reading, and special thanks for posting comments. May you all have a happy and successful 2012!

Fragments vs matrix metalloproteinase-13: avoiding the metal

Matrix metalloproteinases (MMPs), as their name suggests, are metal-dependent proteases that cleave the extracellular matrix. They have been implicated in a wide variety of diseases including cancer and inflammation. MMPs have also been used as model systems to study the effects of fragment linking. (In fact, the first successful example of SAR by NMR was conducted against MMP-3.) Most inhibitors, including those starting from fragments, interact with the catalytic zinc in order to achieve potency. However, with roughly two dozen human MMPs, all dependent on a zinc ion, selectivity has been tricky. A recent paper in J. Med. Chem. mostly from researchers at Boehringer Ingelheim sidesteps this problem nicely.

MMP-13 is one of the more interesting members of the family due to its apparent role in rheumatoid arthritis. The enzyme is crystallographically well-behaved, and has a large substrate-binding pocket (the S1’ pocket) near the catalytic zinc that is dissimilar from other S1’ pockets. Even better, there is an adjacent side pocket (S1’*) that can open when the S1’ pocket is occupied, providing further selectivity.

The researchers started by performing a virtual screen of their entire corporate library to look for fragments that might bind in the S1’ pocket. These were added to an in-house fragment collection, and the combined set of roughly 1000 compounds was screened at 0.5 mM concentration in a biochemical screen. Compounds were also assessed using NMR (saturation transfer difference) and size exclusion chromatography mass-spectrometry. One of the best hits was Compound 1, which came from the virtual screen and was originally made as a synthetic intermediate in a completely different program.

Crystallography revealed that Compound 1 does in fact bind in the S1’ pocket, making several hydrogen bonds, with the amide moiety pointed towards the S1’* portion of the protein. This compound also displayed some selectivity towards two other MMPs. Fragment growing towards the S1’* pocket led to compound 11, with increased potency and ligand efficiency, and ultimately to compound 15, with low nanomolar potency and > 1000-fold selectivity against 9 other MMPs. Crystallography revealed that, as expected, the compound binds with the benzoic acid moiety in the S1’* pocket. And despite the presence of the ethyl ester, compound 15 is orally bioavailable in rats.

The paper gives no indication of where the program is today, but it is another nice example of fragment growing, as well as taking an unconventional approach to achieve selectivity.

Are enthalpic binders more selective than entropic binders?

Thermodynamics is one of those abstract subjects that can have surprising real-world implications. The two components of free energy, enthalpy and entropy, are simplistically associated in drug discovery with polar interactions for the former and hydrophobic interactions for the later. Some researchers have suggested that enthalpically-driven binders are better starting points for optimization, and that best-in-class drugs rely more on enthalpy than entropy. In a recent paper in Drug Discovery Today, Yuko Kawasaki and Ernesto Freire at Johns Hopkins University suggest that enthalpic binders may also be more selective.

Medicinal chemists apply two general strategies to improve selectivity: increase the affinity of a compound for its target more than for off-targets, or decrease the affinity of a compound for off-targets. Kawasaki and Freire argue that the first is more likely to result from entropic interactions, while the second is more likely to result from enthalpic interactions. This is because nonpolar (entropic) interactions are often tolerant of mismatches; a hydrophobic substituent might improve the affinity of your ligand for its target, but, unless it causes a severe steric clash, it may also improve activity for off-targets – though hopefully less. Indeed, recent findings suggest that more lipophilic molecules tend to be more promiscuous than similarly-sized but less lipophlic molecules. On the other hand, due to the highly directional nature of polar interactions, a mismatched polar (enthalpic) interaction in an off-target is likely to be highly detrimental to binding.

The researchers consider two case studies involving HIV-1 protease inhibitors. In one example, adding two (non-polar) methyl groups improves the affinity of the inhibitor for its target as well as for two off-targets, though it improves the potency towards HIV-1 protease more, thus improving selectivity.

In the second case, a non-polar thioether is replaced with a polar sulfone. This slightly decreases the overall binding affinity for HIV-1 protease, but has a much larger negative effect on two off-targets, resulting in greater selectivity. In this case, the enthalpy of binding for HIV-1 protease is considerably improved, though the effect is compensated for by unfavorable changes in entropy. As the authors note, “even if a strong hydrogen bond does not contribute to affinity, it might contribute significantly to selectivity.”

Ideally you would want to use both strategies (improving affinity for your target and decreasing affinity for off-targets). However, since you probably don’t know all your off-targets, focusing on enthalpic binders may be the way to go, as mismatched polar interactions are likely to exclude lots of unknown off-targets.

Of course, two examples may not make a trend, but they do make a testable hypothesis. For example, there is a veritable plethora of kinase inhibitors with known specificity profiles: it would be interesting to correlate these with their thermodynamic profiles. But at any rate, this is yet another reason to hold down the hydrophobicity of your compounds.