08 July 2015

Merging Fragments for Matriptase

We often talk about methods here: how to screen, how to prosecute those actives, and everything in between.  This is one of those what you do with the actives posts.  In this paper, a group from Aurigene and Orion present their results on Matriptase.  There have been multiple reported matriptase inhibitors, small molecule and peptide based.  Previous work from this group showed compounds that were active in cell-based migration and invasion assays and in mice with tri-substituted pyridyls and benzene compounds.  For this work, they take a SBDD approach:  "structure divulges a trypsin-like S1 cavity, a small hydrophobic S2 subpocket, and a solvent exposed spacious S4 region."

In screening benzamidine fragments (MW less than 300) they found 2 actives, ~80uM (Figure 1).
Figure 1.  Benzamidine screening actives
These were modeled in to the active site and obviously the amidine moiety went into S1.  Cpd 1's benzene moiety went nicely into S4 while 2's piperidyl went into S1'.  S4 easily accepted the more hydrophobic napthyl instead of phenyl and then they decided to see if the napthyl compound and 2 could be "linked" and the beta carbon. [So, my first quibble here is that this is not really a linking approach; this is fragment merging. Linking involves modeling, SBDD, and discovery of different linkers.  Its very difficult to do without specialized methods.  What they did here was see huge spatial overlap of compounds and voila, "we can add something right here".]  Well, not surprisingly, this worked.  They describe their SAR around each pocket to pick the compounds to merge, go read it if that interests you. The did crystallize the merged compound and it confirmed the modeling.  The final compound showed activity in cell-based assays and in mice.  That's good.  

This work can be summarized as follows: if you have significant spatial overlap you have a very good chance of merging disparate moieties.  So, two things bother me here.  First, the actives 1 and 2 are mighty big for fragments (more than 22 HAC).  That's fine, tomato...to-mah-to.  The final compound ends up pretty honking big too (37 HAC).  What is really bothersome, at least to me, is the LE.  Both actives start well below 0.2 (for a protease!) and they never improve on it. Now, Pete may disagree, but metrics have a place in FBDD.  Does the LE metric in this case tell us anything? 


Peter Kenny said...

Of course metrics have a place in FBDD and I enthusiastically endorse Simplistic Estimate of Enthalpy (SEEnthalpy) for its simplicity (and for giving me the opportunity to quote Leonard Cohen lyrics in a drug discovery context). Metrics provide comfort and guidance in times of great uncertainty and the fact one has adhered to them can be invoked (I vas only following metrics) in one's defense when the management are deciding who to cull in the aftermath of a high profile crash and burn.

When we use LE, our perception of the system changes with the units in which the quantities that describe the system are expressed. If a theory for nuclear relaxation behaved in this manner it would have been put out of its misery at the manuscript stage but LE is saved from this fate by the wisdom of crowds (aka herding instinct) in drug discovery. It's worth taking a really close look at the 'theory' section (Box 1) in Nat Rev Drug Discov 13:105–121 http://dx.doi.org/10.1038/nrd4163

Occasionally people calculate 'equibrium constants' or 'free energies' for the linking process and the numerical values of these calculated properties depend on the standard state.

Dan Erlanson said...

Another liability is the benzamidine moiety, which could be responsible for the suboptimal pharmacokinetics. It would be interesting to see if they could replace this with a chlorothiophene as has been done with other trypsin-like protease inhibitors.

Peter Kenny said...
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Peter Kenny said...

Hi Dan, My understanding is that the replacing benzamidine with chlorothiophene typically results in a loss of potency against those serine proteases for which arginine is an important molecular recognition element. This replacement will also lead to an increase in lipophilicity (whether one uses ClogP or logD) and so we should anticipate a large loss of lipophilic efficiency. This is likely to get the Sages of Stevenage spitting feathers and surely they will kindle the auto-da-fe to purge you of heretical thoughts.

Replacing the benzamidine with chlorothiophene adds an aromatic ring as well as lipophilicity and any of those Sages who also consider Property Forecast Index to be Core Doctrine will surely recommend some time in a confessional so that you can repent and purge your mind of these unholy thoughts.

Should you be seeking spiritual guidance form sources closer to home, I should note that your proposed structural modification removes three hydrogen bond donors, (I think?) two hydrogen bond donors but only one rotatable bond which is likely to lead to a decrease in SEEnthalpy.

Repent now (while there's still time)!

Peter Kenny said...

Hi Dan, Actually replacing the benzamidine with chlorothiophene does not add an aromatic ring and I was talking complete bollox. I realized this driving up to the north coast today but decided to continue rather than turning around to correct (very sloppy) error. The Anti-Fat Anti-Flat Movement would still recommend confessional time but not for Aromatic Sin. On an unrelated note, the Anti-Fat Anti-Flat Movement seem to have been rather quiet of late. Apparently they held their annual congress recently. In a Stevenage taxi.