26 June 2013

(Not)Drugging the Undruggable

Well after spending last week at a Structure-based Drug Discovery conference that ended up being horribly academic and computational (think force fields and not the cool Star Trek kind), I come back to my blogging pile to find this paper

In this paper, the authors are looking at HIV Integrase.  HIV integrase has long been considered an "undruggable" target, although I would think that the presence of a marketed drug would kind of kill that perception.  But as we all know, preconceived notions die hard and slowly.  Anyhow, viral evolution necessitates the discovery of next generation integrase inhibitors.  To that end, the authors decided to use GLIDE to dock quinolines to the HIV Integrase-IN−LEDGF/p75 interface because some previous work had shown these molecules to have "been previously explored" for anti-integrase activity.  They quickly found out that 8-hydroxyquinoline made far more favorable contacts (one more hydrogen bond) than quinoline.  

They immediately started testing 8-OH-quinoline fragments for potency (via an Alpha-screen) and found molecules with very low micromolar potency but they do not report LEANs.  [It absolutely should be a requirement for any paper citing itself as "fragment" to include some sort of ligand efficiency metric with its data.] QA, QB, and QC have LEANS of 0.45, 0.41, and 0.37.  Yet, these compounds were cytotoxic.  

To expedite their search for non-cytotoxic, they generated a pharmacophore model.  This was used to screen ~7000 compounds generated from a query of 8-OH-quinoline and found that 5- (typically phenyl) and 7-substituted (typically phenyl) 8-OH-quinolines were the best output.
 In a perfect case of fitting the results to your preconceived notions the authors note: 
Although the pharmacophore identified the neutral form of compounds from the database, we have used the ionized form for the purpose of pharmacophore mapping, as we consider these compounds to be ionized in the context of receptor binding.
Despite adding a tremendous amount of heavy atoms, none of the compounds had activity much better than the original 12 HAC quinoline and were still cytotoxic.  They eventually found that only the 5-substituted-8-OH-quinolines did not have cytotoxicity. However, and please note, the potency is still NOT better than the original fragment hits.  Changing the C5-phenyl for piperazine or piperidine did increase potency (to 0.4uM, 0.35 LEAN) and reduced cytotoxicity.  What about the 8-OH moiety you ask?  Well, they found out that it could be substituted and/or be a thioether.  Of course, these weren't any more potent than the lead fragment and cytotoxicity remained an issue.

Well, to continue in a vein started by Dan, these authors seem to have wasted valuable NIH/NIAID and Campbell Foundation money.  Did they discover inhibitors of HIV Integrase, sure.  Are these useful frameworks?  Proabably not.  Did they establish a robust SAR from which they can move forward?  No.  Their activities floated right around 2 uM, with one or two getting below the uM line.  As I said, your computation is only as good as your experimental follow up.  In this case, it doesn't pass muster.



Dan Erlanson said...

Let me start out by acknowledging that the researchers did several things right, including adding detergent to their assay to diminish the risk of aggregators and running a number of control experiments.

That said, I do have to agree with Teddy that I am not convinced they've found much, if anything. First, the SAR are remarkably flat; major structural changes cause only minor changes in activity. Also, as Teddy already noted, the best molecules are only 7-fold more potent than the initial fragment. Moreover, there is no correlation between biochemical and cell-based potency.

Many of these compounds are likely to be metal chelators, which could play a major role in their activity. (Of course, since the approved integrase inhibitor raltegravir works by chelating metals this is not necessarily a show-stopper, but it is worth investigating.)

More troubling, many of the molecules are phenolic Mannich bases and thus subject to retro-Michael eliminations that generate reactive quinone methides, as shown by researchers at sanofi-aventis; these would then react covalently with nearby biological nucleophiles.

For these reasons, many of these types of molecules have been flagged as PAINS.

Anonymous said...

I am surprised all compounds negative on counterscreen. We use same method for our targets and hydroxyquinoline are active in our hands...