Silver Ain't Bad

For those of you who have been reading this blog for a while, you are familiar with the "Fragments in the Clinic" posts, Jan2015, Jan2013, and Jan2010.  Two of  those slowly making its way through the pipeline is navitoclax, ABT-263, and venetoclax, ABT-199.  Today Abbvie and Genentech announced that it had met its end point in phase II trials.  The companies plan to file for approval by the end of this year.  At that point we will then have TWO compounds approved from fragments.  Congratulations to all of those folks who have worked on this over the years!!!

Tenth Annual Fragment-based Drug Discovery Meeting

Last week marked the tenth anniversary of CHI’s three-day Drug Discovery Chemistry conference in San Diego. The conference consists of six tracks, with three happening simultaneously. The FBDD track is the only one which dates all the way back to the beginning in 2006. In fact, this is the oldest recurring fragment conference, predating both the Royal Society Fragments meetings as well as the independent FBLD meetings.

It’s worth reflecting on how far fragments have come since 2006. Back then, as Rod Hubbard (Vernalis and University of York) noted, most of the talks were prospective and methodological. Even as late as 2010 there were talks describing how dedicated fragment groups needed to be shielded from the larger organization. Now fragments are mainstream: a large fraction of the talks in the protein-protein interaction track involved fragments, as did both plenary keynote addresses to the entire conference.

Harren Jhoti’s keynote focused on lessons learned at Astex over the past 15 years. There has been some debate in the literature over ligand efficiency (LE), and one slide that struck me was a summary of 782 dissociation constants (measured by ITC) against 20 projects. The vast majority of these compounds had LE > 0.3 kcal/mol/atom. Given that Astex has put multiple fragment-derived drugs into the clinic and was acquired by Otsuka in one of the largest M&A events of 2013, the metric appears to have some utility.

Still, it’s important not to be dogmatic, particularly for difficult targets. Harren described a program for XIAP/cIAP where they started with an extremely weak fragment with LE < 0.2, but its binding mode was sufficiently interesting that they were willing to work on it. This program also revealed the importance of biophysical measurements, as functional activity was uninterpretable and even misleading until higher affinity compounds were discovered.

One theme throughout the conference was the observation that fragments bind at multiple sites on proteins. Harren noted that Astex researchers have found fragments bound (crystallographically) to 54 sites on 25 targets – an average of 2.2 sites per target. Some targets are even more site-rich: Joe Patel (AstraZeneca) performed a crystallographic screen on a complex of Ras and SOS and found four binding sites, including one previously discussed here. In this effort, 1200 fragments were screened in pools of 4, and in one case two fragments from the same pool each bound only when they were both present at the same time – each fragment alone showed no binding by NMR or crystallography.

Troy Messick (Wistar) described his work against the EBNA1 protein from Epstein-Barr virus. An HTS screen of 600,000 compounds came up with at best marginal hits, but soaking 100 different Maybridge fragments into protein crystals led to 20 structures, with fragments bound to four different sites. Some of these fragments were then merged to give cell-active compounds with good oral bioavailability.

Rather than exploring different ligands binding at different sites, Ravi Kurumbail (Pfizer) described an interesting case of the same ligand binding at different sites. A screen against the kinase ITK identified a (large) fragment that could bind both in the adenine binding pocket as well as a nearby pocket, as determined crystallographically. Determining the affinities of the same fragment for the two sites necessitated some clever SPR and enzymology, but did lead to a highly selective series.

In terms of targets, BCL-family proteins were certainly well-represented, featuring heavily in talks by Chudi Ndubaku (Genentech, selective Bcl-x_L inhibitors), Mike Serrano-Wu (Broad Institute, MCL-1 inhibitors), Zaneta Nikolovska-Coleska (University of Michigan, MCL-1), Roman Manetsch (Northeastern, Bcl-x_L and MCL-1), and Andrew Petros (AbbVie, BCL-2 and MCL-1). Of course, it was AbbVie (neé Abbott) that pioneered BCL inhibitors as well as FBLD in general, and I was happy to hear that there is a renaissance occurring there, with fragment approaches being applied to all targets, even those undergoing HTS.

Finally, there were some interesting practical lessons on library design. Peter Kutchukian described how the Merck fragment library was rebuilt to incorporate more attractive molecules that chemists would be excited to pursue. There is an ongoing debate as to whether a fragment library should be maximally diverse or contain related compounds to provide some SAR directly out of the screen, and in the case of the Merck library the decision was to target roughly five analogs in the primary library, with a secondary set of available fragments for follow-up studies.

The utility of having related fragments in a library was illustrated in a talk by Mark Hixon (Takeda) about their COMT program. A HTS screen had failed, and even a screen of 11,000 fragments came up with only 3 hits (with an additional close analog found by catalog screening). Remarkably, all of these are extremely closely related, but other analogs in the library didn’t show up; had they not had multiple representatives of this chemotype in their library they would have come up empty-handed.

In the interest of space I’ll close here. Teddy will post his thoughts later this week, and please share your own. CHI has announced that next year’s meeting will be held in San Diego the week of April 19. And there are still several great events on the calendar for this year!

NMR as an Impractical Tool, Again

When I was in grad school, I was faced with the choice of two NMR labs to join (after starting as a organic chemist and flirting with enzymology).  Both used NMR, but with very different goals.  One lab used NMR and found systems to study using NMR.  The other studied interesting problems.  The PI would say if NMR is most appropriate than using, but don't be a slave to it.  I have taken that attitude my entire career.  In industry, it also has to be the mantra: best tool for the problem.  Academics tend to have the opposite mindset: let's make my tool work for anything.  

The Krimm lab has been cited here, here, here, here, and here on the blog and I hold their approach to academic tool creation for drug discovery in good regard.  In this paper, they present a combination computational/NMR method for determining if a fragment induces conformational changes in the target.  In their own words: 

The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding.

Sometimes good people do bad things. 

I am not going to get into the details, but rest assured the science is sound.  Their approach is to evaluate H-N (you could also use H-C, why not) chemicals shifts from titration data to simulated CSPs.  When they did compare experimental with calculated CSPs they could not explain some of these shifts, even when they included ring current-induced shifts.  To further investigate this phenomenon, they used Residual Dipolar Couplings (RDCs) to further explore these unexplained CSPs.  It does.  

What are my problems with this paper?  Practicality, primarily.  Is this another anti-compchem rant?  Nope.  The problem here is that everything they propose to do, and they do it well, relies upon a whole sh!tpile of a priori knowledge: 1. the structure of the protein (typically from X-ray) and 2. the assignments of the protein (not trivial).  Additionally, the RDCs require acquiring two sets of data, aligned and unaligned.  RDCs are wholly impractical.  All of this should red flag this paper as a "Impractical" approach.  It also does not present a method for interrogating structural changes induced by ligands that is any better or more robust than the current standard of analysis.

Fragment linking for specific Bcl-2 inhibitors

One of the most well-known examples of a fragment-based program that has yielded a clinical compound is Abbott’s Bcl-2 effort: ABT-263 is currently in over a dozen trials for various cancers. However, this molecule hits several proteins in the Bcl-2 family, and a more specific inhibitor of Bcl-2 alone may have lower toxicity. Phil Hajduk and colleagues have used SAR by NMR to do this, as they report in the latest issue of Bioorg. Med. Chem. Lett.

The researchers started with a protein-detected NMR screen of 17,000 compounds; compound 1 (see figure) was found to be fairly potent, and also roughly 20-fold selective for Bcl-2 over the related protein Bcl-xL. Hajduk’s team did not have a crystal structure at this point, but they were able to use NMR to determine that the compound lies in a large hydrophobic groove. This is the same groove found to bind biaryl acids in earlier work, so the researchers screened a set of 70 of these to see if they could bind in the presence of compound 1. Interestingly, compound 6 was equally potent in the presence or absence of compound 1, suggesting that both fragments could bind simultaneously.

NMR was then used to determine the ternary structure of fragments related to compound 1 and compound 6 bound to Bcl-2, and linking these led to compound 25, with high nanomolar potency. Although this represents a good boost in potency, the binding energies were not additive (let alone synergistic). An NMR structure of one of the linked molecules revealed that, although it binds in the same groove as its component fragments, its position is shifted, and also that one of the protein side chains moves to deepen a hydrophobic pocket. Additional chemistry to fill this pocket led to compound 29, with 40 nM biochemical potency and measurable cell activity, as well as greater than 1000-fold selectivity for Bcl-2 over Bcl-xL and at least 28-fold specificity over other Bcl-2 family members.

This is a nice example of starting with a modestly selective fragment (albeit a jumbo-sized one) and, through fragment linking, increasing both the potency and specificity towards the target protein.

Fragment specificity

A frequent topic in fragment roundtable discussions concerns specificity: do fragments hit lots of targets, or just a few? Isabelle Krimm and colleagues at the Université de Lyon in France studied this question experimentally and report their results in a recent issue of J. Med. Chem. The paper provides data for the ongoing debate of whether and how much specificity a fragment should exhibit before being pursued for further lead development.

The researchers assembled a diverse set of 150 fragments and used NMR techniques to determine whether they bind to five different proteins. Three of the proteins, Bcl-xL, Bcl-w, and Mcl-1 are related members of the Bcl-2 family of antiapoptotic proteins, and at least the first of these has been successfully targeted using fragment-based methods. The fourth protein, PRDX5, has proven to be much less yielding to inhibitor discovery, while the fifth, human serum albumin (HSA), binds a wide variety of small molecules.

After applying 1D-NMR techniques (WaterLOGSY and STD) to all of their fragments against each of the five proteins, the researchers used more rigorous but less sensitive 2D-NMR (HSQC) to determine the binding sites of the hits. (This later study revealed, in agreement with previous results from the same lab, that the fragments all bind in the “hot spots” or active sites of the proteins.)

More than two-thirds of the fragments bound to at least one protein, a rather high hit rate. However, the hit rates for each protein varied considerably, with only 7 hits for PRDX5 and 72 for HSA (with a close second of 71 for Bcl-xL). Within the Bcl-2 family there was little specificity observed: Mcl-1, with 29 hits, shared all but one hit with either Bcl-xL or Bcl-2 or both; such non-specificity among related proteins has been discussed previously. In the case of HSA and Bcl-xL, although both proteins had similar numbers of hits, just over half of these were in common, demonstrating that fragment specificity is not difficult even with small-molecule sponges such as HSA. That said, many fragments were remarkably nonspecific, with 22 hitting four of the 5 proteins. Amazingly, all 7 of the hits against PRDX5 also hit all four other proteins.

The physicochemical properties of the fragments that hit one or more proteins were compared with those of the library as a whole, and although most of the parameters were similar, the ClogP values (a measure of hydrophobicity) were considerably higher for hits, and highest of all for the non-specific hits.

These findings are more evidence that, as predicted almost a decade ago, fragments can bind to more proteins than can larger, more complex molecules. The follow-up question, how much does this matter, is still up for debate. There are plenty of examples of developing specific inhibitors from non-specific starting points during the course of fragment optimization. But how non-specific is too non-specific? Would you feel comfortable pursuing any of the fragments that hit all of the proteins?

Hot spots for fragments

Although most people try to advance fragments to more potent molecules, some have taken the reverse approach: starting with potent binders and deconstructing them into fragments (see for example here, here, and here). A recent, thorough example in J. Med. Chem. shows how isolated fragments do not necessarily bind in the same manner as they do in fully elaborated molecules.

In this paper, Isabelle Krimm and colleagues at the Université de Lyon in France applied “fragment-based deconstruction” to inhibitors of the anti-cancer target Bcl-xL. This protein is one of the great success stories in fragment-based drug discovery: ABT-263, which is in multiple clinical trials, was discovered by researchers at Abbott using SAR-by-NMR. In that work, fragments were identified binding near each other on the protein (site 1 and site 2) and subsequently linked together. Very extensive medicinal chemistry eventually led to the picomolar inhibitor now in clinical testing.

Krimm and colleagues dissected 9 inhibitors of Bcl-2, including ABT-263, into 22 different fragments and studied their binding by NMR. They first used ligand-observed NMR (WaterLOGSY and saturation transfer difference, or STD) and found that 19 fragments interacted with the protein. When they then turned to protein-observed NMR (proton-15N heteronuclear single quantum correlation, or HSQC), only 13 fragments caused changes to the spectra of Bcl-xL, suggesting that the other six bound too weakly to detect. In fact, the most potent fragment has an affinity of just 2.7 mM, so it is not surprising that some of the fragments were undetectable.

The nice thing about protein-observed NMR is that it can provide insight into where on the protein the fragments bind, and in this case the researchers found that 12 of the 13 fragments that caused NMR shifts in the protein bind to site 1, despite the fact that structures and modeling suggest that some of these fragments should be binding in other sub-sites. (The 13th fragment appears to bind to multiple sites on the protein surface.) In other words, the binding modes of the isolated fragments are not the same as the binding modes of the fragments when assembled.

The authors conclude that fragments “will interact with their preferred binding site, which can be different from the site they occupy when they are included in the larger molecule.”

Interestingly, one of the fragments studied by Krimm (2,3-dihydroxynapthalene) was also tested at Abbott, but found to bind in site 2. The reason? In the Abbott study, this fragment (and a number of others) were tested in the presence of a fragment that binds to site 1. It seems that site 1 is a thermodynamic sink, or hot spot. Unless this site is filled, other fragments will bind there, even if they could also bind elsewhere on the protein. The implication is that, if you want to find fragments that bind to a new site on your protein, it may be worth screening in the presence of a fragment known to bind to an existing site.

Click and Clack

A new paper describes how combining fragment classes that selectively react with each other can yield an inhibitor to a protein-protein interaction.

Most of you are probably familiar with the concept of “click chemistry”, exemplified by the Huisgen cycloaddition of azides and acetylenes to form triazoles, and defined earlier this century by K. Barry Sharpless and colleagues. The idea, put very simply, is to react two molecules selectively and reliably to generate a product in high yield. The approach has obvious applications to fragment-based ligand discovery, and in fact Sharpless and co-workers demonstrated that the enzyme acetylcholinesterase can catalyze the formation of an inhibitor with femtomolar potency, starting from two fairly large and potent “fragments,” one containing an azide, the other an alkyne.

The notion of using a protein as a template on which to assemble an inhibitor dates back further than click chemistry. Huc and Lehn used reductive amination between aldehydes and amines in the presence of carbonic anhydrase to capture molecules that interacted more strongly with the protein than did the starting materials, and the technology even formed the basis of a company, Therascope.

In the latest example of this line of research, Roman Manetsch and colleagues find that the antiapoptotic cancer target Bcl-xL is able to catalyze the formation of an inhibitor from fragments sporting thioacids and sulfonyl azides; the inhibitor itself was previously discovered using different fragment-based methods at Abbott. The reaction appears to be relatively fast, and works even in the presence of a small pool of sulfonyl azides.


The paper, published this month in the Journal of the American Chemical Society, is a nice proof-of-concept study, but it does raise practical questions. First, the authors report the use of only six sulfonyl azides and three thioacids. These generally need to be custom-made rather than purchased; how much of a barrier will this represent to other practitioners? Once assembled, how stable will these fragments be in long-term storage? Finally, the product acylsulfonamide is a rather special entity not commonly found in drugs, and with a limited range of bioisosteres (indeed, it was originally employed at Abbott to replace a carboxylic acid). Still, the paper does provide an interesting - if less conventional - method of fragment-based lead discovery.