Second fragment-based drug approved

Yesterday the US FDA approved venetoclax (VenclextaTM) for certain patients with chronic lymphocytic leukemia (CLL). This drug, which readers may know more familiarly as ABT-199, was co-developed by AbbVie and Genentech. The drug binds to BCL-2 and blocks its interaction with other proteins.

The first fragment-derived drug approved, vemurafenib, illustrated how quickly FBDD could move: just six years from the start of the program to approval. In contrast, venetoclax is the culmination of a program that has been running for more than two decades; Steve Fesik and his colleagues at Abbott published the X-ray and NMR structure of the protein BCL-xL back in 1996! The original SAR by NMR work was done on this protein, leading to ABT-263, which hits both BCL-xL and BCL-2. Subsequent work revealed that a selective BCL-2 inhibitor might be preferable in some cases, and further medicinal chemistry led to venetoclax.

This drug illustrates the power of fragments to tackle a difficult target by accessing unusual chemical space. It also illustrates creative, fearless, data-driven medicinal chemistry: not only does venetoclax violate the Rule of five, it even contains a nitro group, a moiety red-flagged due to its potential for forming toxic metabolites. This is a useful reminder that in our business rules are more appropriately considered guidelines, to be discarded when necessary.

Clinical results were sufficiently impressive that the drug was given breakthrough status and granted priority review, accelerated approval, and orphan drug designation. The ultimate victory is for the thousands of patients with relapsed CLL who have the 17p deletion on chromosome 17. In the registration trial, 80% of patients showed a partial or complete remission. It is rare to create something that works this well. Congratulations to all who played a role.

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!

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.