CHI’s Discovery on Target took place in Boston last week. With >1300 attendees from over two dozen countries, this is the older, larger cousin of the San Diego DDC meeting; at some points ten tracks were running simultaneously. Although more heavily focused on biology, there were still plenty of talks of interest to fragment folks.
Michael Shultz (Novartis) provocatively asked “do we need to change the definition of drug-like properties?” Long-time readers will recall that his earlier papers on ligand efficiency led to considerable debate, which seems to have been settled to everyone’s satisfaction with the exception of Dr. Saysno.
His new study, which has just published in J. Med. Chem., analyzes the molecular properties of all 750 oral drugs approved in the US between 1900 and 2017. Contrary to what strict rule of five advocates might expect, the molecular weight has increased over the past couple decades, as has the number of hydrogen bond acceptors. In contrast, the number of hydrogen bond donors (#HBD) has remained constant, suggesting that this may be more important for oral bioavailability. (Indeed, #HBD is the only Lipinski rule not broken by venetoclax.) Although Shultz did not examine “three dimensionality,” he laudably includes all the raw data – including SMILES – in the supporting information. This will be a useful resource for data-driven debates.
Molecular properties are carefully considered by Ashley Adams, who discussed the four fragment libraries used at AbbVie. The first is a 4000-member “rule of three” compliant library. For tougher targets, a 9000-member Ro3.5 library is available, as is a specialized fluorine library for 19F NMR (2000 members) and a 1000-member “biophysics” library, in which all compounds are less than 200 Da. Fragment optimization is often challenging, and since the C-H bond is most common but perhaps least explored, the AbbVie database is annotated with references on C-H bond activation relevant to each fragment.
Anil Padyana spoke about the metabolic enzymes being targeted at Agios. As we mentioned recently, these are very difficult targets, so the researchers often use parallel (as opposed to nested) screening using different techniques to minimize false negatives. Anil also described an interesting SPR assay in which fragments were introduced to the protein after the addition of an activating substrate.
High-quality protein constructs are essential for any fragment screen, and Jan Schultz described ZoBio’s technology for generating these. The company’s “protein domain trapping” approach entails high-throughput generation and screening of tens or hundreds of thousands of truncations of a given protein and rapidly selecting stable, high-expressing, and active variants.
Trevor Perrior mentioned that Domainex has a similar technology, which has been able to produce soluble protein domains in 90% of its attempts. Trevor also described a separate project in which a 656-fragment compound library was screened using SPR against the enzyme RAS. They found fragments that bind in a previously discovered site but, unlike the earlier work, the Domainex researchers were able to optimize these to nanomolar inhibitors.
Another success story was presented by Dean Brown (AstraZeneca), who described a collaboration with Heptares to discover inhibitors of protease-activated receptor 2 (PAR2). As the name suggests, this GPCR is activated when a protease cleaves the N-terminus, allowing the remaining N-terminal residues to fold back and activate the GPCR. The researchers used a stabilized form of PAR2 in an SPR screen of 4000 fragments and obtained >100 binders in multiple series. This led to AZ8838, which blocks signaling by binding in an allosteric pocket. It also has a slow off-rate, which is often an attractive feature – particularly in the context of intramolecular activation.
A number of talks were focused on protein degraders such as PROTACs (PROteolysis-TArgeting Chimeras). These are generally two-part molecules connected by a linker: one part binds to a target of interest, while the other engages the cellular degradation machinery to destroy the target. As Shanique Alabi, a graduate student in Craig Crews's lab at Yale demonstrated, the molecules are catalytic – a single PROTAC molecule can cause the destruction of multiple copies of a target protein. This “event-driven” pharmacology is thus different from most historical drugs, which are “occupancy-driven.” Is there a role for fragments?
One of the strengths of FBLD is that if a ligandable site exists, it can be found. As Astex demonstrated, the majority of proteins seem to have secondary sites, away from the active site. Although some of these may be allosteric, others probably have no functional activity, particularly in the case of protein-protein interactions where secondary sites may be located some distance from the interface. The power of degraders is that non-functional sites can be made functional. The power of FBLD is that it can find small-molecule binding sites, which could then be used as anchoring sites for one side of a degrader. Watch this space!