24 June 2024

Fragments vs LTA4H: LipE in action

Three years ago we described the discovery of LYS006, an inhibitor of leukotriene A4 hydrolase (LTA4H) from Novartis currently in phase 2 clinical trials. Companies often pursue multiple chemical series for important targets, and in a recent J. Med. Chem. paper Gebhard Thoma and colleagues describe another fragment-derived lead against LTA4H.
A biochemical high-throughput screen yielded compound 2, which is quite potent for a fragment-sized molecule. However, despite good ligand efficiency, the LipE (or LLE) was less impressive due to the high lipophilicity of the fragment. (Note that throughout the paper LipE is calculated based on measured logD rather than logP.) A co-crystal structure revealed that it bound in a similar fashion to other previously characterized LTA4H inhibitors such as compound 1, derived from LYS006 and reported in a J. Med. Chem. paper last year. Adopting elements from these led eventually to compound 12, which though less potent was also much less lipophilic and more soluble while still remaining fragment-sized.
Continuing to borrow from the rich literature around this target, the researchers added a basic amine group to get to the very potent compound 14. This was metabolically unstable, but further optimization led to compound 3.
Compound 3 was profiled extensively in a battery of tests. In addition to good biochemical potency, it showed mid-nanomolar activity in a human whole blood assay and was also active in other assays, including a mouse arthritis model. Other attractive features included a clean profile against a plethora of off-targets, good oral bioavailability in mice, rats, and dogs, and a predicted human oral dose of 40 mg once daily. However, a two week toxicology study in rats and dogs was “slightly less favorable” than compound 1.
This is a lovely example of property and structure-guided drug design, and the researchers are refreshingly open about borrowing elements from other molecules, even from outside Novartis. Interestingly, a crystal structure of compound 3 bound to LTA4H revealed that while the overall binding mode was similar to compound 1, which contains the same left-hand portion, the pyrazole and pyridine rings rotated 180º to make different hydrogen-bond interactions. Another reminder that despite our leaps in predictive capability, molecules can still provide many surprises.

17 June 2024

Fragments vs MAT2a: a chemical probe

As many of us know all too well, traditional methods to treat cancer often result in severe and even intolerable side effects. An emerging, gentler approach is based on synthetic lethality: targeting a protein that is essential only in certain cancer cells but not in normal cells. One prominent target is MAT2a, one of two human methionine adenosyltransferases. We’ve written previously about AG-270, a fragment-derived MAT2a inhibitor that entered the clinic. AstraZeneca has also pursued this target, as we discussed here. In a new J. Med. Chem. paper, Stephen Atkinson, Sharan Bagal, and their AstraZeneca colleagues describe a new chemical probe.
A differential scanning fluorimetry (DSF) screen of about 55,000 compounds at 100 µM, nearly a third of which were fragments, resulted in a healthy 1.5% hit rate. Further DSF as well as biochemical testing ultimately delivered compound 8, which is quite potent for a fragment. A crystal structure of the compound bound to MAT2a demonstrated that it bound in the same allosteric site targeted by other compounds. The methoxy group was pointed towards a couple backbone carbonyl oxygen atoms, and adding a couple fluorine atoms created a weak hydrogen bond donor with a satisfying 50-fold boost in potency.

Adding a hydrogen bond acceptor (compound 12) slightly reduced potency but also decreased lipophilicity. Further inspection suggested opportunities for fragment growing, and free energy perturbation (FEP) calculations suggested that adding the methoxyphenyl group of compound 15 would be fruitful. This turned out to be the case, and further optimization led to AZ’9567. The paper provides plenty of meaty medicinal chemistry, with significant efforts focused on reducing lipophilicity and clearance. FEP was used extensively during the design process, and a retrospective analysis found a good correlation between predicted and measured affinity.
AZ’9567 was studied in considerable detail. It has excellent oral bioavailability and good pharmacokinetics in both mice and rats. The compound does not significantly inhibit cytochrome P450 enzymes or hERG and is reasonably clean against a panel of 86 off-targets. The main liability is poor solubility, a problem also faced by AG-270. Nonetheless, the AstraZeneca researchers were able to develop a liquid formulation.
The paper compares AZ’9567 with AG-270, showing that both compounds are potent in biochemical assays as well as against cell lines in which MAT2a is essential. A mouse xenograft model with AZ’9567 showed considerable and sustained tumor growth reduction.
Unfortunately, AG-270 is no longer in clinical development, and there is no mention of a MAT2a inhibitor in the AstraZeneca pipeline. Nonetheless, having a second well-characterized chemical probe will be useful for further characterizing the biology of MAT2a and assessing whether it will be a productive drug target.

10 June 2024

Fragments vs CDC14 phosphatases

Practical Fragments has periodically written about protein tyrosine phosphatases (PTPs), which remove phosphate moieties from tyrosine side chains in proteins. Despite decades of attention, progress towards selective inhibitors has been slow due to both the similar active sites and their highly charged nature. A new paper in J. Med. Chem. by Zhong-Yin Zhang and colleagues provides some hope.
The researchers were interested in CDC14 phosphatases, so-called dual-specificity phosphatases that can dephosphorylate phosphoserine and phosphothreonine in addition to phosphotyrosine. Two members of this family, hCDC14A and hCDC14B, are widely expressed in humans, but their role in cancer is ambiguous, with some studies suggesting they are oncoproteins while others suggest they may have a protective function. Clearly a chemical probe would be useful.
The researchers started by considering non-hydrolyzable phosphotyrosine mimetics, specifically those replacing the central oxygen with a difluoromethyl moiety; we wrote about this bioisostere back in 2013. Eight fragments were made and assessed at 1 mM in aqueous buffer to demonstrate they did not aggregate. They were then tested in functional assays against a panel of ten PTPs, and compound 9 turned out to be quite potent and selective for hCDC14A. Subsequent experiments showed it to have similar activity against hCDC14B, and Lineweaver-Burk plots revealed it to be a competitive inhibitor of both, as expected.
Although no hCDC14A structures have been reported, modeling the compound into a published structure of hCDC14B gave some insights into the binding mode and selectivity. In particular, hCDC14B has a larger active site than some other PTPs, thus explaining why the tricyclic compound 9 could fit. Further analysis suggested the possibility of growing the compound towards a hydrophobic pocket, so the researchers synthesized a small set of molecules, of which compound 15 turned out to be the most potent.
Compound 15 was tested against 16 PTPs and found to be quite selective against hCDC14A and hCDC14B, with IC50 values 5 µM or worse against the others. Mutagenesis studies in the hydrophobic pocket were consistent with the proposed binding mode. Despite the presence of the highly charged difluorophosphonate moiety, compound 15 showed activity in cells at low micromolar concentration and had some oral bioavailability in mice.
Although better cell activity is probably necessary to make a truly useful chemical probe, this is a nice start. Researchers at AbbVie have taken a competitive inhibitor of a different PTP into the clinic, so perhaps we will start to see more successes against these challenging enzymes.

03 June 2024

Throwing the kitchen sink at IL-1β

Last year we highlighted a paper out of Novartis describing a fragment-to-lead story for interleukin-1 beta (IL-1β), a pro-inflammatory cytokine implicated in numerous diseases. The approved antibody drug canakinumab targets IL-1β, but a small molecule would provide easier oral dosing as well as better access to tissues such as the central nervous system. A new paper in J. Med. Chem. by Anna Vulpetti, Konstanze Hurth, and their Novartis colleagues describes the multiple approaches they've taken. (Anna also presented this work at Fragments 2024.)
The paper starts by summarizing the fragment work we described here. Notably, of nearly 4000 fragments screened, only a single super-sized fragment was validated, and it was quite weak. The researchers were able to optimize this to a molecule that inhibits binding of IL-1β to its receptor with an IC50 = 1.1 µM.
Starting from the initial fragment hit, the researchers performed virtual screens to find alternative binders. Of 281 selected for testing by 19F NMR or TR-FRET, two hits were obtained, one with an affinity of around 230 µM and the other worse than 1 mM. These molecules were similar to each other, and merging them led to a 43 µM binder. All molecules exceeded conventional fragment size, with the smallest containing 24 non-hydrogen atoms. We’ve previously discussed the possible need for larger fragments for difficult targets such as protein-protein interactions.
In addition to FBLD, the researchers also performed DNA-encoded library (DEL) screens using 15 libraries containing >1.6 billion molecules. This led to one family of hits, one member of which inhibited binding of IL-1β to its receptor with an IC50 = 8.3 µM. This molecule contains an aldehyde moiety, a reversible covalent electrophile. Subsequent experiments confirmed that the aldehyde reacts with a lysine residue on IL-1β, and the researchers were able to improve the potency to 1.2 µM. This molecule is even larger than the hit derived from fragments, with >50 non-hydrogen atoms. Interestingly, the molecule binds at a different site on the protein from the initial fragment hit.
Finally, the researchers screened a library of macrocyclic peptides in an mRNA display system. The macrocycles consisted of 10-14 amino acid residues, and the library was impressively large, containing “<1013 unique cyclic peptides.” This effort yielded a 14 µM inhibitor. Strikingly, crystallography revealed that the molecule binds at a site distinct from either the fragment- or DEL-derived hits.
This paper is a tour de force addressing a difficult target. Although the researchers conclude that the protein is “ligandable,” the physicochemical properties of all the hits will need to be improved, along with the affinities, in order to make useful chemical probes, let alone drugs. On the other hand, the fact that the ligands bind to different sites and yet can all inhibit the protein-protein interaction is encouraging, offering multiple opportunities for optimization.