Venetoclax, the second fragment-based drug to reach the market, binds to and blocks the activity of the anti-apoptotic protein Bcl-2, allowing cancer cells to undergo programmed cell death. The drug is effective in certain cancers such as chronic lymphocytic leukemia and small lymphocytic lymphoma. However, a related protein called Mcl-1 is more important in other types of cancers. Like Bcl-2, it binds and blocks the activity of pro-apoptotic proteins, allowing cancer cells to survive even when Bcl-2 is inactivated. A paper in Nat. Comm. by Alexander Hird and a large group of collaborators (mostly at AstraZeneca) describes a successful effort to target Mcl-1.
Given that the researchers were targeting a protein-protein interaction, they took multiple approaches, including their own fragment-based efforts. They also characterized previously reported molecules, such as those the Fesik group identified using SAR by NMR (which we wrote about in 2013). A crystal structure of one of these revealed a surprise: two copies of compound 1 bound to Mcl-1, which had undergone conformational changes to accommodate the second molecule in an enlarged hydrophobic pocket.
Recognizing the potential synergies of linking these together, the researchers prepared a dimer of a related molecule, but unfortunately the affinity of this much larger molecule was actually worse. However, they wisely isolated and tested a side product, compound 4, and found that this had improved potency. A crystal structure of this molecule bound to Mcl-1 revealed that the pocket had expanded to accommodate the added pyrazole moiety. Since compound 4 adopted a “U-shaped” conformation, the researchers decided to try a macrocyclization strategy to lock this conformation and reduce the entropic penalty of binding. This produced compound 5, and adding a couple more judiciously placed atoms led to AZD5991, with a nearly 300-fold improved affinity. The molecule binds rapidly to Mcl-1 and has a relatively long residence time of about 30 minutes. A crystal structure reveals a close overlay with the initial compound 1 (in cyan).
This paper holds several lessons. First, the researchers did extensive mechanistic work (beyond the scope of this post to describe) to demonstrate on-target activity. Second, although the initial dimerization strategy was unsuccessful, the researchers turned lemons into lemonade by pursuing a byproduct; we’ve written previously about how even synthetic intermediates are worth testing. Third, the macrocyclization and subsequent optimization is a lovely example of structure-based design and medicinal chemistry. And finally, the fact that the researchers started with a fragment-derived molecule reported by a different group is a testimony to the community nature of science. Last week we highlighted the Open Source Antibiotics initiative, which is actively encouraging others to participate in advancing their early discoveries. Good ideas can come from anywhere, and it takes a lot of them to make a drug.