Multivalent fragments in the clinic: Muvalaplin

It’s been a couple years since Practical Fragments last updated our “fragments in the clinic” list. Before doing so it makes sense to highlight some of those we’ve missed. Let’s start with an open-access Nature paper from Laura Michael and collaborators at Lilly and Monash University published in 2024. Truth be told I’ve been waiting for a longer discovery paper, but I’ll go with what’s available now.

 

The researchers were interested in lipoprotein(a), or Lp(a), which has been linked to cardiovascular diseases. Lp(a) forms when low-density lipoprotein (LDL) binds to apolipoprotein(a), or apo(a). This is a two step process, in which the ten subtypes of so-called Kringle IV (K_IV) domains in apo(a) bind to lysine residues on LDL, followed by disulfide bond formation between apo(a) and LDL. Blocking the first step in this process should reduce levels of Lp(a).

 

Here's the only description of the initial screen: “Biochemical and biophysical compound screens using purified apo(a) K_IV7-8 protein identified interacting small molecules. Optimization of the initial binding molecules led to…LSN3353871.” Whatever the details, LSN3353871 is unequivocally a rule-of-three compliant fragment. It is also a very ligand-efficient binder with high nanomolar affinity for the K_IV8 domain. LSN3353871 disrupted the formation of Lp(a) in vitro at low micromolar levels and decreased levels of Lp(a) in cynomolgus monkeys when dosed orally.

 

As noted above, the apo(a) protein contains multiple K_IV domains, and a classic method for improving potency is by making dimeric ligands that can bind to two domains simultaneously. The researchers did just this in the form of LSN3441732, which binds to apo(a) and disrupts formation of Lp(a) in vitro at picomolar concentrations.

 

If dimeric ligands are better than monomeric ones, why not go for multimeric ligands? The trimeric molecule LY3473329, or muvalaplin, was synthesized and crystallographically shown to bind to three copies of K_IV8. It blocked formation of Lp(a) in vitro and reduced Lp(a) levels in cynomolgus monkeys.

 

Kringle domains are found not just in apo(a) but also in plasminogen, the zymogen form of plasmin, which is responsible for degrading blood clots. Fortunately, subtle differences between the Kringle domains in apo(a) and human plasminogen provide selectivity for the former protein, especially for multivalent ligands such as muvalaplin, and a phase 1 clinical study showed that Lp(a) could be lowered without affecting plasmin activity.

 

This is a nice application of applying fundamental multivalent principles to develop a potent molecule. It is also another example of a molecule that may not look like a drug but works like one: despite containing four basic nitrogen atoms, three carboxylic acid moieties, and sporting a molecular weight above 700 Da, muvalaplin is orally bioavailable. It is currently in a phase 3 trial in up to 10,450 patients. Cardiovascular disease is the leading cause of death in the developed world, and Practical Fragments wishes luck to everyone involved in these studies.

 

In the meantime, watch for more Practical Fragments posts on new entries to our fragments in the clinic list, which will be updated later this year.