The proteasome is quite the structure. It is the shredding unit of the cell, where no-longer-needed proteins go to be ripped down to their components for recycling, and it’s become a more and more important part of drug discovery over the years. For one thing, all this fashionable targeted protein degradation work is about sending designated proteins off for destruction at will and before their time. But even before that, the opposite process – proteasome inhibition – had made an impact.
That’s because there are cancer cells that (because of their higher metabolism, greater production of various proteins, etc.) are more sensitive to problems with proteasomal function, and will die more quickly when the waste-disposal service is interrupted. The first compound on the market to do this was Velcade (bortezomib), which was approved in 2003 for multiple myeloma. It came out of a small company called Myogenics, then was developed further at Millennium, and was also notable for having a boronic acid head group. Those had been known as enzyme inhibitors for a long time, but were thought by many to be unfit to get all the way through clinical trials (after a number of failed development projects during the 1980s and onward).
Another inhibitor, Kyprolis (carfilzomib) was approved in 2012, and that one has an epoxide as the warhead, which is also a bit unusual (it had its origins in a natural product). In 2015 came Ninlaro (ixazomib), another boronic acid. Still in clinical trials are the epoxide oprozomib, the boronic acid delanzomib, and the unusual beta-lactone marizomib (also known as the marine natural product Salinosporamide A). That last one is notable for having gone from “here’s a new natural product” to “here’s an IND application” in what may be record time. Now, this list might be seen as an egregious example of “me-too” drugs gone crazy. How, you wonder, did the world end up with so many proteasome inhibitors, especially since several of them look so similar to others in the same class?
Because they’re still different. The proteasome is a rather complex structure, and its core is made up of a number of protein subunits that form a broad cylinder. The alpha-subunits are at both ends of this tube of destruction, interacting with separate cap protein assemblies that regulate what gets in, and the beta-subunits contain the proteolytic enzymes that form the cylinder walls (in two layers, yet). That graphic at right is from the abstract of this recent paper, from St. Gallen and Leiden, which is a head-to-head comparison of the different compounds in their activity against these subunits and what the means for multiple myeloma therapy. As you can see, the two epoxide compounds (especially at low dose), shut down only the beta-5 subunit. The three boronic acids, though, are active against both the beta-5 and beta-1 proteins. The epoxide carfilzomib, at higher doses, starts inhibiting the beta-2 subunit as well as the beta-5. And the natural product marizomib hits all three of the proteolytic subunits simultaneously. As you’d imagine, the stress on the cells increases as you shut down more of these, but (as the paper rightly notes) the different functions of these subunits (the three in the inner ring and the three in the outer, not shown in the schematic) are not well understood at all.
It had already been known that beta-5 inhibition by itself was the weakest mode of action, and sufficient to take out only the most sensitive cells. The beta-5/beta-1 and beta-5/beta-2 combinations were known to be more effective, but this paper has evidence from cell studies that the latter is a better bet – in fact, that the amount of beta-2 inhibition added to the beta-5 activity is the single biggest factor in differentiating the drugs. What’s more, allosteric effects (what happens to the inhibition profile of the beta-2 subunit after the beta-5 is already inhibited) should make it a better idea to use two separate specific inhibitor compounds rather than one bispecific one, since you could titrate in the beta-2 inhibition much better that way.
This means that higher doses of carfilzomib are perhaps the best mode of treatment among the existing compounds, but the complication is the possibility of cardiac toxicity when you do that, since you’re hitting both subunits at the same ratio. The heart seems to have fewer active proteasomes in its cells than almost any other tissue, which gives you less of a margin for error in shutting them down. I’m unaware of a compound that has only beta-2 activity, but if that’s even possible, it could well be a valuable drug candidate in combination with one of the specific beta-5 inhibitors. Update: see the comments! Meanwhile, marizomib only inhibits beta-2 in a fairly narrow concentration range compared to its other activities, and if this paper is right, that means that it could have an uncertain future in its clinical results. . .