Tweetorial: Irreversible Inhibitors

15 December 2021

Dec 21, 2021

A confluence of circumstances this month nearly broke me while I was writing this tweetorial. I spent a solid two weeks after Thanksgiving being sick with back-to-back non-COVID illnesses. Regrettably, it seems that rhinoviruses are on the rise again. A combination of my kids bringing stuff home from their daily disease incubator (school) plus something I picked up during my lecture stint at West Chester University the week before Thanksgiving knocked me out pretty hard. Thankfully since I’m still working from home, I could mostly muddle through my work day, but in the evenings and weekends I was in full rest mode. Since that’s normally when I do the reading and writing to support the tweetorials, big delays.

Another factor is that I didn’t understand this topic quite as well as I thought I did heading into the writing. Specifically, there had been some confusion in my mind about the distinction between KI (uppercase ‘I’) and Ki (lowercase ‘i’), because a good amount of literature assumes they’re interchangeable, when technically that’s not always true. It was illuminating to look at the limiting case where k_off » k_inact, where KI does collapse to Ki. This is a direct analogy to the same collapse in Km to Kd in the Michaelis-Menten equation, ignoring the k_cat term present in the Briggs-Haldane treatment of this subject. I learned a lot from my reading, but… learning also takes time.

Then there was the issue of graphics. I try to respect copyright, and obtaining rights to images e.g. in the Strelow paper I refer to frequently in the thread can be costly and annoyingly time-consuming. I’ll put a plug in here for more authors to take advantage of open source journals and/or at least make use of highly portable Creative Commons licenses. The upshot is that I spent a fair amount of time noodling in Excel and GraphPad Prism to recreate some of these lovely images in my own hands. That was time well spent though, because nothing enhances understanding of math-y topics like rummaging around in the numbers, changing parameters, and seeing what happens to the graphs. Powerful way to learn.

Once I had all of that squared away in my own mind, the first 28 posts came together pretty easily. But then I realized I was 28 posts into the thread and had said nothing about the impact on medicinal chemistry. I try to keep these tweetorials in the 40-50 post max range, which is already a small novella. Rather than crack open the literature and run through case studies, I decided to keep it general. The important takeaway is that potency optimization for irreversible inhibitors is fundamentally a two parameter optimization. Awareness of both k_inact and KI is needed, and these SARs, like any two SARs, can be moving in opposite directions.

It’s also an unfortunate truth that the literature is replete with folks who optimized (or tried to, anyway) their irreversible inhibitors with IC50s. This is a bad idea, because it results in an epic reductio ad absurdum if taken to the logical extreme. If inhibitors with vastly different k_inact and KI values are incubated for long enough, the enzyme will become fully inactivated. In that scenario, every IC50 becomes the same, which is clearly not right.

I also made a choice not to talk about the continuum of time-dependent inhibitors. The takeaway from that one is to have early awareness of the possibility that inhibitors may be time-dependent. Medicinal chemists tend to be fairly clued in on the possibility of time-dependent CYP inhibition on the ADME side, but less aware that anything — including the primary target of interest — can potentially be subject to time-dependent inhibition. Simple preincubation biochemistry studies early in the project can help to tease this out.

Anyway, enough preamble. Here’s the post:

Tweetorial: Irreversible Inhibitors

15 December 2021

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