There’s a trick that every medicinal chemist learns very early, and continues to apply every time its feasible: take two parts of your compound, and tie them together into a ring.
The reason that works so well may not be immediately obvious if you’re not a medicinal chemist, so let me expand on them a bit. The first thing to know is that this method tends to work either really well or not at all – it’s a “death or glory” move. And that gives you a clue as to what’s going on. The idea is that the rotatable bonds in your molecule are, under normal conditions, doing just that: rotating. Any molecule the size of a normal drug has all kinds of possible shapes and rotational isomers, and room temperature is an energetic enough environment to populate a lot of them.
But there’s only one of them that’s the best for fitting into your drug target, most likely. So what are the odds? As your molecule approaches its binding pocket, there’s a complicated energetic dance going on. Different parts of your drug candidate will start interacting with the target (usually a protein), and that starts to tie down all that floppy rotation. The question is, does the gain resulting from these interactions cancel out the energetic price that has to be paid for them? Is there a pathway that leads to a favorable tight-binding situation, or is your molecule going to approach, flop around a bit, and dance away?
Several things are at work during that shall-we-dance period. The different conformations of your compound vary in energy, depending on how much its parts are starting to bang into each other, and how much you’re asking the bonds to twist around. The closer that desired drug-binding shape is to the shape your molecule wants to be in anyway, the better off you are, from that perspective. So tying back the molecule and making a ring in the structure does one thing immediately: it cuts down on the range of conformations it can take, in the same way that tying a rope between your ankles cuts down on your ability to dance. You’ve handcuffed your molecule, which would probably be cruel if they were sentient, but then, a lot of organic chemistry would be pretty unspeakable if molecules had feelings.
That’s why this method tends to be either a big winner or a big loser. If the preferred binding mode of your compound is close to the shape it takes when you tie it down, then you’ve suddenly zeroed in on just the thing you want, and the binding affinity is going to take a big leap. But if it’s not, well, you’ve now probably made it impossible for the thing to adopt the conformation it needs, and the binding affinity is going to take a big leap over a cliff.
There’s another effect to reducing the flexibility of your compound, and that has to do with entropy. All that favorable-interaction business is one component of the energy involved, namely the enthalpy, but entropy is the other. Loosely speaking, the more disordered a system, the higher its entropy. A floppy molecule, when it binds to a drug target, has to settle down into a much tighter fit, and entropically, that’s unfavorable. Energetically, you’re paying to do that. But if your molecule is already much less flexible, there’s not much of a toll as it fits into the pocket. If loss-of-floppiness is a bad thing, then don’t start out with so much of it.
So, how much do I and my medicinal chemistry colleagues think about this stuff, day to day? A fair amount, but there are parts of it that we probably don’t pay enough attention to. Entropy gets less respect from us than it deserves, I think. It’s easy to imagine molecules bumping into each other, sticking and unsticking, but the more nebulous change-in-disorder part of the equation is just as important. And it doesn’t just apply to our drug molecules – proteins get less disordered as they bind those molecules (or more disordered, in some cases), and those entropic changes can mean a lot, too.
I also mentioned molecules finding a pathway to binding, and that’s something that we don’t think about as much, either. We probably make things all the time that would be potent binders, if they just could get past some energetic hump and wedge themselves into place. But there are no crowbars available; our drug candidates have to be able to work their way in on their own. The can’t-get-there-from-here cases come back from the assays as inactive. The tendency is to imagine these in the binding site already, and to try to think of what could be going wrong in there – but it may be that they’d be fine, but that their structures won’t allow them to come in for a landing.
Picturing this accurately is very hard indeed. We have enough trouble with good representations of static pictures of our molecules bound to their targets, so making a movie of the process is a whole different story. Each frame is on a femtosecond scale – molecules flip around rather quickly – and every frame would have to be computed accurately (drug structure, protein structure, and the energetics of the whole system) for the resulting video clip to make sense. It’s been done, but not all that often, and we’re not good at it.