Archive for August, 2009

I had a printout of the structure of maitotoxin on my desk the other day, mostly as a joke to alarm anyone who came into my office. “Yep, here’s the best hit from the latest screen. . .I hear that you’re on the list to run the chemistry end. . .what’s that you say?”

This is, needless to say, one of the largest and scariest marine natural product structures ever determined (and that determination has been no stroll past the dessert table, either).

But that’ hasn’t stopped people from messing around with it. And there’s much speculation that other people are strongly considering messing around with it, too – you synthetic chemists can guess the sorts of people that this might be, and their names, and what it might be like to sit through the seminars that result, and so on.

I fear that a total synthesis of maitotoxin would be largely a waste of time, but I’m willing to hear arguments against that position. Just looking at it, though, inspires thought. This eldrich beastie has 98 chiral centers. So let’s do some math. If you’re interested in the SAR of such molecules, you have your choice of (two to the 98th) possible isomers, which comes out to a bit over (3 times ten to the 29th) compounds. This is. . .a pretty large number. If you’re looking for 10mg of each isomer to add to your screening collection (no sense in going back and making them again), then you’re looking at a good bit over half the mass of the entire Earth. And that’s just in sheer compounds; we’re not counting the weight of vials, which will, I’d say, safely move you up toward the planetary weight of a low-end gas giant. We will ignore shelving considerations in the interest of time.

Recall that yesterday’s post gave a number of about 27 million compounds below 11 heavy atoms. You could toss 27 million compounds into a collection of ten to the 29th and never see them again, of course. But that brings up two points: one, that the small-compound estimate ignores stereochemistry, and we’ve been getting those insane maitotoxin numbers by considering nothing but. The thing is, with only 11 non-hydrogen atoms, there aren’t quite as many chances for things to get out of control. The GDB compound set goes up only to 110 million or so if you consider stereoisomers, which actually isn’t nearly as much as I’d thought.

But the second point is that this shows you why the Berne group stopped at 11 heavy atoms, because the problem becomes intractable really fast as you go higher. It’s worth remembering that the GDB people actually threw out over 98% of their scaffolds because they represented potential ring structures that are too strained to be very stable. And they only considered C, N, O and F as heavy atoms (even adding sulfur was considered too much to deal with, computationally). Then they tossed out another 98 or 99% of the structures that emerged from that enumeration as reactive and/or unstable. Relax your standards a bit, allow another atom or two, bump up the molecular weight, do any of those and you’re going to exceed anyone’s computational capacity. Update: the Berne group has just taken a crack at it, and managed a reasonable set up to 13 heavy atoms, with various simplifying assumptions to ease the burden. If you want to mess around with it, it’s here, free of charge).

Source: Corante