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January 9, 2012
A Look Into the Future?
For a look into a possible drug-discovery future (from the computational optimist viewpoint), you might want to check out a brief bit of science fiction, "Alpha Shock", in the Journal of Computer-Aided Molecular Design. Some excerpts to give you the general idea:
". . .Of course, the compounds were of little value if they couldn’t be formulated. Sanjay was pressed for time, and nanobot development still took several weeks, so he had to go “old school.” Sanjay accessed World Crystallography Repository’s (WCR) formulation suite and entered the 2D structures of his compounds. The system linked to the Amazon Hyper-Cloud and initiated a series of quantum chemical calculations to develop a custom force field for the solid phase simulations. Unfortunately the preliminary results were disappointing, even after more than 100 million combinations of excipients, particle sizes, focusing tails, and polymorphs had been analyzed in detail. He would run a more complete search overnight, but the chances were that the 10-min simulation was telling him what he needed to know: don’t expect these exact compounds to be quite right. . .
. . .“In fact,” Dmitri continued, “I think the best tactic is to turn down the interaction of this transcription factor”—a protein popped out of one node on the map—“with that protein”—another protein materialized—“and this stretch of DNA.” A 3D model of the complex assembled in front of him, slowly rotating, with the most likely binding sites and points of intervention highlighted. “Of course, you only want to disrupt this interaction in the hippocampus, and only when D7 receptor functioning is high.” The relevant pathway maps showed the effects of the blockage on downstream signaling. “Oh, and naturally you also want to turn down oxphos in the mitochondria. So we need either a single molecule that can do both things, or a two-drug combo.”
The overall impression is a bit like Charles Stross, in its deliberate you-haven't-extrapolated-wildly-enough approach. But Stross doesn't put in as many computational chemistry inside jokes, which is probably better for his sales. My first impulse is the same one I have to, say, Ray Kurzweil, that all this stuff may (in fact probably is) on its way, but not by the dates stated. That position allows me to take flak from both sides, which must be some sort of feature that I value.
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