05 February 2018

Pointless stereochemistry

Designing fragments to be more “three dimensional” than the flatter aromatic molecules that dominate most libraries is a topic often discussed in fragment library design. One way to make fragments more shapely is to introduce a stereocenter, but doing so often complicates the synthesis. In fact, new methods for efficient enantioselective synthesis constitute a major theme of organic chemistry research. In a recent paper in Angew. Chem. Int. Ed., Niklaas Buurma (Cardiff University), Andrew Leach (Liverpool John Moores University) and collaborators at Hawler Medical University Erbil and AstraZeneca demonstrate that the effort is sometimes not worthwhile.

Because proteins are chiral, different enantiomers can have profoundly different activities. The classic case is thalidomide, the racemic mixture of which was sold as a sedative in the 1950s, leading to the birth of thousands of babies with profound birth defects. Only one enantiomer appears to be responsible for the teratogenic effects, and many people are taught that had the manufacturer sold just one enantiomer, the disaster would have been averted. Unfortunately, biology is not so simple: the hydrogen atom attached to the chiral center is slightly acidic, and thalidomide rapidly racemizes at physiological pH.

Such racemization is more common than generally appreciated. The researchers experimentally measured the racemization of a couple dozen compounds using either circular dichroism (CD) spectroscopy or NMR (in the latter case, this involved dissolving the molecule in deuterated buffers and measuring the rate of deuterium incorporation, which occurs through an achiral intermediate).

The experimental results were then compared with those obtained through computational methods. Initially these were intensive quantum mechanical calculations, but the researchers also developed a rapid and effective approach by considering each of the attached substituents around the stereocenter independently. Importantly, the details for doing this are provided in the supporting information.

How much of a problem is this? The researchers provide four examples of what they call “potentially pointless stereoselective syntheses,” all published in high profile journals in 2016 (interestingly, three are fragment sized).

According to calculations, all of these molecules would undergo 19 to 70% racemization in 24 hours under physiological conditions.

So before embarking on any onerous stereoselective synthesis, it would be worth running a quick calculation. If the molecule goes forward you’ll still need experimental evidence for stability, but at least you’re less likely to be unpleasantly surprised by the answer.


Paul Savage said...

I can't help feeling that most steroselective synthesis for fragments is pointless. Chiral pool is fine, but the added effort of genuine steroselective synthesis is hard to justify. Back in the day, fragment libraries were often run as mixtures of 10 or so different compounds, remember? So I can't see the harm of having two enantiomers or even diasteriomers for that matter in the well. If the protein is really selective for one isomer (and that happens less often than you might think) it be sorted out later. The main criterion for screening is efficiency, and complex steroselective routes don't cut it in my view.

Anonymous said...

How much would these fragments have to alter to increase the half-life?

Dan Erlanson said...

Hi Paul,

You bring up good points, and in fact according to our recent
poll almost everyone includes racemates in their libraries. That said, if you do get a racemic hit, testing the pure enantiomers individually can be a useful (though not absolute) indicator as to whether the hit is real or not.

The issue the authors are concerned about is that even if you do find a chiral hit, it will rapidly racemize, so a stereoselective synthesis is not worthwhile.

One potential solution would be to lock the stereocenter by replacing the hydrogen with, for example, a methyl group, though this may not be tolerated, and could also be synthetically challenging.