16 May 2012

Halogenated fragments stabilize mutant p53


Practical Fragments recently discussed using fluorinated fragments for 19F NMR, but there are other halogens out there – are these useful for constructing fragment libraries? SGX Pharmaceuticals had a collection of fragments enriched with bromine atoms, the thought being that this atom would facilitate crystallography. Halogens can also make productive interactions with proteins, including so-called “halogen bonds” to backbone carbonyl atoms or pi-systems. With this in mind, Andreas Joerger at Cambridge University and Frank Boeckler at Eberhard-Karls University and their colleagues have assembled and screened a “halogen-enriched fragment library.” Their results are reported in a recent issue of J. Am. Chem. Soc.

The library consists of 79 non-reactive, soluble aromatic compounds containing bromine or iodine. Because these elements are so large, the researchers used a modified rule of 3 – instead of a molecular weight limit of 300, they limited the fragments to no more than 22 heavy atoms (see also our recent post on this topic here). They then screened this library against the Y220C mutant form of p53, which contains a surface crevice that destabilizes the protein and contributes to cancer cell survival. Thermal shift assays were used as the primary screen, with hits being confirmed by 2D NMR and ITC. This resulted in the discovery of compound 3, which crystallography confirmed was making a halogen bond to a backbone carbonyl.



Modifying the amine substituent improved potency modestly, and building off the phenyl ring towards a nearby pocket improved the potency further, albeit at a cost in ligand efficiency. Still, this compound (PhiKan5196) does represent the most potent Y220C binder reported, and represents an order of magnitude improvement over previous work. Moreover, the molecule induces apoptosis in p53 Y220C containing human cancer cell lines but not in matched wild-type p53 cell lines. (Unfortunately the compound also appears to be generally cytotoxic.)

This library is an interesting approach in part because it is somewhat heretical: for various reasons most library designers exclude molecules containing bromine or, especially, iodine. That said, the thyroid hormones do contain iodine aplenty, and MEK kinase seems to have a predilection for bromine or iodine as well. What do you think? Are halogenated fragments a useful tool for certain targets, or an unproductive diversion?

9 comments:

Dr. Teddy Z said...

An atom's an atom. It's the ends that justify the means. If the final compound does what you want, who cares if it contains "non-traditional" atoms. I think the hurdle here is that typically (and I recognize the generalization here) chemists want to make easy molecules and shy away from chemistry that can be long and hard. Of course, who can blame them in the current climate where they graded on the number and not necessarily the quality of the compounds they make.

Dr. Rettul said...

Indeed, working with unusal atoms is a very interesting approach. Unfortunately, some other atoms are still negelected. I predict germanium and selenium to play an important role in drug design, too. I bet, in a few years, prof Joerger (university of Cambridge) will present a new milestone-paper in nature with very special compounds containing Germanium. No doubt!

Dr. Teddy Z said...

Derek Lowe has selenophenol on his "Things I won't work with" list
http://pipeline.corante.com/archives/2012/05/15/things_i_wont_work_with_selenophenol.php

Anonymous said...

Is there a review or paper you would recommend on setting up and optimizing thermal shift assays?

Dan Erlanson said...

I've never done thermal shifts myself, but James Kranz and Celine Schalk-Hihi have what looks to be a very thorough review (Chapter 11) in the 2011 Methods in Enzymology volume.

Troy said...

I think that bromines are especially useful for deconvoluting a fragment from pools of 5-8 fragments soaked into crystals. Especially at a synchrotron where you can tune the wavelength to 0.92 Angstroms, you can capitalize on the anomalous signal from bromine. If the goal is to get a structure and screen through lots of crystals so you can get your foot in the door, then why not use halogenated compounds. You can always take them out later if they don't help.

Anonymous, another resource for thermal shift assays is http://thermofluor.org.

Pete said...

Bromine and iodine are likely to compromise aqueous solubility to a greater extent than chlorine. However, the heavier halogens are likely to form stronger halogen bonds. The key is to ensure that heavy halogens pay their way in affinity for their physicochemical property debit. Just like accountancy really except perhaps a bit more exciting?

I seem to remember that there might be a metabolic stability issue/concern with iodo on aromatic rings. Not looked at this for a while.

Selenium ((as selenomethionine) gets used in protein crystallography. I think selenium sulfide gets used in anti-dandruff shampoo. You occasionally come across the suggestion of replacing carbon in marketed drugs with silicon to get round IP. This doesn't make a lot of sense since you're still going to have to do the clinical trials and the silicon-based analog will need to be significantly better than the original drug if money is to be made. It would be a lot better to be creative in exploiting the special properties of silicon. There are drugs with antimony.

Dr. Teddy Z said...

Silicon is in simethicone, given to infants as an anti-gas compound...and is a major anti-foam in bioprocessing. Selenium is naturally occuring and an important trace element, doesn't mean I want to necessarily ingest it as part of a metabolizable drug.
Replacing carbon is interesting, total new atom. Is it also necessary to do all new trials when replacing protons with deuterons?

Pete said...

I think that one would need to do the trials because tinkering with metabolism by deuteration could lead to different reactive metabolites. If you invoke similarity to the original drug in attempt to reduce the amount of clinical work required, you run the risk of being sued for infringement on the grounds that the deuterated compound is 'obvious'. Also the deuterated compound will contain some of the 'undeuterated' compound which presumably still belongs to the company that introduced it. As would also be the case for a 'siliconated' drug, the deuterated drug is likely to fall off the same patent cliff as the parent compound. I believe there are companies whose business plans involve 'siliconation' and/or 'deuteration' of marketed drugs. One for the patent attorneys, I suggest?