28 May 2013

A slew of sites for fragments in HIV Reverse Transcriptase

The protein HIV-1 reverse transcriptase (RT) has been something of an Achilles heel for HIV; 13 approved drugs inhibit this enzyme! However, HIV is more adaptable than Achilles, and can develop resistance to drugs, creating a need for new molecules. With this in mind, Eddy Arnold and colleagues at Rutgers University performed an extensive fragment campaign against this target; their work was recently published in J. Med. Chem.

The researchers assembled a library of 775 fragments, 500 from Maybridge and most of the rest from Sigma-Aldrich and Acros. These were combined into 143 pools of 4 to 8 fragments, each at 100 mM in DMSO. Crystals of RT grown with the drug rilpivirine were soaked with each of the pools; rilpivirine stabilizes the protein and yields crystals that diffract to high resolution. The researchers also added 80 mM arginine and 6% trimethylamine N-oxide (TMAO) to the soaking solutions; arginine helped solublize some of the more hydrophopic fragments and improved electron density, while TMAO improved diffraction.

Overall, the researchers found 34 fragments that bound to HIV RT, a hit rate just over 4%. Interestingly, halogenated fragments seemed to give a much higher hit rate: 7 of 29 fluorine-containing fragments produced structures, as did 4 of the 17 brominated fragments and one of the two chlorinated fragments. I don’t recall seeing halogens previously over-represented among fragment hits, though last year we did write about halogen-enriched fragment libraries. The sample sizes reported here are small, but if the findings hold up in other studies, fluorine fetishism may be further justified.

But just as interesting as the composition of the fragment hits is the number of binding sites in the protein: 16, with names ranging from the descriptive (“NNRTI Adjacent” and “Incoming Nucleotide Binding”) to the concise (“399”) to the downright thuggish (“Knuckles”). In the case of three of these sites, some of the fragments also inhibited enzymatic activity.

There is a lot of nice information here, and eight co-crystal structures have been deposited in the protein data bank. Still, I am left a bit dizzy at the sheer number of sites. In fact, one fragment (4-bromopyrazole) bound to all of the 16 sites! What are we to make of this – is this a privileged fragment or a promiscuous binder? And as for the sites with no known functional activity, are these useful? What do you think?


LJStewartTweet said...

Dan. Thanks for covering this RT fragments story that has emerged from Eddy's lab. I'd like to point readers to an interesting paper from Skolnik and Gao recently published in PNAS.


They point out that an anlysis of 1,284,577 entries extracted from the ChEMBL15 and BindingDB "more than 1,400 ligands, each binds to 40 or more nonhomologous proteins.

See also the post on this at In the Pipeline.

I tend to think that most protein interactions are with proteins. In a folded protein, most residue interactions are with other residues. Thinking of it this way means that small molecules have to "mimic" protein residues / functional groups in order to "trick" their way into binding proteins.

By this logic, 4-bromopyrazole is "Crafty" "Tricky" Think of it like Run DMC would describe this molecule ...."its tricky to rock a rhyme, its tricky tricky ttttricky"

Just look at 4-bromopyrazole structure. Per unit area its chemical structure packs a tremendous number of possible types of interactions with proteins. I used to think Tyrosine was really "tricky", capable of H-bond donor acceptor, Pi stack, cation, edge binding. But 4-bromopyrazole is looking pretty darn tricky too now.

Dr. Teddy Z said...

So, I have been mulling this over...it comes down to your definition. Something that binds is an active, it is is active in two or more orthogonal assays, it becomes a hit. Hits are what should be discussed, actives are of no interest. The "some" fragments that showed enzymatic inhibition are the interesting ones, everything else is promiscuous until proven otherwise.