Field of Science

Post-docking as a post-doc, and some fragment docking

I am now ready to post-doc. I am also now ready to post-dock, that is, engage in activities beyond docking. Sorry, I could not resist cracking that terrible joke. It's been a long journey and I have enjoyed every most moments of it. Thanks to everyone in the chemistry blogworld who regaled, informed, provoked and entertained on this blog. I am now ready to move on to the freakingly chilly Northeast. Location not disclosed for now, but maybe later.

Speaking of docking, here is a nice paper from the Shoichet group in which they use fragment docking to divine hits from a large library for a beta-lactamase. Fragment docking can often be tricky compared to "normal" docking since fragments being small usually demonstrate promiscuity, low-affinity and non-selectivity in binding. Fragment docking thus is not yet a completely validated technique.

In their study, the present authors screen their ZINC library for fragments binding to the ß lactamase CTX-M by docking using the program DOCK. They also screen a lead-like library for larger molecules. The top hits from the fragment docking results were assayed and showed micromolar inhibition against the lactamase. These included tetrazole scaffolds not seen before. Importantly, five of these hits could be crystallized and the high-res crystal structures validated the docking modes.

What was interesting was that the same tetrazole scaffolds in the larger lead-like library were ranked very low (>900) and would not have ever been selected had their tetrazole fragments not showed up at the top in the fragment docking results. These compounds, when assayed showed sub-milimolar to micromolar activity against the lactamase. Thus, the protocol essentially demonstrated that fragment docking can reveal hits that can be missed by docking larger lead-like molecules. One of the reasons DOCK succeeds in this capacity is because of its use of a physics-based scoring function that has no bias against fragments. It also helps that the active site of CTM-X is relatively rigid with little protein motion.

The fragments were also assayed against another lactamase for Amp C. Usually, hits for CTM-X and Amp C are mutually exclusive. What was seen was that the higher the potency of the fragments for CTX-M, the higher the specificity for CTX-M, not surprising considering that increased potency translates to a much better complementary fit of the fragments for CTX-M.

Fragment docking can be messy since fragments can bind non-selectively and haphazardly to many different parts of many different proteins. But this study indicates that fragment docking is not an uninteresting strategy to possibly find hits from other lead-like libraries that may be otherwise concealed.

The potencies of the compounds found may look pretty weak, but because there are extremely few molecules inhibiting these medicinally important lactamases, such advances are welcome. Lactamases are of course an important target for overcoming resistance in antibiotic treatment.

Chen, Y., & Shoichet, B. (2009). Molecular docking and ligand specificity in fragment-based inhibitor discovery Nature Chemical Biology DOI: 10.1038/nchembio.155


  1. Congratulations! I hope your defence went well; perhaps you could write a short post on that experience ...

    And good luck for your post-doc!

  2. Thanks! The defence went very well and I could indeed contemplate writing about the experience sometime.

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