Constancy of the discodermolide hairpin motif

Our paper on the conformational analysis of discodermolide is now up on the ACS website. The following is a brief description of the work.

Discodermolide (DDM) is a well-known highly flexible polyketide that is the most potent microtubule polymerization agent known. In this capacity it functions very similar to taxol and the epothilones. However the binding mode of DDM will intimately depend on its conformations in solution.

To this end we have performed multiple force field conformational searches on DDM and the first surprising thing we noticed was that all four force fields located the same global minimum for the molecule in terms of geometry. This is surprising because, given the dissimilar parameterization criteria used in different force fields, minima obtained for flexible organic molecules are usually different for different force fields. Not only that, but all the minima closely superimposed on the x-ray structure of DDM which we call the "hairpin" motif. This is also surprising since the solid state structure of such a highly flexible molecule should not generally bear resemblance to a theoretically calculated global minimum.

Next, we used our NAMFIS methodology that combines parameters from conformational searches to coupling constants and interproton distances obtained from NMR data to determine DDM conformations in two solvents, water and DMSO. We were again surprised to see the x-ray/force field global minimum structure existing as a major component of the complex solution conformational ensemble. In many earlier studies, the x-ray structure has been located as a minor component so this too was unexpected.

However, this same structure has also been remarkably implicated as the bioactive conformation bound to tubulin by a series of elegant NMR experiments. To our knowledge, this is the first tubulin binder which has a single dominant preferred conformation in the solid-state, as a theoretical global minimum in multiple force field conformational searches, in solution as well as in the binding pocket of tubulin. In fact I personally don't know of any other molecule of this flexibility which exists as one dominant conformation in such extremely diverse environments; if this happened to every or even most molecules, drug discovery would suddenly become easier by an order of magnitude since all we would have to do to predict the binding mode of a drug would be to crystallize it or to look at its theoretical energy minima. To rationalize this very pronounced conformational preference of DDM, we analyze the energetics of three distributed synthons (methyl-hydroxy-methyl triads) in the molecule using molecular mechanics and quantum chemical methods; it seems that these three synthons modulate the conformational preferences of the molecule and essentially override other interactions with solvent, adjacent crystal entities, and amino acid elements in the protein.

Finally, we supplement this conformational analysis with a set of docking experiments which lead to a binding mode that is different from the earlier one postulated by NMR (as of now there is no x-ray structure of DDM bound to tubulin). We rationalize this binding mode in the light of SAR data for the molecule and describe why we prefer it to the previous one.

In summary then, DDM emerges as a unique molecule which seems to exist in one dominant conformation in highly dissimilar environments. The study also indicates the use of reinforcing synthons as modular elements to control conformation.

Jogalekar, A., Kriel, F., Shi, Q., Cornett, B., Cicero, D., & Snyder, J. (2009). The Discodermolide Hairpin Structure Flows from Conformationally Stable Modular Motifs Journal of Medicinal Chemistry DOI: 10.1021/jm9015284

Does a protein-bound ligand exist in only one conformation?

I have been thinking a lot recently about studies in which people have determined the bound conformation of a ligand by transfer-NOESY experiments, essentially by transferring magnetization off another ligand to the protein and then back to the ligand of interest. With the known bound conformation of the first ligand, one can apparently locate the conformation of the second one. Many such unknown protein-bound conformations have been worked out. In my field of research, the ones which are relevant are of agents that bind to tubulin, especially discodermolide. In this case, the conformation of discodermolide was deduced via competition transfer-NOESY experiments with epothilone. These experiments are non-trivial to carry out and, as is the case for other biomolecular NMR studies, should be interpreted carefully. But in the end they look like nifty techniques that can shed light on unknown bioactive conformations, something that's very valuable for drug design.

Essentially it's again a problem of fitting the bound conformation NMR data to a single conformation. In solution we know for sure that this is a fallacious step. The (not so) obvious assumption in doing this for bound conformations is that there's got to be only one conformation in the active site too. But I have always wondered if a ligand in a protein active site could also have multiple conformations. MJ's comments on a past post and the discussion there makes me think that even in a protein active site, there could possibly be multiple conformations of a ligand, something that runs counter to what we conventionally think. How diverse those conformations might be is a different question; one would probably not expect large conformational changes. But even 'small' conformational changes could be significant enough to distinguish between different conformations in the active site. It's a problem worth thinking about.

Another much-feared chemical agent bites...tubulin

Bisphenol A this time. In a long list of tubulin binding agents. Unlike taxol and some of these agents however, it does not actually stabilize microtubules. What next in the list of tubulin binders? Water? Of course that.

Discodermolide unraveled?

Drugs affecting microtubule dynamics are familiar chemical players in med chem by now. First came Taxol, then the epothilones, then discodermolide, and the list continues with peluroside, eleutherobin, and dictyostatin to name a few of the better known entities.

Like it is for other drugs, one of the major questions asked about these molecules is how they bind to their target. Taxol and epothilone have been subjected to immense SAR and analog preparation by some of the hard hitters in the synthetic arena. Their binding conformations have been postulated with reasonable confidence. The common pharmacophore hypothesis, tempting but misleading and not true in this case, has been convincingly questioned. But for discodermolide, the binding conformation is not yet known. Now, groups from Spain and the UK have applied the "INPHARMA" NMR methodology to probe the interaction of disco with tubulin.

Admittedly, INPHARMA is a nifty technique- here is the original reference. It relies on magnetization transfer to a protein proton from a proton of a molecule that binds in the active site. This magnetization is then again transfered from the protein proton to a proton of another molecule that binds to the same site. For this to happen, the rate constants for binding have to be much smaller than the relaxation times for the protons.
Thus, the magnetization transfer sequence for two ligands A and B that bind to the same active site is

H(A)------>Protein proton------->H(B)
Naturally, this happens if both H(A) and H(B) are close to the same protein proton. Thus you see cross peaks between two protons A and B of two different ligands, mediated by a protein proton. Information from many such cross peaks allows us to map the protein protons to the ligand protons that are near them. In the end, not only does a picture emerge of the binding conformation of both ligands separately, but this information also allows us to suggest a common pharmacophore for the two ligands. And Paterson has now used this technique for disco and epothilone.

I am sure the technique has to be done carefully and that it was, and I also don't doubt the postulated conformation of disco. Most of the paper is really interesting and it's a neat study. But what concerns me is the fact that the end result, the binding conformation of disco can be mapped onto the x-ray conformation of disco proposed earlier, as well as the solution conformation of dictyostatin. Where my mind snags is in accepting this conclusion, because a single or even one dominant conformation for a flexible molecule derived in solution is unrealistic. It's what is called a 'virtual' solution. It's virtual simply because it's an average conformation. And since the average is a juxtaposition of all possible individual conformations, it simply does not exist in solution by itself. It's like saying that the contiguous structure of fan blades seen when a fan is moving very fast actually exists. It does not, because it is an average, and the resolution time of our eye is not short enough to capture individual positions of the fan blades.

So I wonder how the binding conformation of disco could be mapped onto the conformations of one x-ray conformation and one single dominant conformation in solution. Now I am sure there is more to this story, and I am still exploring the paper, but for commonsense reasons, a little red light in my brain always turns on (or at least should turn on) when a single or dominant conformation for a highly flexible molecule in solution is postulated.

More cogitations to come soon.