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More Whitesides on Ligand Binding

George Whitesides and his lab have another paper out on the details of how ligands bind to proteins. They’re still using the favorite model enzyme of all time (carbonic anhydrase), the fruit fly and nematode of the protein world. Last time around, using a series of ligands and their analogs with an extra phenyl in their structure. The benzo-ligands had increased affinity, and this seemed to be mostly an enthalpic effect. After a good deal of calorimetry, etc., they concluded that the balancing act between enthalpy and entropy they saw over the group was different for ligand binding than it was for logP partitioning, and that means that it doesn’t really match up with the accepted definition of a “hydrophobic effect”.
In this study, they’re looking at fluorinated analogs of the same compounds to see what that might do to the binding process. That makes the whole thing interesting for a medicinal chemist, because we make an awful lot of fluorinated analogs. You can start some interesting discussions about whether these are more hydrophobic than their non-F analogs, though, and this paper lands right in the middle of that issue.
The first result was that the fluorinated analogs bound to the enzyme (in their X-ray structures) with almost identical geometry. That makes the rest of the discussion easier to draw conclusions from (and more relevant). It’s worth remembering, though, that very small changes can still add up. There was a bit of a shift in the binding pocket, actually, which they attribute to an unfavorable interaction between the fluorines and the carbonyl of a threonine residue. But the carbonic anhydrase pocket is pretty accomodating – the overall affinity of the compounds did not really change. That led to this conclusion:

Values of DG8bind, combined with an overall conserved binding geometry of each set of benzo- and fluorobenzo-extended ligands suggest that binding depends on a fine balance of interactions between HCA, the ligand, and molecules of water filling the pocket and surrounding the ligand, and that a simple analysis of interactions between the protein and ligand (Figure1E) is insufficient to understand (or more importantly, predict) the free energy of binding.

But although the overall free energy didn’t change, the enthalpic and entropic components did (but arrived at the same place, another example to add to the long list of systems that do this). The differences seem to be in the Coulombic interaction with the binding pocket (worse enthalpy term – is that what shifted the structure over a bit in the X-ray?) and changes in energy of solvation as the ligand binds (better entropy term). Matched pairs of compounds didn’t really show a difference in how many waters they displaced from the binding site.
So the take-home is that the hydrophobic effect is not all about releasing waters from protein binding surfaces, as has been proposed by some. It’s a mixture of stuff, and especially depends on the structure of the water in the binding pocket and around the ligands, and the changes in these as the compounds leave bulk solvent and find their way into the binding site.
That makes things tricky for many compounds. Hydrophobic effects seem to be a big part of the binding energy of a lot of drug molecules (despite various efforts to cut back on this), and these Whitesides studies would say that modeling and predicting these energetic changes are going to be hard. Computationally, we’d have an easier time figuring out direct interactions between the protein and the ligand, the way we do with enthalpic interactions like hydrogen bonds. Keeping track of all those water molecules is more painful – but necessary.

10 comments on “More Whitesides on Ligand Binding”

  1. Pete says:

    From what I can remember, sulfonamides deprotonate when they bind to carbonic anhydrase and the pKa of the unfluorinated benzothiazole sulfonamide is around 8. Changes in ligand pKa associated with fluorination probably need to be considered when interpreting thermodynamic measurements of binding of ligands to this enzyme.

  2. nitrosonium says:

    i see one of your Vertex coworkers is on this paper!

  3. Hap says:

    See this paper – it gives the pKas of fluorinated benzenesulfonamides (2-F, 3-F, 4-F, 2,6-F2, 3,5-F2, pentafluoro). I don’t know what the current paper looks like, but I assume it would have similar data for the compounds used.

  4. A. Postdoc says:

    Get back to me when Whitesides isn’t trying to sell software for Schrodinger, then maybe I’ll believe some of their conclusions. When your goal is to sell software, it warps your reality to make that software look good.

  5. nitrosonium says:

    of course…we all know it. selling software is exactly what George Whitesides is known for!! been doing it for decades now. i think that is why he received the Priestly medal!!

  6. H2L says:

    @Postdoc…I am sure Whitesides really cares about selling Schrodinger software. Please remind us all how that helps him with anything that he cares about? In this paper, it looks like the same conclusions from the computational method could have been drawn from any molecular modeling software that accounts for solvation and a careful analysis of the energetics. Nothing Schrodinger-related here, although it does emphasize the potential value of using computational tools to gain insights. I think that is becoming more accepted in the med chem field (i.e. we are all “designers” now). The software might not be able to make perfect predictions, but it can lead to insights and testable hypotheses.

  7. A. Postdoc says:

    @H2L #6 please show me what testable hypothesis Schrodinger software provided and was tested in this paper. They did all the science, then ‘processed’ the results with software. No hypothesis, no testing, no science.

  8. H2L says:

    @Postdoc…interesting definition of science. To me, gaining a fundamental understanding of an experimental observation seems like science, but I do not have postdoc experience like you, so I guess you must know more about science than me.

  9. A. Postdoc says:

    @H2L #8 well, I used your definition. You claimed they tested hypothesis, they didn’t, I called you out on it. Nice ad hominem attack btw. Good job distracting from the point, that Schrodinger (and this whole paper) test no hypotheses and we should probably quit accepting their papers, even if they are with Whitesides.

  10. Why? says:

    @A.Postdoc
    What on earth gives you the impression that Whitesides cares about selling software besides the fact that he used it in a paper? What does he have to gain?
    I’m guessing you’ve never met the man. I can assure you that he cares less about personal wealth than any professor I’ve ever met.

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