Wednesday, 29 June 2011

Lipophilicity teaser

This post got prompted one by Dan at Practical Fragments and I'm going to ask you to first take a look at that and at the comments. Now I'd like you to look at some measured octanol/water logP values that I pulled from the Sangster Research Laboratories logPow database. The question I'd like to put to you is whether you think that these measured logP values truly reflect the energetic costs of moving the different isomeric methylimidazoles from water to a truly non-polar environment like a hydrophobic binding pocket in a protein.



Let's take a look these figures. The least lipophilic compound of the set is N-methylimidazole in which the hydrogen bond donor of imidazole has been capped, although the partition coefficients for the three compounds are all very similar. It seems that the octanol/water partitioning system just doesn't seem to 'see' the hydrogen bond donors of the 2-methyl and 4/5-methyl isomers.

Octanol has a hydroxyl group and, in the context of a shake-flask logP determination, gets pretty wet (~2M), making it a unconvincing model for the hydrophobic core of a lipid bilayer or a hydrophobic binding pocket. In contrast, alkanes lack hydrogen bonding capability which also means that they also dissolve less water. The catch is that alkane/water partition coefficients are more difficult to measure than their octanol/water equivalents since polar solutes are poorly soluble in alkane solvents.

The difference between octanol/water and alkane/water logP values for a compound (often termed ΔlogP) is one measure of the polarity of the compound. The octanol/water logP of phenol is 1.5 and it would be reasonable to describe it as lipophilic. However in the alkane/water system the situation is reversed and the logP of -0.6 would lead to phenol being described as hydrophilic.

I'll leave things here for now because this post is really just a teaser and I will be returning to the theme in more depth in the future. If you're interested in finding out more take a look at my harangue from the March 2011 PhysChem Forum at Syngenta and the article that goes with it. I'd also recommend reading this review by Wolfenden if you're interested in the relevance of alkane/water logP values to protein structure and function.

Literature cited

Toulmin, Kenny & Wood, Toward prediction of alkane/water partition coefficients. J. Med. Chem. 2008, 51, 3720-3730. DOI

Wolfenden, Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins. J. Gen. Physiol. 2007, 129, 357-362. DOI

4 comments:

Dan Erlanson said...

You bring up some excellent points, and I look forward to the next installment.

One question is how relevant octanol is as a proxy for a hydrophobic binding site; I agree it has problems, but I suspect a pure alkane might be too hyrophobic and not representative either. After all, many binding sites are solvated (albeit often poorly), and some functionalities even in the interior of proteins are more polar than pure alkanes.

A second question is how well different measures of lipophilicity correlate with one another. Has anyone plotted a large set of known logP values (octanol-based) vs alkane/water partition coefficients? I'm sure there will be outliers, but do they more or less track? For example, are all the cresols more lipophilic than phenol itself?

Pete said...

I agree that hydrophobic pockets are likely to be solvated to some degree although it's not clear that the water in them behaves like bulk water (e.g density & hydrogen bonding patterns). However, when thinking about hydrophobicity in the context of binding, the main issue is the nature of the contact between the molecular surfaces of ligand and protein.

Hydrogen bonds do of course occur at binding interfaces. However, these are discrete, highly-directional entities and we normally model them on an individual basis rather than trying to account for them in an average way using a solvent with some hydrogen bonding capability. Solven enclosure is another problem (even for hydrocarbon/ water) since thye water molecules may be even less happy in a pocket than when in contact with a flat apolar surface.

The difference between the alkane/water and octanol/water logP values reflects the ability of the molecule to form hydrogen bonds. For something like anisole the differences are small but for a 4-pyridone (even when N-alkylated) the octanol/water logP is more than 4 units higher than the the hexadecane/water logP.

In analog series the hydrogen bonding groups are often conserved so the variation in the logP values across the series is likely to be similar for the two partitioning systems even though the absolute values may be be quite different. The trouble starts when performing analyses across many series. You can find (especially in retrospective analyses of large datasets that are fashionable) some very creative and imaginative approaches to making the trends look stronger than they really are.

morten_g said...

A spot of confusion for me here.

Isn't LogP investigated because of it's influence on ligand-membrane interactions? I.e. too hydrophilic and the ligand won't pass membranes and too lipophilic and the ligand won't go into solution?
You guys are talking about how well octanol/water mimics protein binding sites but every binding site is going to be different and since you are probably working in a target driven context can't you simply measure dH and dS?

What I don't get is why it isn't a water/micelle partitioning system that is used.

Pete said...

I would agree that logP was originally introduced in the context of permeability. However, there can be a big difference between association with a membrane and transport through it. For example a lipophilic amine in its cationic form could conceivably associate with a lipid bilayer with the cation group exposed to solvent and/or anionic head groups of the lipid. In contrast we would not normally expect the cationic form of an amine to be found in hydrocarbon core of the lipid bilayer. This is one reason why the micelle partitioning would not be expected to be particularly predictive of permeability. Also I believe the experiments to be time-consuming.

When I compare octanol and alkane as models for binding sites I'm simply saying that to a ligand a lipophilic binding site looks more like alkane than octanol. For real ligands (and binding sites) one needs think in terms of the contributions that the different portions of the ligand make to logP. I would argue that the alkane/water logP is more relevant in this regard than the octanol/water logP.

I remain unconvinced that measuring the enthalpy and entropy changes associated with binding would be much use. The association of enthalpy changes with polar interactions is frequently asserted but less frequently demonstrated. A characterisation of molecular surface as either polar or non-polar is quite simply not good enough for quantitative studies.