A paper in PNAS by Ned Wingreen at Princeton uses first-principles quantum molecular dynamics to look at the hydrophobic interaction of two hydrated methane molecules. I’d say this is primarily a methodological paper – that’s pretty much the angle Guilia Galli takes in her accompanying commentary – in that it aims to establish how well classical simulation approaches do in capturing the nature of the interaction. The answer is: not particularly. Classical force fields predict two free-energy minima, one at methane-methane contact and a second, rather shallow, at a small separation corresponding to one intervening solvent layer. But the relative stability of these minima is rather sensitive to the precise force-field parameters and can be reversed for some values. The quantum simulations reveal a deeper potential well at contact – this is always the stable configuration. But there is a succession of shallow minima at several other methane-methane separations, implying the existence of several relatively stable hydration cages. The authors talk about these configurations in terms of ‘clathrate-like cages’, but in fact it seems that they don’t have any well-defined hydrogen-bonding arrangements: two independent simulations at a specific methane-methane separation gave water structures that could not be superimposed. (There was, however, apparently some consistency in the ‘hydrogen-bonded rings’ in between the two methanes.) Wingreen and colleagues suggest that the shallow minima are the result of relatively well packed configurations for water in the hydration shells. But I don’t really know what this means. Normally, considerations of molecular packing in liquids are governed by the short-ranged repulsion between molecules. But ‘well packed’ is an ambiguous term for water, where optimal hydrogen bonding means that the waters sit rather further apart than equivalent spherical molecules would do. I’m assuming ‘well packed’ here refers to unbroken, unstrained H-bonding configurations…?
“Until a few years ago it was common practice to ignore water molecules in protein binding sites”, say Jonathan Essex and colleagues at Southampton University in an interesting paper in JACS. But now, they point out, there is increasing interest in designing ligands that will displace particular water molecules in drug binding. Conceivably, this might make the ligands more selective and the binding energy more favourable.
But it’s not clear whether that will necessarily be so. Despite the entropic advantage of expelling bound water from a binding cleft, one can’t generalize about the consequent free energy change. Whether or not it is advantageous to incorporate a water molecule at the binding interface hinges on a delicate balance. Confining a water molecule clearly has an entropic penalty, but this might be repaid by the enthalpic gains of hydrogen-bond formation – an issue that must itself be weighed against the average number of hydrogen bonds that a bulk water molecule engages in. Jack Dunitz (Science 264, 670 (1994); Chem. Biol. 2, 709-712 (1995)) has estimated that transferring a water molecule from an ordered binding site where it is bound by an ‘average’ hydrogen bond to the bulk involves an overall free-energy change that is close to zero. So it is not obvious which way the scales will tip in any instance. John Ladbury and his coworkers (D. A. Renzoni, M. J. J. M. Zvelebil, T. Lundbäck & J. E. Ladbury, in J. E. Ladbury & P. R. Connelly (eds), Structure-Based Drug Design: Thermodynamics, Modeling and Strategy 161-180, Landes Bioscience (1997)) have thought about the implications for drug design.
The message is illustrated in the binding of various inhibitors of HIV-1 protease, one of the key targets in AIDS therapies. Crystal structures show that some of these, such as KNI-272, bind to the enzyme via a bridging water molecule. Other inhibitors, such as DMP450, have been designed specifically to exclude this water molecule while mimicking its hydrogen-bonding capacity, and have found to bind more strongly. Li and Lazaridis (JACS 125, 6636-6637 (2003)) have calculated that displacement of the bound water by DMP450 is in itself unfavourable relative to KNI-272, but that this cost is outweighed by the lower cost of desolvating DMP450 to form the bound complex. So the consequences of eliminating the water molecule are both highly specific and not obvious.
With all this in mind, Essex and colleagues have sought a way of classifying water molecules in protein binding sites according to how easily displaced they are by ligands. By studying the thermodynamics of six proteins complexed with a variety of ligands, they say that the water molecules in the binding sites seem to come in two classes: those that are readily displaced (by at least some ligands), and those that never are. The latter, unsurprisingly, turn out to be more tightly bound according to MC simulations. All the same, the authors say that “no linear correlation exists between the binding free energies of water molecules and the change in binding affinity of ligands displacing the water molecules.” Yet they conclude that if we can identify the ‘conserved’ water molecules – those that do not get displaced come what may – then these can be usefully used in the design of drug docking: in effect, they serve as ‘part of the protein’, available for hydrogen bonding to the ligand. This paper supplies some heuristics for deciding which water molecules are conserved or displacable.