Field of Science

Myths about disrupting protein-protein interactions with small molecules
The first era of medicinal chemistry was finding small molecules to target proteins. It's still going strong and will continue to do so. The second era that promises a treasure trove at least in principle is finding small molecules for disrupting protein-protein (PP) interactions. So many important processes in our body are regulated by these crucial interactions that finding small molecules to modulate them could promise a bonanza of new therapies.

But disrupting PP interactions is fundamentally different from designing a small molecule to bind to a (mostly) well-defined active site on a protein. PP interaction surfaces are rather flat and expansive and depend on subtle interactions between amino acids that add up to provide substantial binding affinity. Designing a small molecule to disrupt such interactions is somewhat like disrupting the sliding of one door hinge against another by lodging a grain of sand between the two. However, the picture has been simplified somewhat in recent years by the identification of "hotspots"- key amino acid epitopes that provide the bulk of binding interaction. If one could design a small molecule that could provide this major contribution to the free energy of binding, one could have an effective drug that could target PP interactions. After all, a grain of sand can indeed inhibit hinge sliding if it's placed in the right position.

One of the big players in investigating small molecule PP interaction agents has been Jim Wells, formerly at Genentech and Sunesis and now at UCSF. He has a nice Nature review that traces recent successful examples of small molecule PP interaction antagonists. Wells considers six or seven successful stories involving important proteins playing key roles in health and disease. For example, disrupting the inhibition of the pro-apoptotic BAD and BAK by the anti-apoptotic Bcl-2 and Bcl-xl, disrupting the binding of interleukin IL-2 to its receptor, and disrupting the binding of HDM2 to the tumour suppressor p53.

But more importantly, Wells then address some widely held myths about PP interactions that seem to drive pessimism in the field. They are worth taking a look at:

Myth 1: It's very difficult to find a small molecule that would lodge between the rather disordered flat surfaces of two proteins.

While this is true, in practice as is exemplified by almost all the examples, the protein surface does not remain flat when a molecule binds to it. Loops and side chain adapt and form shallow pockets and dents to which the molecule can bind. The fallacy in believing the myth is to assume that small-molecule protein surface binding is a rigid body interaction. It's not, and there's a strong element of induced fit in the process. This is probably the single most important thing to keep in mind, that small molecules will form their own small pockets and bind well to initially flat protein surfaces.

Myth 2: Small molecules that disrupt PP interactions are too large to be drugs

This is part of the partly substantiated myth that large molecules usually don't become drugs, because of many factors including ROF problems. But many molecules disrupting PP interactions cited in the review are about 500-700 Da, perhaps a little large but not intractable as drugs. The authors also calculated the ligand efficiency which is the free energy of binding per non-hydrogen (heavy) atom for the ligands, and found that it was comparable to that of kinase or protease inhibitors. Clearly with sound med chem efforts, it won't be too difficult to have such drugs. Interestingly, since the molecules occupy about half the binding site that the parts of the native protein partner do, their ligand efficiency is almost twice.

Myth 3: Small molecules disrupting PP interactions won't be potent

Just not true. Almost all the molecules found in the cited examples had mid to low nanomolar Ki values, almost as good as the binding constants for the partner proteins.

Myth 4: Screening would not help find novel small molecule PP modulators

Again, not true. Most of the cited molecules were found by HTS. Interestingly, there may be even more wealth in HTS than we have now. As the authors explain, HTS hits are fundamentally going to be limited by chemotypes present in the libarries. After all we can do only as well as chemical space in existing libraries. Existing libraries contain many molecules targeted against kinases, GPCRs and other well-known targets for which common privileged structures have been deduced. But because of the diversity of PP interactions, it is improbable that common scaffolds will exist for disrupting them, and libraries will have to contain novel scaffolds to get better hits. Given this fact, it's impressive and encouraging that the existing libraries could come up with such potent structures for disrupting a few PP interactions. Remarkably, even with such different scaffolds, the ligand efficiency remains more or less constant for the cases studied.

Clearly the field of small-molecule-PP interactions is alive and kicking. In the next few years, hopefully computational, screening and NMR approaches will converge to discover novel agents for these important processes.

Wells, J.A., McClendon, C.L. (2007). Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature, 450(7172), 1001-1009. DOI: 10.1038/nature06526


  1. Nice post. BUT -- have a look at Proc. Natl. Acad. Sci. vol. 105 pp. 6795 - 6796, 6959 - 6964 '08 for a guess of how many protein/protein interactions humans have. They come up with 650,000 which, if correct, implies that we've found only 1/300th of them. So targeting a known interaction may affect many more as well.


  2. protein-protein interactions are quite common and also diverse in nature. for example, many small molecules interacting with microtubule network biochemically are protein-protein interaction inhibitors per se. maybe one minor problem of this field is the definition of the terms, I guess.

  3. wow. that's a lot of interactions. i guess the question is one of selectivity, but there could be cause for optimism i think. consider what they said about targeting kinases; so many similar kinases are around that it was considered very difficult to selectively target kinases. but now we have several drugs which do that. so i think it should be possible to exploit the disruption of PP interactions. in fact it seems to me to be one of those interesting situations where finding a solution may be hard but doing it selectively may just be possible precisely because it is so hard to target such interactions. anon's comment is interesting. how do you classify a molecule that binds in a protein pocket but then also prevents that protein from binding to another one? do you call it a PP interaction disrupter or a regular small molecule binder? or both?

  4. All is not hopeless -- have a look at [ Proc. Natl. Acad. Sci. vol. 101 pp. 14326 - 14332 '04 ] also. Abeta42 amyloid is the main constituent of the senile plaque found in the brain in Alzheimer's disease. Beware -- there is some controversy about whether Abeta42 is the culprit in the disease. It might be a result of the way the neuron is defending itself (e.g. a pile of spent bullets rather than the smoking gun).

    A screen of 3000 small molecules for the ability to disrupt the structure of Abeta42 amyloid fibrils came up with 4,5, dianilinophthalimide (DAPH). The compound disrupts the pre-existing fully formed fibrils (at microMolar concentrations). Amorphous materials without fibrils, but apparently containing some protofibrils and smaller forms are produced. When Abeta42 is incubated with DAPH fibrils aren't formed. DAPH was included in the library because it is a tyrosine kinase inhibitor (with specificity for the epidermal growth factor receptor kinase).


  5. One should also consider the possibility of using allosteric PP interaction inhibitors in medicine. The advances here have so far mostly been accidental, but the potential is interesting. Check out PNAS 104(41) p. 16074-9, for example.


Markup Key:
- <b>bold</b> = bold
- <i>italic</i> = italic
- <a href="">FoS</a> = FoS