Frustrated PROTACs: Exceptions or the rule?
Discomfort may be productive
Drug discovery has long been guided by a simple equation: a molecule binds a protein, and the tighter the binding, the stronger the effect. This binary view - one ligand, one target - has shaped the way chemists think about potency, selectivity, and mechanism. The tighter the embrace between protein and ligand, the more potent the drug.
PROTACs break this rule. These bifunctional molecules, which recruit an E3 ubiquitin ligase to a target protein to mark it for destruction, behave in ways that routinely confound classical expectations. In a PROTAC system, the binary affinities of each end of the molecule - for the target and for the ligase - do not straightforwardly predict the potency of ternary complex formation or the efficiency of degradation. A weak binder can sometimes trigger potent degradation; a tight binder can sometimes fail. The relationship between binary binding, ternary affinity, and degradation is nonlinear and often counterintuitive. This is not unique to PROTACs. All ternary complex systems, including molecular glues, where a small molecule stabilizes the interaction between two proteins, share this curious property. The formation of a ternary complex introduces new thermodynamic and kinetic landscapes, where emergent interactions can amplify, dampen, or even invert the effects seen in binary systems. For medicinal chemists trained to think in terms of classical structure–activity relationships, PROTACs and glues are a jolt: they reveal that the rules governing binary interactions are not abolished but transcended.
A very interesting new paper in Nature Communications by Ma and colleagues reveals that this same principle- long known as “frustration” in the protein folding field - may hold the key to understanding one of the most enigmatic features of PROTACs, the bifunctional molecules that have transformed drug discovery. The success of a PROTAC often hinges on a slippery quantity called cooperativity - the degree to which the presence of one partner enhances the binding of the other. Positive cooperativity means the ternary complex (target–PROTAC–ligase) is more stable than either binary pair; negative cooperativity means the opposite. Cooperativity governs degradation potency, but it has long defied prediction. As we know well, crystal structures offer snapshots, not explanations. Two complexes may look similar on paper yet behave very differently in cells.
Ma et al. took a fresh angle. Instead of asking how tightly the proteins fit together, they asked how uncomfortable their interface is. Starting from high-resolution structures of SMARCA2 (the target) and VHL (the E3 ligase) bound to a panel of PROTACs, they performed long, microsecond molecular dynamics simulations; allowing the complexes to wriggle, bend, and explore their energy landscapes. For each frame, they computed the degree of interfacial frustration using a mutational scanning approach that scores how energetically suboptimal each residue pair is compared to plausible alternatives.
The result is striking: PROTACs that show high cooperativity tend to create interfaces rich in highly frustrated contacts. In other words, when the two proteins are brought together in a way that leaves certain residues energetically ill at ease, the resulting complex is more cooperative. Low-cooperativity PROTACs, by contrast, form interfaces that are too comfortable—too optimized, perhaps, to allow the subtle dynamic adjustments that a cooperative complex requires. Perhaps unsurprisingly, these frustrated contacts cluster in flexible loop regions, not rigid helices or sheets. The authors found amino acids like proline, glutamine, and asparagine frequently involved in these frustrated interactions. The picture that emerges is not of a perfect molecular handshake but of a sort of wrestling match, in which temporary strains and mismatches drive the system toward productive alignment. The beauty of this finding lies in its inversion of expectation. Traditional computational scoring methods such as MMGBSA binding energies fail to predict cooperativity reliably. But frustration, usually treated as a nuisance, turns out to be a signal. By quantifying how “unhappy” the interface is, the authors could distinguish between PROTACs with strong and weak cooperativity, even for cases where no experimental structures existed.
Why should frustration paradoxically promote cooperativity? One plausible answer is that having a bunch of amino acids sit uncomfortably next to each other also gives them the freedom to break apart and form a more cooperative, more productive complex. Frustrated contacts keep the interface dynamically poised, allowing it to adapt upon ternary complex formation. Instead of locking into a single rigid conformation, the system remains flexible enough to find mutually favorable arrangements as both partners settle in. Frustration thus acts as a kind of energetic lubricant, preventing the interface from getting stuck in local minima.
One reason I like this paper is because this insight, though developed in the specialized world of targeted protein degradation, resonates more broadly. Biological systems thrive not in spite of their imperfections, but because of them. A perfectly packed protein might be inert; a slightly frustrated one can breathe and function. Likewise, a perfectly complementary protein–protein interface may bind stably but fail to cooperate. A little unhappiness goes a long way. If frustration proves to be a general predictor of cooperativity, it could change how PROTACs are designed. Instead of seeking the tightest possible fit between target and ligase, chemists might deliberately engineer interfaces that are almost right—flexible, dynamic, and strategically discontented. In the subtle art of molecular matchmaking, harmony may not be the goal. A bit of friction can be the source of strength.
The big take home message is that nature seldom builds perfect machines. Proteins, for all their exquisite precision, are not clockwork mechanisms. In the tangled network of attractions and repulsions that shape a protein, some local interactions must remain discontented. This residue of dissatisfaction, of energetic frustration, gives proteins their vitality. It allows them to breathe, to flex, and to act.