Researchers Christian Ottmann, Luc Brunsveld and Lech Milroy discover new way to improve and develop drug molecules

Being well-balanced is essential for our health. This applies to day-to-day food intake or exercise and rest, but also to processes inside our body. On the cellular level, an imbalance can be a sign of disease and drugs can often be developed to repair this imbalance.
Christian Ottmann, Luc Brunsveld and Lech Milroy, researchers based in the Chemical Biology group within the Biomedical Engineering department of the TU/e are specialists in this field. Their most recent discovery will potentially lead to the optimization of drugs and development of new drugs.

Out of balance

In healthy individuals, cells exist in a state of dynamic equilibrium. In cases of disease, such as cancer or neurodegenerative disorders, dysfunctions in the expression, folding or function of individual proteins is often sufficient to tip the cell out of equilibrium. One way to redress this imbalance and therefore treat disease is by developing small molecules capable of selectively targeting dysfunctional proteins.

Small molecules for disease treatment

The Chemical Biology group are convinced that small molecules are the way forward to treat disease, and have one target class in mind – protein-protein interactions (PPIs). PPIs are the molecular events that relay signals throughout healthy and diseased cells and thereby represent viable drug targets.

Inhibitors versus stabilizers

The use of small molecules to inhibit PPIs has blossomed over the last two decades into a viable therapeutic strategy. By inhibiting a protein, the designed molecule halts or changes the activity of this protein. If this protein is dysfunctional and out of balance, and therefore associated with a disease, the designed molecule can redress the imbalance and restore the equilibrium in the cell. Techniques such as X-ray crystallography and NMR spectroscopy have played a big part in this increase in the development of inhibitors, by making the design of new inhibitors molecules more predictable.

By contrast, the use of small molecules to stabilize PPIs has received little attention. The potential of stabilizers is evident though, judging by the existence of blockbuster stabilizer drugs such as the immunosuppressant rapamycin (Rapamune®) and the microtubule stabilizer paclitaxel (Taxol®). Stabilizers bind to the protein and stabilize the folding of the protein, or binding to other proteins associated with the development of a disease

The task of discovering novel stabilizers is at least an order of magnitude more complex than the discovery of inhibitors. The stabilizing molecule in many cases should be capable of fitting more than one protein simultaneously within a protein complex.

Design of new stabilizers

In their article, recently published in Angewandte Chemie, Christian Ottmann et al. propose a possible solution to this complex problem, which aims to capitalize on the molecular duality of inhibitor and stabilizer compounds. They adopt a structure-guided drug design approach to design more potent and selective ligands, which makes use of structural data derived from the crystal structures of protein-ligand complexes.

There is nothing new in this approach per se, as it is a proven method for the discovery of PPI inhibitors. The novelty of their work, they argue, lies in the observation that inhibitor and stabilizers both target different though proximal sites of PPIs, opposite sides of the PPI interface where both inhibitor and stabilizer bind to the protein (see image). Because of this close linkage of inhibitor and stabilizer, the structure of the inhibitor is closely related to the structure of the stabilizer (and vice versa). This structural information can inform the design of stabilizers and inhibitors.

Illustrative example: Protein-protein interaction 14-3-3 / Tau

14-3-3 is an intracellular protein, which binds to proteins regulating the function, localization and degradation of the guest protein. By binding to the protein Tau, 14-3-3 prevents Tau from binding to microtubules which are important for i.e. the structural integrity of the cell. The binding of Tau to the microtubules leads to degeneration in neuronal cells. Therefore inhibition of 14-3-3 in Tau may yet prove to be an effective strategy to treat neurodegenerative disorders such as Alzheimer’s disease.

To illustrate their point on use of the stabilizers and to highlight the potential of the approach, they use structural information derived from 14-3-3 stabilizer complexes to guide the optimization of inhibitors of 14-3-3/Tau. Using the synthetic Tau (peptide) binding interface as the chemical starting point – readily accessible by solid-phase peptide synthesis– the Chemical Biology group developed a potent inhibitor of (full-length hyperphosphorylated) Tau by focusing on improvements to the inhibitor-stabilizer interface. Most significantly, these improvements could be attributed to a stabilizer-like interaction.

The future

The team of scientists are in the first instance using PPI stabilizers to optimize the binding properties of PPI inhibitors. What they are ultimately aiming for is to exploit the easy-accessibility of PPI inhibitors to access the less-accessible PPI stabilizers. While still early days, this rational approach to the design of PPI stabilizers may pay off in the form of new drug molecules with improved target selectivity and therefore reduced toxicity.