Plenty of medicines are protein inhibitors, meaning the drug binds to a protein to block its function. One example of a common inhibitor medication is angiotensin-converting enzyme (ACE) inhibitors used for high blood pressure. ACE is an enzyme in the blood that creates angiotensin II, a molecule responsible for constricting blood vessels. ACE inhibition limits this constriction, alleviating high blood pressure. A second example of an inhibitor medicine is selective serotonin reuptake inhibitors. These drugs bind to serotonin transporters, allowing serotonin (the happy neurotransmitter) to stay in neuronal synapses longer and are therefore used to treat depression.
Old School - Attacking the active site
Both ACE inhibitors and serotonin reuptake inhibitors bind to proteins at their active sites: the central place of function in a protein. ACE inhibitors bind to the catalytic site – the portion of the protein that creates angiotensin II, while serotonin reuptake inhibitors bind and block the channel that serotonin passes through.
It's intuitive that to inhibit an enzyme, a researcher designs a small molecule that binds and directly impedes a protein's active site. This strategy for inhibitor design is favored for a few reasons:
But never fear; scientists are innovative. To increase the number of possible pharmaceutical targets, researchers are designing inhibitors to target a new class of pharmaceutical targets, protein-protein interactions.
New School - Protein-protein interaction inhibitors
Active sites aren't the only essential interface of a protein. Protein interaction interfaces are also necessary for several reasons.
From a protein's point of view, cells are large and confusing places. So, proteins bind to one another to ensure they are in the proper place at the right time to do their jobs. Additionally, proteins are often made of multiple subunits and function similar to a machine. The subunits of these molecular machineries are held together by protein-protein interactions. Therefore, inhibiting a protein-protein interaction can block a protein's function by displacing its localization in the cell or breaking apart a protein complex.
For some time, protein-protein interactions were deemed "undruggable" because, unlike active sites, protein-protein interfaces are large, flat, and hydrophobic. Overall, most protein-protein interfaces have a suboptimal shape and chemistry for small-molecule inhibitors to bind. However, in the last decade, research has shown that although protein-protein inhibitors' design might be taxing, it's certainly possible.
Dealing with the large interfaces
Although protein-protein interfaces are large (averaging 28 amino acids), researchers have found that a small portion of amino acids, termed "hot spots," are responsible for most of the energy required for protein binding. Therefore, the entire protein-protein interface is not the target for site; rather, the hot spot amino acids are.
Struggling with flat target sites
At first glance, most protein-protein interfaces seem flat, but that isn't necessarily the case. Hot spot residues often reside in "pockets" of a protein surface comparable to the size of an active site. And even if it seems hot spots reside on a flat surface, proteins are dynamic, and interfaces may have pockets that appear upon binding to its partner protein.
Combatting the hydrophobicity issue
When it comes to hydrophobic and hydrophilic properties, "like likes like." Hydrophilic molecules bind hydrophilic molecules, while hydrophobic molecules bind hydrophobic molecules. So, a hydrophobic interface will bind hydrophobic inhibitors.
Hydrophobic inhibitors perform poorly in the human body since we are made of mostly water. Therefore, scientists can optimize hydrophobic inhibitors by adding hydrophilic chemical groups to the inhibitor and removing unnecessary hydrophobic groups. And although the core of the protein-protein interaction is often hydrophobic, charged residues often support the interface, which an inhibitor can also target.
Where we stand now
Tirofiban, an integrin disrupter, has earned FDA approval to treat stroke patients. Its mechanism of action is to break apart integrins in the blood and prevent blockages in the brain's blood vessels. Additionally, MDM2-P53 disruptors are undergoing clinical testing for cancer. These inhibitors selectively kill cancer cells by breaking apart the MDM2-P53 interaction. MDM2 inhibits P53, a protein that signals cell death during stress. Stabilizing P53 activity allows P53 to amplify the cell death signal in cancer cells.
Since the strategy for targeting protein-protein interactions is new, few approved drugs target protein-protein interactions. However, the mere fact that some protein-protein inhibitors are undergoing clinical testing is astronomical, considering this class of drugs was once declared impossible. The success of tirofiban and MDM2-P53 inhibitors garners optimism that more protein-protein inhibitors will develop into novel medicine.
Will protein-protein inhibitors replace active site inhibition? Likely not. However, this new class of inhibitors will significantly increase the number of protein targets and hopefully improve our chance of creating new life-saving and life-improving drugs.
This post is a science communication piece derived from my recent review article: "Targeting Protein-Protein Interactions in the DNA Damage Response Pathways for Cancer Chemotherapy" published in RSC Chemical Biology. The information shared here encompasses the first half of the paper. A second post about targeting the DNA Damage Response for cancer chemotherapies is soon to follow.