Proteins are important biomolecules, fulfilling tasks in every cell of your body and with a central role in health and disease.
Dr. Harald Weinstabl and Dr. Will Farnaby lead collaboration at Boehringer Ingelheim and the University of Dundee working on PROTACs, a new class of molecules with the potential to selectively target and destroy disease-causing proteins.
Drs. Weinstabl and Farnaby’s interdisciplinary research team has achieved significant tumor growth inhibition in mice, and this molecule is freely available to other researchers.
Read their original research: https://doi.org/10.1038/s41467-022-33430-6
Image Source: Choksawatdikorn / Shutterstock
Hello and welcome to ResearchPod. Thanks for listening and joining us today. In this episode, we will discuss the collaborative research of a joint team led by Dr. Harald Weinstabl and Dr. Will Farnaby, from Boehringer Ingelheim RCV in Vienna, Austria and the University of Dundee Centre for Targeted Protein Degradation, or CeTPD, in Scotland, respectively. The team is part of a larger drug discovery collaboration between Professor Alessio Ciulli, the Director of CeTPD, and Boehringer Ingelheim, that is focussed around the identification of molecules to selectively target and destroy disease-causing proteins.
Proteins are important biomolecules, fulfilling tasks in every cell of your body and coming in many forms. Some act as building blocks for the tissues of the body. Others, such as hormones, deliver messages between different parts of the body. Some proteins work as enzymes, speeding up many physiological processes that would not be feasible in their absence. Those enzymes work within a complex network, depending on other proteins and biomolecules to control many metabolic processes, and take a central role in health and disease.
Enzymes convert smaller molecules, or substrates, into useful products. The enzyme-substrate interaction takes place within the enzyme’s active site, that is to say, a cavity or a fold buried within the complex 3D structure of the enzyme with a shape and electrical charge complementary to those of the substrate. Enzyme reactions can be disrupted by small molecules known as enzyme inhibitors.
Why do many researchers look at enzymes as drug targets to treat disease? Simply because the interaction between enzymes and their substrates can sometimes become dysfunctional and lead to many health conditions, which include cancer, diabetes, and an array of cardiovascular, inflammatory and autoimmune diseases. Scientists have long used the action of enzyme inhibitors as a pharmacological tool to target and halt disease-causing enzyme reactions. Unfortunately, for some types of cancer and many other diseases, enzyme inhibitors either lack efficacy, resulting in resistance to treatment, or fail to selectively bind to their target protein, causing poor tolerability and toxicity issues.
The team around Drs. Weinstabl and Farnaby have demonstrated a solution for the many diseases that do not respond to the action of classic enzyme inhibitors. The scientists explain that a promising class of molecules, discovered around 20 years ago, are capable of targeting disease-causing proteins and flagging them for destruction by the body. These molecules are known as PROTACs, an acronym that stands for proteolysis targeting chimeras. To achieve their pharmacological action, PROTACs bind to two proteins at the same time, facilitating their physical proximity; the first is the target protein, while the second is known by the name of E3 ligase. The proximity of the two proteins causes another molecule, ubiquitin, to bind to the target protein. Ubiquitin acts as a tag, which instructs the proteasome, a system of molecules responsible for the controlled disassembly of proteins, to degrade the target protein.
PROTACs are both selective and effective in the elimination of their targets and offer hope that they could pose a solution to therapeutic resistance for hard-to-treat diseases like cancer. One challenge to the use of PROTACs, however, is the scarcity of orally available options among the degrader molecules designed to date. Orally bioavailable drugs offer several advantages over drugs that are injected intravenously, including higher patient acceptance, easier and cost-effective large-scale manufacturing, and the possibility of self-administration in non-sterile conditions. The team has investigated the bioavailability and the in vivo efficacy of a selective and orally available PROTAC that recruits a specific subtype of E3 ligase, known as ‘von Hippel-Lindau’ E3, or VHL for simplicity. The team published a study in the journal Nature Communications in 2022, demonstrating the remarkable selectivity of an orally available, VHL-recruiting PROTAC, known as ACBI2. ACBI2 is capable of specifically degrading a protein target SMARCA-2, which is expressed in cancer cells. The molecule can distinguish between SMARCA-2 and the highly similarly structured SMARCA-4 protein, and its selectivity over SMARCA-4 is of utmost importance, as the simultaneous knockdown of both SMARCA-2 and SMARCA-4 could lead to tolerability issues elsewhere in the body.
The SMARCA2 protein plays a significant role in regulating DNA structure, allowing cancer cells to grow and proliferate; its selective destruction would constitute an effective strategy to arrest or slow the progression of hard-to-treat cancers. This strategy is particularly promising in the treatment of some types of lung cancer where SMARCA-4 deficient cancer cells rely on SMARCA-2 to survive. The SMARCA-2 dependent destruction of lung cancer cells is an example of synthetic lethality. Scientists define synthetic lethality as a combination of two genetic mutations that lead to cell death. While the mutation of either of two genes individually has no effect, the combined mutations lead to an unfavourable cellular environment for cancer cells. Many researchers have already used synthetic lethality successfully in several clinical trials looking at treatments for breast, ovarian, prostate, and pancreatic cancers.
To achieve optimal oral bioavailability and efficacy for their lead compound, ACBI2, which selectively targets SMARCA-2 over SMARCA-4, the researchers studied the high-resolution crystal structure of several small molecules, selecting those that could bind effectively and selectively to the SMARCA2 target protein while retaining the water-solubility and absorption characteristics required for the oral route of administration. Once the candidate molecule with optimal structure for the SMARCA-2 binder was identified, it was further modified with the addition of small carbon-containing units to enhance the SMARCA-2 binding and degrading capability of ACBI2.
The interdisciplinary research team conducted experiments in human whole blood and several cell culture samples, demonstrating that ACBI2 was responsible for the preferential degradation of SMARCA-2 of at least 30-fold over SMARCA-4. To assess the in vivo efficacy of the treatment, the researchers tested the SMARCA-2 degradation in tumour-bearing mice that were treated with orally administered ACBI2. This resulted in a significant inhibition of tumour growth and correlated to a dramatic reduction in the levels of SMARCA-2. The treatment was also well tolerated by the mice, suggesting low toxicity. Taken together, these data led the team to conclude that the orally bioavailable VHL-recruiting degrader ACBI2 is capable of SMARCA-2 dependent synthetic lethality towards SMARCA-4 deficient cancer cells and that the anti-cancer properties of the compound, either alone or in combination with other drugs, warrant further investigation. Farnaby and Weinstabl hope that other researchers and drug developers can benefit from the study. To help the scientific community design other potent and selective orally bioavailable protein degraders, they have made ACBI2 freely available to any institution that requests it.
In summary, the research team has synthesised ACBI2, a new and exciting anti-cancer molecule that targets disease-causing proteins for destruction by the body’s immune system. The novel drug offers several advantages over classic enzyme inhibitors. The scientists tested ACBI2 in mice and in several cell lines, finding that the molecule significantly inhibited tumour growth in mice bearing lung cancer. The team has agreed to make the molecule freely available to other researchers upon request.
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