How Researchers Are Turning Poison into Medicine

The main principle of classical targeted therapy is that drugs act as "blockers" – they suppress the mutant protein in the cell. However, this type of treatment has a significant drawback: the genetic instability of the tumor causes its cells to constantly mutate, developing resistance to the drug, which ultimately renders it ineffective.

An alternative approach is based on proteolysis – the cell's natural system for clearing "old" or "broken" proteins. 

"For this purpose, a PROTAC* is created, a chimeric molecule that acts as a messenger. The molecule consists of two ligand fragments connected by a linker. One 'claw' of this 'chimera' binds to the target protein to be destroyed. The second 'claw' locates a special 'executioner' protein from the E3 ligase family in the cell, such as cereblon (CRBN). The linker physically brings the target and the 'executioner' together," explains Alexander Bunev, Director of the Center for Medicinal Chemistry (CMC) at TSU. "When both 'claws' capture their targets, cereblon marks the target protein for death, and the cell sends it to its waste-processing system, the proteasome."

This mechanism takes the fight against disease to a whole new level: instead of blocking it, it initiates a program to completely destroy the affected cells.

CRBN is a key component of chimeric molecules. The discovery of its interaction with the ligand thalidomide played a fundamental role in understanding its work.

"Thalidomide is a notorious drug that caused severe birth defects in children in the mid-20th century. It turns out that by binding to cereblon, it alters it, causing it to attack completely different target proteins, including those responsible for normal embryonic development. However, it was precisely this 'erroneous' activity that proved key to the treatment of myeloma (a malignant disease of the blood system – Ed.)," notes Alexander Bunev. "Myeloma cells have their own 'survival proteins' – Ikaros and Aiolos. Thalidomide, by altering cereblon, causes it to recognize and target these proteins for destruction."

Deprived of its critical components, the cancer cell dies. But here, scientists faced a dilemma.

"Thalidomide is an excellent, yet unpredictable, 'hook' for cereblon," continues Alexander Bunev. "If a PROTAC were created using it to treat, say, lung cancer, once it enters the bloodstream, it would similarly destroy the Ikaros and Aiolos proteins present in healthy hematopoietic cells, causing severe side effects. This has created a new challenge for modern pharmaceuticals: creating molecules that bind to cereblon without altering anything within cereblon or compromising other proteins."

A team of scientists from St. Petersburg State University, the Center for Medicinal Chemistry at Togliatti State University, and the Max Planck Institute for Physics (Munich, Germany) is successfully working on this problem. The research is structured as a multi-stage pipeline. Chemists in St. Petersburg are creating new promising ligands for cereblon, while scientists at the TSU Center for Medicinal Chemistry are using computer modeling and cellular assays to test how the new molecules penetrate and interact with cells – the Center for Medicinal Chemistry has an impressive collection of cell lines. Professor Markus Hartmann's group in Germany is using X-ray crystallography to obtain precise 3D models of ligand binding to cereblon.

"We at the Center for Medicinal Chemistry conducted a Thermal Shift Assay and experimentally demonstrated that the ligands synthesized by our colleagues do indeed stabilize cereblon in cells using a specific method. But another important question remained unanswered. Cells contain a huge number of proteins. What if our ligands cause CRNB to destroy other, previously unknown proteins?" says Alexander Bunev.

To answer this question, Professor Eric Fisher's research group from Harvard Medical School, a world leader in quantitative proteomics (a field of analytical chemistry dedicated to the identification and quantitative analysis of proteins), joined the work. The American researchers' method allows them to "count" all the thousands of proteins in a cell before and after drug exposure. If the concentration of a protein drops, it means it has been degraded.

The results of the experiments were brilliant: the scientists not only confirmed that their ligands do not affect known "off-target" proteins (Ikaros, Aiolos), but also proved that no new ones are created. This is critically important for the development of drugs against solid* tumors, where blood side effects have been a major limitation.

"Despite the fact that collaboration with scientists from other countries currently presents a number of challenges, this joint study has proven highly effective. We have developed a universal methodology for searching for new active compounds based on a specific chemical structure – glutarimide. Most importantly, we have validated biologically active structures, which serve as ready-made 'building blocks' for constructing fully functional 'chimeras.' In other words, our findings pave the way for the creation of new anticancer drugs with a fundamentally new mechanism of action," comments Dmitry Dar'in, Professor in the Department of Medicinal Chemistry at the Institute of Chemistry at St. Petersburg University.

Based on the data obtained, the researchers plan to carry out large-scale work on the design and synthesis of new, more effective compounds.

"The ultimate goal is to create a molecule that, using internal cellular mechanisms, will specifically destroy a protein vital to cancer cells, leading to their death. This is an ambitious but entirely achievable goal, made possible by our effective international collaboration," emphasized Dmitry Dar'in.

The scientists described the experimental results in an article published in the European Journal of Medicinal Chemistry.

Background information:

PROTAC (Proteolysis-Targeting Chimeras) is a technology for targeted protein degradation. In 2024, Pfizer first submitted an application to the FDA for approval of a drug based on this technology for the treatment of prostate cancer, confirming its clinical significance.

Solid tumors are a large group of neoplasms characterized by the formation of a dense tissue mass. They account for the vast majority of all cancer cases.