Scientists at Scripps Research have discovered a critical feature required by a promising new class of cancer drugs, known as CELMoDs, for them to be effective. CELMoDs are designed to attack cancer in a novel way, by binding to a regulatory protein called cereblon, which then triggers the degradation of key cancer-driving proteins. The Scripps team has discovered that these drugs, in order to work, need to cause a critical shape change in cereblon when they bind to it. They suggest that their findings will help researchers reliably design effective CELMoDs.

“There are a lot of research groups that have spent considerable time making drugs that bind very tightly to cereblon, but have then scratched their heads in puzzlement that these drugs fail to work,” said study senior author Gabriel Lander, PhD, professor in the Department of Integrative Structural and Computational Biology at Scripps Research.

Lander, together with first author was Randy Watson, PhD, a postdoctoral researcher in the Lander lab, and colleagues, reported on their findings in Science, in a paper titled “Molecular glue CELMoD compounds are regulators of cereblon conformation,” in which they concluded, “Our results provide mechanistic insights into the therapeutic efficacy of CELMoD compounds, a class of molecules that epitomize molecular glues and are central players in the field of targeted protein degradation.”

Cereblon (CRBN) works as part of a major protein-disposal system in cells. This system tags targeted proteins with molecules called ubiquitin, effectively marking the proteins for destruction by roving protein-breaking complexes known as proteasomes. “Eukaryotic proteins are targeted for degradation through covalent attachment of ubiquitin moieties to specific residues, primarily lysine side chains,” the authors explained.

The ubiquitin-proteasome system is used not only to destroy abnormal or damaged proteins, but also to help regulate the levels of some normal proteins. Cereblon is one of hundreds of “adaptors” used by the ubiquitin-proteasome system to guide the ubiquitin-tagging process towards specific sets of target proteins.

Scientists now recognize that some cancer drugs, including the myeloma drug lenalidomide, work by binding to cereblon. They do so in a way that forces the ubiquitin-tagging, and consequent destruction, of key proteins that promote cell division—proteins that couldn’t be targeted easily with traditional drugs. Inspired in part by that recognition, scientists are working to developing cereblon-binding drugs—CELMoDs, also known as protein-degradation drugs—that will work even better against myeloma and other cancers. “The CELMoD agent lenalidomide (Revlimid) has been used as a first-line therapy for multiple myeloma and other hematological malignancies for more than a decade, and next-generation CELMoD compounds markedly improve patient outcomes in clinical trials,” the team continued.

One enduring problem for the field has been the fact that while some of these drugs bind tightly to cereblon, they fail to cause sufficient degradation of their protein targets. Understanding why this happens has been difficult. Scientists have wanted to use high-resolution imaging methods to map cereblon’s atomic structure and study its dynamics when bound by CELMoDs. But cereblon is a relatively fragile protein that has been hard to capture with such imaging methods. “Prior crystallographic studies defined the drug-binding site within CRBN’s thalidomide-binding domain (TBD), but the allostery of drug-induced neosubstrate binding remains unclear,” the scientists noted.

For the newly reported study, Watson spent more than a year devising a recipe for stabilizing cereblon in association with a ubiquitin-system partner protein, in order to image it with low-temperature electron microscopy (cryo-EM). In this way, he was able ultimately to resolve the cereblon structure at near-atomic scale. Watson also imaged the cereblon-partner complex with CELMoD compounds and target proteins. “We performed cryo–electron microscopy analyses of the DNA damage-binding protein 1 (DDB1)–CRBN apo complex and compared these structures with DDB1-CRBN in the presence of CELMoD compounds alone and complexed with neosubstrates,” the scientists explained.

The structural data revealed that CELMoDs must bind to cereblon in a way that changes its shape, or conformation. Cereblon, the researchers determined, has a default “open” conformation, but must be switched to a particular “closed” conformation for the ubiquitin-tagging of target proteins. “Association of CELMoD compounds to the TBD is necessary and sufficient for triggering CRBN allosteric rearrangement from an open conformation to the canonical closed conformation.”

The main significance of the finding is that drug companies developing CELMoDs now have a much better idea of what their candidate drugs must do to be effective. “Companies have been developing cereblon-binding protein-degradation drugs that they can see are better degraders, but they didn’t know this was because the drugs are better at driving this closed conformation,” Watson said. “So now they know, and they can test their drugs for this key property.”

The results, the researchers commented, “highlight previously unappreciated allosteric effects for consideration in the design of CRBN-directed molecular glue therapeutics. By characterizing the conformational rearrangements inherent to the CRBN-DDB1 system, and showing how three distinct degrader molecules affect allostery and neosubstrate-binding capacity, we reveal how conformational control of the mobile drug-binding TBD within CRBN has cryptically driven the therapeutic success of neosubstrate-targeting agents.”

Watson’s breakthrough recipe for stabilizing cereblon in preparation for cryo-EM imaging also is now being adopted widely by researchers in this field. Lander says his lab hopes now to facilitate the development of protein-degradation drugs that work by binding to other ubiquitin-proteasome adaptor proteins besides cereblon. He notes that the big attraction of the protein-degradation drug strategy is that it can be used to hit virtually any disease-relevant protein, including the very large class of proteins that can’t be targeted with traditional drugs.

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