Exploiting cellular degradation machinery as a potential treatment strategy for RAS-driven cancers

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Exploiting a cell’s built-in mechanism to degrade and destroy proteins is a promising strategy to combat RAS-driven cancers, according to a recent study published in the journal Science authored by RAS Initiative scientists at the Frederick National Laboratory for Cancer Research in collaboration with NYU School of Medicine. 

Cells continuously make proteins, many of which are degraded within 24-48 hours as part of normal turnover and quality control. Biochemical, cell-biological, and structural analyses revealed a process that the scientists say could lead to the ubiquitination – a cellular system for tagging proteins for degradation – of oncogenic KRAS.  

RAS cycles between its active (GTP-bound) and inactive (GDP-bound) states, a process that controls fundamental processes in the cell. Disruption of this cycle ultimately leads to disease, including a third of all cancers. Most RAS-related cancers are caused by mutant KRAS. 

Dhirendra Simanshu, Ph.D., who leads the Structural Biology Research Team within the RAS Initiative, said the team’s work built on previous studies that discovered the protein LZTR1 (Leucine Zipper-like Transcription Regulator 1) binds to RAS-like proteins through the Kelch domain in its first half. The other half of LZTR1 connects these RAS proteins to the cell’s recycling system, which tags them for destruction and breaks them down. 

The 2019 study led by Pau Castel at New York University and Frank McCormick at the University of California, San Francisco, showed that LZTR1 binds strongly to and promotes degradation of the normal, or wild-type, RAS-like protein RIT1, but binds weakly to oncogenic RIT1 mutants, preventing their degradation.  

In this recent study, the Frederick National Laboratory team used the X-ray crystallography technique to reveal the atomic details of how LZTR1 interacts with different RAS family members, including RIT1, MRAS and KRAS. The biochemical results demonstrated that LZTR1 binds tightly to only GDP-bound forms RIT1 and MRAS, while its interaction with GDP-bound classical RAS proteins (HRAS, KRAS, NRAS) is much weaker. 

 Strengthening the LZTR1-KRAS affinity to promote KRAS degradation  

The team analyzed the strong LZTR1 affinity with RIT1 with the intent to replicate it between LZTR1 and KRAS. They found that KRAS mutations T35A and E62A formed a higher-affinity interaction with LZTR1 and, as a result, these mutant proteins were degraded more quickly in cells. They used these KRAS mutations to crystallize and determine the structure of the KRAS–LZTR1 complex. 

“Cells already have a natural mechanism to recognize RAS protein for degradation through LZTR1,” Simanshu said. “If we could design a small molecule that acts like molecular glue to strengthen the interaction between KRAS and LZTR1, we might be able to promote degradation of mutant KRAS.” 

The study “provides a proof-of-concept that a glue-like compound, which acts like those mutations (T35A and E62A) and increases the LZTR1-KRAS affinity, could lead to more degradation of the KRAS protein in the cell,” he said. 

Research article in Science led by Frederick RAS team

Science is one of the world’s most prestigious scientific publications, and the Frederick National Laboratory for Cancer Research's RAS scientists have previously co-authored papers in the journal. In this case, most of the work was carried out at FNLCR by co-first authors Srisathiyanarayanan  Dharmaiah, and Daniel  A.  Bonsor, with Castel and Simanshu as corresponding authors. Structure-based cell biological studies were conducted in collaboration with Castel’s group at the NYU School of Medicine.  

Dwight Nissley, Ph.D., head of the National Cancer Institute’s RAS Initiative at the Frederick National Laboratory, said this recent Science publication is an important milestone for the program, which launched in 2013.  

“It’s extremely exciting and is a tribute to the capabilities of the RAS Initiative and Frederick National Laboratory,” he said. “It’s gratifying to see the evolution of the RAS Initiative from a state of ‘audacious aspiration,’ to a team that is discovering new drugs, therapeutic targets and cancer biology.” 

Exploring KRAS degradation as a potential strategy to limit drug resistance 

The Frederick National Laboratory's RAS Initiative scientists co-developed three investigational drugs targeting RAS-related cancers in the last six years, which are now in human clinical trials. These were developed in partnership with BridgeBio Oncology Therapeutics and Lawrence Livermore National Laboratory.  

Existing KRAS inhibitors and similar drugs in development target specific KRAS mutations, and Simanshu acknowledged that cancers treated with these drugs develop new mutations, causing the treatment to stop working. Degradation could be an antidote to resistance. 

“When you degrade a protein, it makes it harder for the disease to fight back by causing resistance mutations,” Simanshu said. “Destroying the protein works better than just blocking it.” 

Additional authors include Albert Chan, Simon Messing, Matthew Drew, Dominic Esposito and Nissley of FNLCR and Stephanie Mo, Alvaro Fernandez-Cabrera and Martha Vega of NYU.