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Patterns of substrate affinity, competition and degradation kinetics underlie biological activity of thalidomide analogs

Adam S. Sperling, Michael Burgess, Hasmik Keshishian, Jessica A. Gasser, Shruti Bhatt, Max Jan, Mikołaj Słabicki, Rob S. Sellar, Emma C. Fink, Peter G. Miller, Brian J Liddicoat, Quinlan L. Sievers, Rohan Sharma, Dylan N. Adams, Elyse A. Olesinski, Mariateresa Fulciniti, Namrata D. Udeshi, Eric Kuhn, Anthony Letai, Nikhil C. Munshi, Steven A. Carr and Benjamin L. Ebert

Key Points

  • Sensitivity to thalidomide analogs is determined by an interplay between the level of CRBN and multiple potential substrates.

  • Substrates compete for access to a limiting pool of the CRBN E3 ligase substrate adaptor in the presence of thalidomide analogs.

Abstract

Pharmacologic agents that modulate ubiquitin ligase activity to induce protein degradation are a major new class of therapeutic agents, active in a number of hematologic malignancies. However, we currently have a limited understanding of the determinants of activity of these agents and how resistance develops. We developed and utilized a novel quantitative, targeted mass spectrometry (MS) assay to determine the relative activities, kinetics, and cell-type specificity of thalidomide and four analogs, all but one of which are in clinical use or clinical trials for hematologic malignancies. Thalidomide analogs bind the CRL4CRBN ubiquitin ligase and induce degradation of particular proteins, but each of the molecules studied have distinct patterns of substrate specificity that likely underlie the clinical activity and toxicities of each drug. Our results demonstrate that the activity of molecules that induce protein degradation depends on the strength of ligase-substrate interaction in the presence of drug, the levels of the ubiquitin ligase, and the expression level of competing substrates. These findings highlight a novel mechanism of resistance to this class of drugs mediated by competition between substrates for access to a limiting pool of the ubiquitin ligase. We demonstrate that increased expression of a non-essential substrate can lead to decreased degradation of other substrates that are critical for anti-neoplastic activity of the drug, resulting in drug resistance. These studies provide general rules that govern drug-dependent substrate degradation and key differences between thalidomide analog activity in vitro and in vivo.

  • Submitted November 19, 2018.
  • Revision received April 27, 2019.
  • Accepted April 26, 2019.