Profiling the Landscape of Drug Resistance Mutations in Neosubstrates to Molecular Glue Degraders
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Abstract
Targeted protein degradation (TPD) holds immense promise for drug discovery, but mechanisms of acquired resistance to degraders remain to be fully identified. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)-suppressor scanning to identify mechanistic classes of drug resistance mutations to molecular glue degraders in GSPT1 and RBM39, neosubstrates targeted by E3 ligase substrate receptors cereblon and DCAF15, respectively. While many mutations directly alter the ternary complex heterodimerization surface, distal resistance sites were also identified. Several distal mutations in RBM39 led to modest decreases in degradation, yet can enable cell survival, underscoring how small differences in degradation can lead to resistance. Integrative analysis of resistance sites across GSPT1 and RBM39 revealed varying levels of sequence conservation and mutational constraint that control the emergence of different resistance mechanisms, highlighting that many regions co-opted by TPD are nonessential. Altogether, our study identifies common resistance mechanisms for molecular glue degraders and outlines a general approach to survey neosubstrate requirements necessary for effective degradation.
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Both deep mutational scanning (DMS) and CRISPR tiling have recently highlighted hotspots in ligase and POI that are functionally relevant for degrader activity.
“For instance, both DMS and CRISPR tiling have recently highlighted hotspots in ligase and POI that are functionally relevant for degrader activity.237,238”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [238]
A complementary CRISPR-suppressor scanning strategy identifies resistance-causing mutations localized in neo-substrates of known molecular glue degraders.
“Moreover, an elegant recent study described a complementary approach, which is based on a CRISPR-suppressor scanning strategy, to identify resistance-causing mutations that are localized in neo-substrates of known molecular glue degraders48.”
From Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders (2023) · cites this paper as [48]
Several functional genomics campaigns have helped map how the repertoire of CRLs and their regulators shape degrader efficacy, outlining putative resistance mechanisms.
“Several functional genomics campaigns in recent years have helped map how the repertoire of CLRs and their regulators shape degrader efficacy, thus also outlining putative resistance mechanisms.141-151”
From Chasing molecular glue degraders: screening approaches (2022) · cites this paper as [150]
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Chasing molecular glue degraders: screening approaches
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Self-citationAdvancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
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- Authors
- Gosavi, P. M., Ngan, K. C., Yeo, M. J. R., Su, C., Li, J., Lue, N. Z., Hoenig, S. M., & Liau, B. B.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Liau, Brian B.
- ORCID
- Venue
- ACS Central Science
- Publisher
- American Chemical Society (ACS)
- Published
- 2022-02-14
- Volume
- 8
- Issue
- 4
- Pages
- 417-429
- ISSN
- 2374-7943 (ISSN-L)
- 2374-7951
- PMC
- PMC9052798
- OpenAlex
- W4226498581
- Cited by
- 56
- References
- 48
- Citations by year
- 2026: 13 · 2025: 9 · 2024: 10 · 2023: 12 · 2022: 12
- FWCI
- 3.51
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- Locations
- ACS Central Science (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Ono Pharma Foundation (Ono Pharma Breakthrough Science Initiative Award)
- National Science Foundation (DGE-1745303)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- targeted protein degradation, molecular glues, drug resistance mutations, GSPT1, RBM39, cereblon, DCAF15, mutational constraint, sequence conservation, resistance mechanisms
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