De novo design of Ras isoform selective binders
Jason Z Zhang1, Xinting Li2, Alexa Rane Batingana3
1Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA 98195, USA.
Abstract:
The four major isoforms encoded by RAS proto-oncogenes are differentially associated with cancer, but there are few isoform-specific binding reagents becasue the sequence differences are confined to their disordered C termini. To overcome this limitation, we use deep learning-based methods to design Ras isoform-specific binders (RIBs) for all major Ras isoforms de novo by targeting the Ras C terminus. The RIBs bind to their target Ras isoforms both in vitro and in cells with remarkable specificity, disrupting their membrane localization and inhibiting Ras activity. The RIBs enable dissection of the distinct roles of Ras isoforms during RasG12C inhibitor resistance, demonstrating their utility in understanding Ras biology and disease and suggesting potential therapeutic applications.
Insights
Researchers developed novel Ras isoform-specific binders (RIBs) using deep learning to target cancer-associated Ras proteins. These RIBs demonstrate high specificity, inhibiting Ras activity and offering potential for cancer therapy and understanding resistance mechanisms.
Area of Science:
- Oncology
- Molecular Biology
- Bioinformatics
Background:
- RAS proto-oncogenes encode four major isoforms implicated in cancer.
- Limited availability of isoform-specific binding reagents hinders research due to conserved sequences, except for C-terminal differences.
Purpose of the Study:
- To design novel, de novo Ras isoform-specific binders (RIBs) targeting the Ras C-terminus.
- To overcome the challenge of limited isoform specificity in existing reagents.
- To explore the utility of RIBs in understanding Ras biology and cancer.
Main Methods:
- Deep learning-based methods were employed to design RIBs targeting the Ras C-terminus.
- In vitro and cellular assays were used to validate RIB binding and specificity.
- RIBs were used to investigate Ras isoform roles in RasG12C inhibitor resistance.
Main Results:
- De novo designed RIBs demonstrated high specificity for target Ras isoforms.
- RIBs effectively bind both in vitro and within cells.
- RIBs disrupt Ras membrane localization and inhibit Ras activity.
- RIBs facilitated the dissection of distinct Ras isoform roles in RasG12C inhibitor resistance.
Conclusions:
- Deep learning enables the creation of highly specific Ras isoform binders.
- RIBs are valuable tools for dissecting Ras isoform functions in biological processes and disease.
- RIBs show promise for therapeutic applications in cancer treatment.
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