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Updated: Aug 6, 2025

Selection of Transporter-Targeted Inhibitory Nanobodies by Solid-Supported-Membrane SSM-Based Electrophysiology

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Targeting Ras-binding domain of ELMO1 by computational nanobody design.

Chunlai Tam^1,2, Mutsuko Kukimoto-Niino³, Yukako Miyata-Yabuki⁴

¹Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.

Communications Biology

|March 18, 2023

Summary

Researchers designed a novel nanobody, Nb29, targeting the ELMO1 protein

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Area of Science:

Biochemistry
Structural Biology
Drug Discovery

Background:

Cell movement regulation is crucial for cancer metastasis.
ELMO1 protein is involved in cytoskeletal regulation and cancer cell migration.
Targeting protein-protein interactions offers therapeutic strategies for anti-metastasis.

Purpose of the Study:

To determine the structure of ELMO1's Ras-binding domain (RBD) alone and with RhoG.
To computationally design nanobodies targeting ELMO1-RBD.
To validate nanobody binding and inhibitory potential against ELMO1-RBD/RhoG interaction.

Main Methods:

X-ray crystallography for structural determination.
Computational nanobody design using a dock-and-design approach.
Affinity maturation and molecular dynamics simulations for optimization and validation.

Main Results:

Successfully determined the structure of ELMO1-RBD in complex with RhoG.
Designed Nb01, a novel nanobody binder, from scratch in the first design round.
Generated 17 enhanced binding variants, with Nb29 inhibiting ELMO1-RBD/RhoG interaction.

Conclusions:

Computational nanobody design is effective for targeting protein-protein interactions.
Nb29 demonstrates therapeutic potential by inhibiting ELMO1-RBD/RhoG interaction.
Stabilizing mutations in nanobody CDRs contribute to enhanced binding affinity.