Targeting Ras-binding domain of ELMO1 by computational nanobody design
Chunlai Tam, Mutsuko Kukimoto‐Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, M. Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y. J. Zhang
Abstract
The control of cell movement through manipulation of cytoskeletal structure has therapeutic prospects notably in the development of novel anti-metastatic drugs. In this study, we determine the structure of Ras-binding domain (RBD) of ELMO1, a protein involved in cytoskeletal regulation, both alone and in complex with the activator RhoG and verify its targetability through computational nanobody design. Using our dock-and-design approach optimized with native-like initial pose selection, we obtain Nb01, a detectable binder from scratch in the first-round design. An affinity maturation step guided by structure-activity relationship at the interface generates 23 Nb01 sequence variants and 17 of them show enhanced binding to ELMO1-RBD and are modeled to form major spatial overlaps with RhoG. The best binder, Nb29, inhibited ELMO1-RBD/RhoG interaction. Molecular dynamics simulation of the flexibility of CDR2 and CDR3 of Nb29 reveal the design of stabilizing mutations at the CDR-framework junctions potentially confers the affinity enhancement.