Structure-based discovery of neoandrographolide as a novel inhibitor of Rab5 to suppress cancer growth

Jing Zhang; Yue Sun; Li-Ye Zhong; Nan-Nan Yu; Lan Ouyang; Run-Dong Fang; Yang Wang; Qing-Yu He

doi:10.1016/j.csbj.2020.11.033

Structure-based discovery of neoandrographolide as a novel inhibitor of Rab5 to suppress cancer growth

Comput Struct Biotechnol J. 2020 Nov 30:18:3936-3946. doi: 10.1016/j.csbj.2020.11.033. eCollection 2020.

Authors

Jing Zhang^{1

2}, Yue Sun², Li-Ye Zhong², Nan-Nan Yu², Lan Ouyang², Run-Dong Fang², Yang Wang², Qing-Yu He^{1

2}

Affiliations

¹ The First Affiliated Hospital, Jinan University, Guangzhou 510632, China.
² MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.

Abstract

Rab5 is a small GTPase that plays a crucial role in oncogenic signal transduction, which was considered as an attractive target for cancer therapy. Rapid GDP/GTP exchange in the packet of Rab5 sustains its high activity for promoting cancer progression. However, Rab5 currently remains undruggable due to the lack of specific inhibitor. Herein, we reported the discovery of a novel Rab5 inhibitor, neoandrographolide (NAP), by using high-throughput virtual screening with a natural product library containing 7459 compounds, which can occupy the surface groove of Rab5, competing with GDP/GTP for the binding. Ser34 is the most important residue in the groove of Rab5, as it forms most hydrogen-bond interactions with GDP/GTP or NAP, and in silico mutation of Ser34 decreased the stabilization of Rab5. Moreover, fluorescence titration experiment and isothermal titration calorimetry (ITC) assay revealed a direct binding between NAP and Rab5. Biochemical and cell-based assays showed that NAP treatment not only diminished the activity of Rab5, but also suppressed cell growth of cancer cell. This finding firstly identifies NAP as a novel inhibitor of Rab5, which directly binds with Rab5 by occupying the GDP/GTP binding groove to suppress its functions, highlighting a great potential of NAP to be developed as a chemotherapeutic agent in cancer therapy.

Keywords: Cancer therapy; Neoandrographolide; Rab5; Virtual screening.