Evolution-guided design of mini-protein for high-contrast <i>in vivo</i> imaging.

Nongyu HUANG; Yang CAO; Guangjun XIONG; Suwen CHEN; Juan CHENG; Yifan ZHOU; Chengxin ZHANG; Xiaoqiong WEI; Wenling WU; Yawen HU; Pei ZHOU; Guolin LI; Fulei ZHAO; Fanlian ZENG; Xiaoyan WANG; Jiadong YU; Chengcheng YUE; Xinai CUI; Kaijun CUI; Huawei CAI; Yuquan WEI; Yang ZHANG; Jiong LI

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Evolution-guided design of mini-protein for high-contrast in vivo imaging.

Author: Nongyu HUANG ¹ ; Yang CAO ² ; Guangjun XIONG ¹ ; Suwen CHEN ¹ ; Juan CHENG ¹ ; Yifan ZHOU ¹ ; Chengxin ZHANG ³ ; Xiaoqiong WEI ⁴ ; Wenling WU ¹ ; Yawen HU ¹ ; Pei ZHOU ¹ ; Guolin LI ¹ ; Fulei ZHAO ¹ ; Fanlian ZENG ¹ ; Xiaoyan WANG ¹ ; Jiadong YU ¹ ; Chengcheng YUE ¹ ; Xinai CUI ⁵ ; Kaijun CUI ⁶ ; Huawei CAI ⁷ ; Yuquan WEI ¹ ; Yang ZHANG ⁸ ; Jiong LI ¹
Author Information

1. Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
2. Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610000, China.
3. Department of Computational Medicine and Bioinformatics, University of Michigan, MI 48109, USA.
4. Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, VA 22903, USA.
5. CDUTCM-KEELE Joint Health and Medical Sciences Institute, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
6. Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China.
7. Department of Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
8. Department of Biochemistry, Yong Loo Lin School of Medicine, Department of Computer Science, School of Computing, and Cancer Science Institute of Singapore, National University of Singapore, Kent Ridge 117417, Singapore.
Publication Type:Journal Article
Keywords: Affibody; EvoDesign; HER2-positive breast cancer; In vivo image; Lower liver uptake; Mini-protein; Protein design; Spatial aggregation properties
From: Acta Pharmaceutica Sinica B 2025;15(10):5327-5345
CountryChina
Language:English
Abstract: Traditional development of small protein scaffolds has relied on display technologies and mutation-based engineering, which limit sequence and functional diversity, thereby constraining their therapeutic and application potential. Protein design tools have significantly advanced the creation of novel protein sequences, structures, and functions. However, further improvements in design strategies are still needed to more efficiently optimize the functional performance of protein-based drugs and enhance their druggability. Here, we extended an evolution-based design protocol to create a novel minibinder, BindHer, against the human epidermal growth factor receptor 2 (HER2). It not only exhibits super stability and binding selectivity but also demonstrates remarkable properties in tissue specificity. Radiolabeling experiments with ^99mTc, ⁶⁸Ga, and ¹⁸F revealed that BindHer efficiently targets tumors in HER2-positive breast cancer mouse models, with minimal nonspecific liver absorption, outperforming scaffolds designed through traditional engineering. These findings highlight a new rational approach to automated protein design, offering significant potential for large-scale applications in therapeutic mini-protein development.