Computer-Aided Directed Evolution Generates Novel AAV Variants with High Transduction Efficiency

Zengpeng Han; Nengsong Luo; Fei Wang; Yuxiang Cai; Xin Yang; Weiwei Feng; Zhenxiang Zhu; Jie Wang; Yang Wu; Chaohui Ye; Kunzhang Lin; Fuqiang Xu

doi:10.3390/v15040848

Computer-Aided Directed Evolution Generates Novel AAV Variants with High Transduction Efficiency

Viruses. 2023 Mar 26;15(4):848. doi: 10.3390/v15040848.

Authors

Zengpeng Han^{1

2

3}, Nengsong Luo⁴, Fei Wang⁵, Yuxiang Cai⁴, Xin Yang⁶, Weiwei Feng⁶, Zhenxiang Zhu^{1

2

3}, Jie Wang^{1

2}, Yang Wu^{1

2}, Chaohui Ye^{1

2}, Kunzhang Lin³, Fuqiang Xu^{1

2

3

4

7}

Affiliations

¹ State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
² University of Chinese Academy of Sciences, Beijing 100049, China.
³ Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, the Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China.
⁴ Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China.
⁵ iDrugDance Technology Co., Ltd., Shenzhen 518055, China.
⁶ ZhunAo Biotechnology Co., Ltd., Wuhan 430056, China.
⁷ Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.

Abstract

Adeno-associated viruses (AAVs) have become safe and effective tools for therapeutic in vivo gene drug delivery. Among many AAV serotypes, AAV2 is the most well-characterized. Although many studies have been carried out on the engineering of the capsid VR-VIII region, few attempts have been made in the VR-IV region. Here, we targeted amino acid positions 442-469 of the VR-IV region and established an engineering paradigm of computer-aided directed evolution, based on training samples from previous datasets, to obtain a viral vector library with high diversity (~95,089). We further examined two variants selected from the library. The transduction efficiency of these two novel AAV variants, AAV2.A1 and AAV2.A2, in the central nervous system was 10-15 times higher than that of AAV2. This finding provides new vehicles for delivering gene drugs to the brain.

Keywords: Cap gene library; adeno-associated virus; computer-aided design; directed evolution; transduction efficiency.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Capsid Proteins* / metabolism
Capsid* / metabolism
Dependovirus / physiology
Gene Library
Genetic Therapy
Genetic Vectors / genetics
Transduction, Genetic

Substances

Capsid Proteins

Grants and funding

This work was supported by the STI2030-Major Projects (2021ZD0201003), the National Natural Science Foundation of China (31830035, 31771156, 21921004, 82151309), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB32030200), the Shenzhen Key Laboratory of Viral Vectors for Biomedicine (ZDSYS20200811142401005), and the Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration (2022ZDZ13).