Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy

Wenting Guo; Xiaojia Li; Jingyu Fan; Hongwei Li; Yan Wen; Chunyan Meng; Haitao Chen; Zhipeng Zhao; Yuling Zhang; Yushen Du; Baixing Wu

doi:10.1016/j.isci.2023.107672

Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy

iScience. 2023 Aug 18;26(9):107672. doi: 10.1016/j.isci.2023.107672. eCollection 2023 Sep 15.

Authors

Wenting Guo¹, Xiaojia Li¹, Jingyu Fan², Hongwei Li^{1

3}, Yan Wen^{1

4}, Chunyan Meng¹, Haitao Chen⁵, Zhipeng Zhao⁶, Yuling Zhang^{1

3}, Yushen Du², Baixing Wu¹

Affiliations

¹ Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
² Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
³ Department of Cardiology, Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology and Guangzhou Key Laboratory of Molecular Mechanism and Translation in Major Cardiovascular Disease, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
⁴ Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
⁵ School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China.
⁶ Department of Basic Medical Sciences, Taizhou University, Taizhou, Zhejiang 318000, China.

Abstract

Non-natural nucleobase isocytosine (IC) is the isomer of cytosine; its chemical derivate 5-fluoroisocytosine (5-FIC) together with the isocytosine-specific deaminase (ICD) VCZ was suggested to be potential practical enzyme/prodrug pair for cancer therapy through gene-directed enzyme-prodrug therapy (GDEPT) method. In this study, we have determined the crystal structures of apo-VCZ and its complex with 5-FU. We identified the critical residues for substrate binding and catalytic reaction. We also captured the substrate-induced conformational changes of VCZ, then proposed the conjectural reaction procedures of VCZ for converting the IC into the uracil. Moreover, we evaluated the therapeutic effect of wildtype or the mutated VCZ protein in the colorectal cancer cell lines. Our studies will shed light on optimizing the ICD/5-FIC pairs by modifying either the enzyme or the prodrug based on the structural observations, thereby improving the possibility of applying the ICD/5-FIC pair in clinical trials.

Keywords: Biochemistry; Biological sciences; Biomolecules; Natural sciences; Pharmacology; Protein; Protein structure aspects; Structural biology.