Suppression of HIV-1 Integration by Targeting HIV-1 Integrase for Degradation with A Chimeric Ubiquitin Ligase

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RESEARCH ARTICLE

Suppression of HIV-1 Integration by Targeting HIV-1 Integrase for Degradation with A Chimeric Ubiquitin Ligase Zuopeng Zhang1 • Sen Yuan1 • Shuting Xu1,3 • Deyin Guo1,2 • Lang Chen1 • Wei Hou1



Min Wang1

Received: 14 March 2020 / Accepted: 14 September 2020 Ó Wuhan Institute of Virology, CAS 2020

Abstract Human immunodeficiency virus (HIV) attacks human immune system and causes life-threatening acquired immune deficiency syndrome (AIDS). Treatment with combination antiretroviral therapy (cART) could inhibit virus growth and slow progression of the disease, however, at the same time posing various adverse effects. Host ubiquitin-proteasome pathway (UPP) plays important roles in host immunity against pathogens including viruses by inducing degradation of viral proteins. Previously a series of methods for retargeting substrates for ubiquitin-proteasome degradation have been successfully established. In this study, we attempted to design and construct artificial chimeric ubiquitin ligases (E3s) based on known human E3s in order to manually target HIV-1 integrase for ubiquitin proteasome pathway-mediated degradation. Herein, a series of prototypical chimeric E3s have been designed and constructed, and original substrate-binding domains of these E3s were replaced with host protein domains which interacted with viral proteins. After functional assessment screening, 146LI was identified as a functional chimeric E3 for HIV-1 NL4-3 integrase. 146LI was then further optimized to generate 146LIS (146LI short) which has been shown to induce Lys48-specific polyubiquitination and reduce protein level of HIV-1 NL4-3 integrase more effectively in cells. Lymphocyte cells with 146LIS knock-in generated by CRISPR/ Cas-mediated homology-directed repair (HDR) showed remarkably decreased integration of HIV-1 NL4-3 viral DNAs and reduced viral replication without obvious cell cytotoxicity. Our study successfully obtained an artificial chimeric E3 which can induce Lys48-specific polyubiquitination and proteasome-mediated degradation of HIV-1 NL4-3 integrase, thus effectively inhibiting viral DNA integration and viral replication upon virus infection. Keywords HIV-1  Integrase  Iduna  LEDGF  Chimeric E3s  Ubiquitination

Introduction In eukaryotic cells, the ubiquitin-proteasome pathway (UPP) plays important roles in many cellular events by targeting certain regulatory proteins for 26S proteasome & Min Wang [email protected] & Wei Hou [email protected] 1

School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China

2

Centre for Infection and Inmunity Study (CIIS), School of Medicine, Sun Yat-sen University, Guangzhou 518107, China

3

Renmin Hospital of Wuhan University, Wuhan 430060, China

degradation. This process is carried out in two consecutive steps: (1) tagging the substrate with a specific type of ubiquitin chain and (2) subsequent degradation of the tagged substrate by the 26S proteasome complex (Saeki 201