Harnessing the arenavirus polymerase for antiviral drug design

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Infectious diseases have long been serious public threats along the human history, especially those acute emerging viral pathogens, such as influenza virus, Ebola virus, Nipah virus, Lassa virus (LASV), severe acute respiratory syndrome coronavirus (SARS-CoV), middle-east respiratory syndrome coronavirus (MERS-CoV), as well as the ongoing pandemic COVID-19 virus. All these viral infections have caused massive destructions for human lives and the economy. The prevention and control of these emerging infectious diseases have been greatly hindered by their unpredictability and the lagging time for developing vaccines and specific drugs. Unfortunately, for most of these viruses, there are no available vaccines or effective drugs. The global crisis of COVID-19 teaches us once more that the destiny of all human beings is well connected around the globe and no one can survive with others suffering. It also highlights the urgent need of proactive efforts to get well-prepared for potential pandemics or epidemics.

The Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology in Institute of Microbiology, CAS (IMCAS) is one of the leading institutes in the research field of emerging infectious diseases in China. In 2016, I joined the group of Prof. Yi Shi, who works on the mechanisms of RNA virus replication and antiviral drug design, to pursue my PhD. In the past five years, I mainly focused on the structural and functional studies on the replication machinery of arenaviruses, a group of enveloped segmented negative-sense RNA viruses (sNSVs), which include many highly virulent and life-threating human pathogens, as exemplified by LASV. LASV is classified as a biosafety level 4 (BSL-4) agent and its infection can cause severe hemorrhagic fever diseases with a high mortality rate. Even though there are no infection cases of LASV or other arenaviruses reported in China so far, we should suit up to the best of our ability to prevent the potential outbreak of epidemics or pandemics in any region of the world. Our research efforts would be an indispensable prerequisite to achieve this goal.

Arenaviruses encode their own RNA-dependent RNA polymerase (RdRp) for replication and transcription of the viral genome, and this molecule is quite conserved among different viral species, which therefore indicates a very important antiviral therapeutic target. However, the working mechanism of this viral machinery was yet poorly understood which was partially hindered by the challenges in recombinant expression and purification of the polymerase. To tackle this problem, we tried different expression systems and constructs, and finally successfully obtained the biologically active protein samples for structural and functional studies. In 2020, our team reported the first near-atomic resolution structure of arenavirus polymerase, as well as its complex with viral RNA promoter1. In these structures, we identified a conserved 3’-RNA binding site in different sNSV polymerases. This site would thus be a promising candidate target for developing broad-spectrum antiviral drugs. Besides, we also found the 5’-vRNA regulates the switch between transcription and replication, and the self-dimerization is crucial for the activity of the polymerase1. These findings constitute a basic framework for understanding the mechanism of arenavirus replication, but yet many further questions remain.

One intriguing phenomenon attracted my interest that the viral matrix protein Z can down-regulate the activity of the polymerase. I therefore turned to investigate the mechanism of this specific regulation between arenavirus polymerase and Z protein. This project opened a new world for me and added substantial value to my PhD. I am so grateful to all my team members and collaborators for this fantastic cooperative journey. In this project, we performed comprehensive structural and biochemical studies and found Z protein binding alters the conformational dynamics of the key catalytic motifs of the polymerase, thus inhibiting the catalytic activity by allosteric effect2. We also identified the key structural determinant of Z protein governing its inhibitory activity to the polymerase, which is highly conserved across all arenaviruses. This observation is quite remarkable. It indicates the regulatory effect of Z protein on polymerase might be a universal mechanism among all arenaviruses, and also suggests the possibility of cross-inhibition between different viruses, which is supported by our in vitro polymerase activity assays2. These findings again provide a new strategy for developing broad-spectrum antiviral drugs against different arenaviruses.

Developing antiviral drugs targeting the viral polymerases is a very important strategy for proactive preparation for potential pandemics or epidemics. I am so excited to be involved in this field and sincerely hope our findings would someday be translated to benefit the health of all mankind.

References:

  1. Peng, R. et al. Structural insight into arenavirus replication machinery. Nature 579, 615-619 (2020).
  2. Xu X. et al. Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals. Nat. Microbiol. (2021). DOI: 10.1038/s41564-021-00916-w.

Xin Xu

Ph.D. student, Institute of Microbiology, Chinese Academy of Sciences