Structure of Ebola virus polymerase

On September 28, a team of researchers from the Chinese Academy of Sciences’ Institute of Microbiology published a paper in Nature, which resolved the 3D structure of Ebola virus polymerase for the first time and revealed the molecular mechanism by which it works. At the same time, this study discovered how the classic drug—suramin inhibits the activity of Ebola virus polymerase.

For nearly 50 years, the Ebola virus has been raging in Africa, causing tens of thousands of deaths and a disease death rate of up to 90%. Scientists around the world have not stopped researching the Ebola virus, and developing small molecule drugs that can effectively inhibit the Ebola virus has been an international hotspot and challenge.

Filoviruses, including the Ebola virus, are non-segmented negative sense RNA viruses with seven genes and belong to the order Monoviridae. In recent years, antiviral therapies have pointed to different processes of the Ebola virus life cycle. The most developed area of antiviral development is focused on the entry process and includes monoclonal antibodies and small molecule inhibitors. However, these small molecule inhibitors have shown poor clinical outcomes. Therefore, there is an urgent need for broadly reactive drugs to control infection with different filoviruses. However, there are currently knowledge gaps in the understanding of the mechanism of filovirus RNA synthesis that hinder the development of such drugs.

The research team noted that the transcription and replication process of the Ebola virus genome is carried out by a complex formed by the viral polymerase L protein and other helper proteins. Since the polymerase complex is highly conserved among different filoviruses, it is a very ideal target for broad-spectrum antiviral drug development. However, there is an urgent need to clarify the replication mechanism of the Ebola virus and elucidate the molecular basis for the function of its polymerase, both for structural optimization of existing drugs targeting polymerase and for the development of new drugs targeting the conserved sites of polymerase. However, the large molecular weight, instability, and susceptibility to degradation of the Ebola virus polymerase have made the resolution of its 3D structure a worldwide challenge, thus severely limiting the development of drugs targeting polymerase.

After many years of work, the Chinese research team has successfully expressed and purified the Ebola virus polymerase complex protein (L-VP35 complex) and used cryo-electron microscopy to resolve its high-resolution 3D structure.

Structural analysis revealed that the polymerase L protein of Ebola virus forms a stable complex with the VP35 protein tetramer, and its polymerase active and capped structural domains are similar in structure to those of other fellow unsegmented negative-stranded RNA viruses such as respiratory syncytial virus (RSV) and rabies virus (RABV), suggesting that unsegmented negative-stranded RNA virus polymerases are conserved during evolution. The team noted that the N-terminal structural domain of Ebola virus polymerase has a filovirus-specific insertional domain and is essential for Ebola virus polymerase to be active, which could be a potential target for antiviral drug development.

Suramin, a drug discovered more than 100 years ago, was used to treat parasitic diseases such as African trypanosomiasis sleeping sickness. Following the Ebola outbreak, some studies suggested that sulforaphane had good in vitro anti-Ebola activity, but the precise molecular mechanism was unknown.

Suramin effectively inhibited Ebola virus polymerase activity in vitro using enzyme activation and cell replicon assays, and the structure of the complex between Ebola virus polymerase and suramin was resolved using cryoelectron microscopy, revealing that suramin exerts its inhibitory effect by binding to the polymerase’s NTP entry channel and blocking substrate from entering the enzyme activation center. The molecular details of sulforaphane drug interaction with L protein provide critical reference information for further modification and optimization of suramin.

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