Study and therapeutic targeting of m6A methylations in paramyxovirus RNA for the development of innovative antivirals against emerging viruses in this family

"Paramyxoviruses pose a significant global health risk, causing severe infections and ranking among the top three causes of death worldwide. Nipah virus (NiV) and Hendra virus (HeV) are particularly dangerous among them, with mortality rates ranging from 40% to 100%. Currently, there is no vaccine or treatment available for these airborne outbreaks that can be transmitted from human to human. These viruses share a similar non-segmented, negative-sense RNA genome with other significant paramyxoviruses, including the measles virus (MeV) and the Atlantic salmon paramyxovirus (ASPV). A key yet underexplored aspect of paramyxovirus biology is the presence of N6-methyladenosine (m6A) on their genomic RNA. This epitranscriptomic modification appears to contribute to the virus' ability to evade the host immune system, although its exact role remains largely unknown. Our project aims to target these RNA m6A modifications as a novel therapeutic strategy. We hypothesise that specific RNA motifs act as structural switches that promote viral replication or prevent immune detection when methylated. Our approach is built around three main objectives: Precisely mapping m6A sites on the genomic RNAs of NiV, MeV and ASPV. Identify m6A sites that influence viral function and immune evasion. Design and synthesise new antiviral compounds that target viral methylation, focusing on NiV while using MeV and ASPV as BSL2 models. Our multidisciplinary consortium adopts a 'One Health' approach, recognising the interconnectedness of human and animal health. This project's innovation lies in its focus on how methylation impacts RNA structure, representing the first in-depth evaluation of paramyxovirus genome methylation. This could lead to the development of novel antiviral treatments that incorporate immune evasion mechanisms. The key steps in our project include: Mapping m6A sites on the viral RNA of NiV, MeV and ASPV using nanopore sequencing while observing changes in host cell RNA; Understanding the role of m6A modifications by modelling their effect on viral RNA structure using SHAPE technology and identifying critical m6A motifs via machine learning for targeted drug development. We will also test how m6A-modified viral RNA motifs interact with immune receptors (TLRs and RLRs) in epithelial and immune cells, to improve our understanding of immune evasion. Developing compounds that target m6A modifications, including bisubstrate inhibitors of host methyltransferases such as METTL3/14, as well as covalent inhibitors. We will also design molecules that bind directly to m6A sites on viral RNA to interfere with methylation or modify recognition by host 'reader' proteins. Testing and validating antiviral compounds: After an initial selection based on in vitro and enzymatic assays, promising compounds will be tested for their ability to inhibit MeV replication in cells and then validated using NiV in BSL4 conditions. We will use lung organotypic cultures (LCOs) to bridge the gap between in vitro and in vivo studies and test the selected compounds in vivo using a salmon paramyxovirus model to assess survival rates and reductions in viral load. By combining host- and pathogen-targeted strategies, we aim to overcome the limitations of traditional antivirals and pave the way for a new generation of effective therapies against these deadly pathogens. "