Mechanisms of Virus Entry into Cells and Antiviral Barriers Limiting Entry

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Work in this project relates to the functional and structural characterization of CD225 protein family, which are united by the presence of a CD225 domain that controls membrane trafficking processes via mechanisms that are poorly understood. My lab has published a number of articles describing the mechanistic activity of CD225 family members known as IFITM proteins and our findings have been extended to other CD225 family members involved in neurotransmission and glucose signaling. We published two articles pertaining to this project in 2020 (Ahi et al., mBio, 2020; Rahman et al., eLife 2020), two articles in 2022 (Rahman et al., Journal of Molecular Biology, 2022; Majdoul et al., Nature Reviews Immunology, 2022), one in 2024 (Shi et al., Nature Communications, 2024), one article in 2025 (Rahman et al., EMBO Journal, 2025), and two additional articles are in the process of being submitted/reviewed. Our work provides extensive insight into the function of IFITM proteins as well as the extended CD225 protein family to which they belong and will provide leverage for the development of new antiviral therapies. Notably, we identified an amphipathic alpha helix that is required for the antiviral activity of IFITM3 against multiple viruses, including HIV-1, Zika virus, and Influenza A virus. We showed that the amphipathic helix is required for the ability of IFITM3 to alter the biophysical properties of cellular membranes (membrane rigidity and curvature (Rahman et al. eLife, 2020) and we also described how IFITM3 forms functional oligomers in this study. As a follow up, we identified interaction partners of IFITM3 using an unbiased proteomics based approach and identified the related IFITM1 as an interaction partner. More specifically, we found that IFITM1 and IFITM3 form heteromultimers and we provide evidence that these heteromultimers are functional antiviral units active in endosomes, where a variety of enveloped viruses enter cells via membrane fusion (Wilt et al. bioRxiv, 2025 (submitted)). Additionally, we demonstrated that the amphipathic helix of IFITM3 exhibits direct cholesterol binding activity (Rahman et al. Journal of Molecular Biology), providing a plausible mechanism for how IFITM3 restricts membrane fusion pore formation through cholesterol regulation. We are now building on our findings by incorporating in silico analyses like molecular dynamics simulations and structural approaches like cryoelectron microscopy to further pin down the mechanistic basis for IFITM3-mediated virus restriction. Most recently, we discovered that the CD225 domain contains a SNARE-like motif that enables CD225 family members, including IFITM3, to bind cellular SNARE fusogens and regulate their assembly, a process that is critical to the coordinated membrane fusion during vesicular trafficking events in cells (Rahman et al. EMBO Journal, 2025). Importantly, we have also characterized the existence of viral countermeasures that enables evasion of the antiviral activities of IFITM3. For example, we have recently found that Nef from early/acute primary HIV-1 infection exhibits the capacity to antagonize human IFITM3 and, in doing so, restores infectivity to HIV-1 virions (Agarwal et al. bioRxiv, 2025 (in revision). The mechanism by which Nef performs this activity involves inhibition of IFITM3 oligomerization and restoration of membrane fluidity in the presence of IFITM3. Our findings will allow us to better understand the cellular roles played by IFITM3 and related proteins in regulating the biophysical properties of host and viral membranes. An understanding of the host-virus interplay involved in evading IFITM3 will reveal key molecular insights into membrane properties required for efficient virus infection, which could be targeted for antiviral therapy. Furthermore, our findings on CD225 proteins will provide mechanistic insight into their poorly characterized tumorigenic roles and provide a basis for their inactivation.