8ZFV | pdb_00008zfv

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.

(2025) J Struct Biol 217: 108197-108197

• PubMed: 40113149 Search on PubMed
• DOI: https://doi.org/10.1016/j.jsb.2025.108197
• Primary Citation of Related Structures:  
  8W6W, 8ZFV, 9IN1


• PubMed Abstract: 
  

  The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18?±?1.3?μM), cefuroxime (55?±?4.2?μM), and ampicillin (28?±?1.2?μM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC ₅₀ ranging from?～?12 to 18?μM and K _D values between 24?μM to 32?μM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 ?) and N-CTD-Ampicillin (2.2 ?), along with the structure of apo N-CTD (1.4 ?). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.

   View More

---

Organizational Affiliation: 

Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.