T-705-modified ssRNA in complex with Lassa Virus Nucleoprotein exhibits nucleotide splaying and increased water influx into the RNA-binding pocket.

Lassa virus infection is clinically characterized by multi-organ failure in humans. Without an FDA-approved vaccine, ribavirin is the frontline drug for treatment but with attendant toxicities. 6-fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) is an emerging alternative drug with proven anti-Lassa virus activity in experimental model. One of the mechanisms of action is its incorporation into nascent single strand RNA (ssRNA) which forms complex with Lassa nucleoprotein (LASV-NP). Here, using Molecular Dynamics simulation, the structural and electrostatics changes associated with LASV-NP- ssRNA complex has been studied when none, one or four of its bases has been substituted with T-705. The results demonstrated that glycosidic torsion angle χ (O4'-C1'-N1-C2) rotated from high-anti- (-110° and -60°) to the syn- conformation (+30) in with increased T-705 substitution. Similarly, increased T-705 substitution resulted in increased splaying (55°-70°), loss of ssRNA-LASV-NP H-bond interaction, increased water influx into the ssRNA binding pocket and decreased electrostatic potentials of ssRNA pocket. Furthermore, strong positively correlated motion observed between α6 residues (aa: 128-145) and its contact ssRNA bases (5-7) is weakened in apo biosystem and transitioned into anti-correlated motions in ssRNA-bound LASV-NP biosystem. Finally, LASV genome may become more accessible to cellular ribonuclease access with T-705 incorporation due to loss of NP interaction. This article is protected by copyright. All rights reserved.