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

‐705‐modified ssRNA is associated with out‐of‐plane spaying of the modified bases within the RNA resulting in loss of base‐stacking interaction

T‐705‐modified ssRNA bound to Lassa virus nucleoprotein ssRNA binding pocket promotes the influx of water into the ssRNA binding pocket with resultant loss of electrostatic potentials of the amino acids lining the pocket

T‐705‐modified ssRNA bound to Lassa virus nucleoprotein ssRNA binding pocket alters essential dynamics of the protein

Abstract

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.

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