Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP
RNA Synthesis The RNA template, 5′-rUrUrUrUrUrCrArUrArArCrUrUrArArUrCrUrCrAr- CrArUrArGrCrArCrUrG-3′, and RNA primer 5′-rCrArGrUrGrCrUrArUrGrUr- GrArGrArUrUrArArGrUrUrArU-3′ were prepared by solid-phase synthesis on an ÄKTA oligopilot plus 10 (Cytiva). RNAs were cleaved from the solid support by treating with 4 mL of a 1:1 mixture of 28% wt NH3/H2O solution and 33% wt CH3NH2/EtOH solution at 55 °C for 30 min; then the silyl protecting groups were removed by treating with 3 mL of 1:1 mixture of triethylamine trihydrofluoride and dimethyl sulfoxide at 55 °C for 90 min. Then, 30 mL of cold 50 mM NaClO4 in acetone was added to precipitate the RNA product. After centrifugation, the pellet of RNA was dissolved in 5 mL of water and passed through a Sep-Pack C18 Cartridge, 5 g sorbent (Waters). Eluates containing RNA were combined and lyophilized. Mass spectroscopy of the template RNA found m/z ([M-7H+]) = 1,341.8 (theoretical 1,342.1) and found m/z ([M-6H+]) = 1,565.6 (theoretical 1,565.9); mass spectrometry of the primer RNA found m/z ([M-6H+]) = 1,278.6 (theoretical 1,278.9) and found m/z ([M-5H+]) = 1,534.5 (theoretical 1,534.9).
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It’s a report on the structure of favipiravir tri-phosphate, a ribonucleotide analog, complexed with the SARS2 RNA polymerase and a portion of its viral RNA substrate determined by cryogenic-electron microscopy (as opposed to more conventional X-Ray crystallography.
Favipiravir triphosphate inhibits the viral polymerase, thus inhibiting viral activity and is therefore a possible drug to treat Covid-19. This study is trying to determine the structural determinants of this enzyme inhibition at a detailed molecular level which can be of use in further development of this molecule or screening for or designing related molecules that may work even better at in hitting viral replication.