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Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FPV), an active pharmaceutical component of the drug discovered and registered in March 2014 in Japan under the name Avigan, with an indication for pandemic influenza, has been studied. The study of this compound was prompted by the idea that effective processes of recognition and binding of FPV to the nucleic acid are affected predominantly by the propensity to form intra- and intermolecular interactions. Three nuclear quadrupole resonance experimental techniques, namely 1H-14N cross-relaxation, multiple frequency sweeps, and two-frequency irradiation, followed by solid-state computational modelling (density functional theory supplemented by the quantum theory of atoms in molecules, 3D Hirshfeld Surfaces, and reduced density gradient) approaches were applied. The complete NQR spectrum consisting of nine lines indicating the presence of three chemically inequivalent nitrogen sites in the FPV molecule was detected, and the assignment of lines to particular sites was performed. The description of the nearest vicinity of all three nitrogen atoms was used to characterize the nature of the intermolecular interactions from the perspective of the local single atoms and to draw some conclusions on the nature of the interactions required for effective recognition and binding. The propensity to form the electrostatic N−H···O, N−H···N, and C−H···O intermolecular hydrogen bonds competitive with two intramolecular hydrogen bonds, strong O−H···O and very weak N−H···N, closing the 5-member ring and stiffening the structure, as well as π···π and F···F dispersive interactions, were analysed in detail. The hypothesis regarding the similarity of the interaction pattern in the solid and the RNA template was verified. It was discovered that the -NH2 group in the crystal participates in intermolecular hydrogen bonds N–H···N and N–H···O, in the precatalytic state only in N–H···O, while in the active state in N–H···N and N–H···O hydrogen bonds, which is of importance to link FVP to the RNA template. Our study elucidates the binding modes of FVP (in crystal, precatalytic, and active forms) in detail and should guide the design of more potent analogues targeting SARS-CoV-2. Strong direct binding of FVP-RTP to both the active site and cofactor discovered by us suggests a possible alternative, allosteric mechanism of FVP action, which may explain the scattering of the results of clinical trials or the synergistic effect observed in combined treatment against SARS-CoV-2.

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The pure nuclear quadrupole resonance spectra of 14N have been measured in tris-sarcosine calcium chloride (TSCC), deuterated TSCC, and sarcosine using nuclear double resonance in the laboratory frame. In TSCC two chemically nonequivalent nitrogen sites have been found at room temperature, one with a quadrupole coupling constant e2Qq/h =1040 kHz and an asymmetry parameter η=1 and another one with e2Qq/h = 940 kHz, η=1. The 14N results in deuterated TSCC differ from those in undeuterated TSCC by less than 10%. The corresponding 14N data for sarcosine are e2Qq/h = 1440 kHz, η=1 and e2Qq/h = 1470 kHz, η=0.79. In the ferroelectric phase at 77 °K only one nitrogen site has been found in TSCC with e2Qq/h = 1010 kHz and η=0.89. In TSCC, ν (35Cl) =2160 kHz and ν (37Cl) =1710 kHz, and deuterated TSCC 35Cl and 37Cl quadrupole resonance lines were found in the paraelectric phase, whereas in the ferroelectric phase no chlorine lines could be observed.