Additionally, it was observed that porcine delta coronavirus (PDCoV) Nsp9 mutant (Nsp9 without the N-finger motif) is monomeric in solution 16. SARS-CoV Nsp9 forms a dimer from a conserved region called "GxxxG" α-helical motif, where the interruption of key residues within this region reduces RNA binding and SARS-CoV proliferation 14, 15. CoV Nsp9s have diverse forms of dimerization that promote their biological function. In addition, Nsps are considered important for viral replication during the human cell infection phase 13, 14. Nsp9 along with Nsp7, Nsp8, and Nsp10 are located within the replication complex and thus, are likely to be members of this process 12. All Nsps are considered essential for transcription, replication, and translation of viral RNA, except Nsp1 and Nsp2 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14. During the replication process of the virus, polyprotein processing releases RNA polymerase along with several non-structural proteins (Nsps) that facilitate RNA synthesis and may play a key role in the replication process, although they are not included in the viral envelope 7, 8, 9, 10, 11.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently a global pandemic, which has spread rapidly throughout the world since December 2019 when it was first reported 1, 2, 3, 4, 5, 6. Overall, we provide a detailed study on the Nsp9 dimer of SARS-CoV-2 that may aid in the development of new strategies for the treatment and prevention of COVID-19. In addition, the energetic and lipophilic analysis reveal that the higher binding energy in the native dimer can be deduced since it is more lipophilic than the mutant one, increasing non-polar interactions, which is in line with the result of MM-GBSA and SIE approaches where the van der Waals energy term has the greatest weight in the stability of the native dimer. Besides, clustering results for the native dimer showed accessible cavities to drugs. On the other hand, Gly100 and Gly104, are responsible for stabilizing the α-helices and making the dimer interface remain stable in both, native and mutant (without N-finger motif) systems. The results reveal for the native dimer that the N-finger contributes favorably through hydrogen bond interactions and two amino acids bellowing to the hydrophobic region, Leu45 and Leu106, are crucial in the formation of the cavity for potential drug binding. Additionally, we presented a virtual N-finger mutation to investigate whether this motif contributes to dimer stability. Here, we present a structural, lipophilic and energetic study about the Nsp9 dimer of SARS-CoV-2 through computational methods that complement hydrophobicity scales of amino acids with molecular dynamics simulations. The dimeric forms of coronavirus Nsp9 increase their nucleic acid binding affinity and the N-finger motif appears to play a critical role in dimerization.
In SARS-CoV-2 replication complex, the Non-structural protein 9 (Nsp9) is an important RNA binding subunit in the RNA-synthesizing machinery.