Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach

Abstract

In this study, the Nsp12-Nsp8 complex of SARS-CoV-2 was targeted with structure-based and computer-aided drug design approach because of its vital role in viral replication. Sequence analysis of RNA-dependent RNA polymerase (Nsp12) sequences from 30,366 different isolates were analysed for possible mutations. FDA-approved and investigational drugs were screened for interaction with both mutant and wild-type Nsp12-Nsp8 interfaces. Sequence analysis revealed that 70.42% of Nsp12 sequences showed conserved P323L mutation, located in the Nsp8 binding cleft. Compounds were screened for interface interaction, any with XP GScores lower than À7.0 kcal/mol were considered as possible interface inhibitors. RX-3117 (fluorocyclopentenyl cytosine) and Nebivolol had the highest binding affinities in both mutant and wild-type enzymes, therefore they were selected and resultant protein-ligand complexes were simulated for analysis of stability over 100 ns. Although the selected ligands had partial mobility in the binding cavity, they were not removed from the binding pocket after 100 ns. The ligand RX-3117 remained in the same position in the binding pocket of the mutant and wild-type enzyme after 100 ns MD simulation. However, the ligand Nebivolol folded and embedded in the binding pocket of mutant Nsp12 protein. Overall, FDA-approved and investigational drugs are able to bind to the Nsp12-Nsp8 interaction interface and prevent the formation of the Nsp12-Nsp8 complex. Interruption of viral replication by drugs proposed in this study should be further tested to pave the way for in vivo studies towards the treatment of COVID-19.

Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients

“…NSP12 creates the core polymerase complex with NSP7 and NSP8 ( Hillen et al, 2020 ; Peng et al, 2020 ; Wang et al, 2020 ), and site 323 locates near the binding interface of NSP8 and NSP12 ( Hillen et al, 2020 ). The proline (P) amino acid creates hydrogen bond with NSP8 ( Mutlu et al, 2020 ). The P→L mutation is preferable to NSP8–NSP12 binding and thus promotes viral replication ( Kannan et al, 2020 ).…”

Comparative study of predicted miRNA between Indonesia and China (Wuhan) SARS-CoV-2: a bioinformatics analysis

“…This mutation is highly associated with the infectious rate on human lung cells, and colon cells (Yurkovetskiy et al 2020 ). Additionally, the combination of Spike D614G and NSP12 P323L in all detected SARS-CoV-2 variants indicates the importance of these two mutations in terms of transmission and pathogenicity rate (Hartley et al 2020 ; Kannan et al 2020 ; Mutlu et al 2020 ). A study from Vietnam cases, which also found D614G and P323L as the most common mutations, suggests that there is a high probability of the European origin of viruses in their samples as these two mutations are highly dominant in European samples (Nguyen et al 2020 ).…”

Analysis of the SARS-CoV-2-host protein interaction network reveals new biology and drug candidates: focus on the spike surface glycoprotein and RNA polymerase

“…Importantly, SARS-CoV-2 NSP8 K58 could affect viral replication [ 100 ] and this amino acid is required to interact with the nascent RNA strand [ 89 ]. Moreover, Multu et al targeted the interaction between NSP8 and NSP12 by using computational structure-based models [ 101 ]. SARS-CoV-2 NSP12 mutations (A97V, A185V, I201L, P323L, L329I A466V and V880I) were detected in different patients [ 102 ].…”