Comparative mutational analysis of the Zika virus genome from different geographical locations and its effect on the efficacy of Zika virus-specific neutralizing antibodies

Aziz, Abdul; Suleman, Muhammad; Shah, Abdullah; Ullah, Ata; Rashid, Farooq; Khan, Sikandar G.; Iqbal, Arshad; Luo, Sisi; Xie, Liji; Xie, Zhixun

doi:10.3389/fmicb.2023.1098323

Cited by 2 publications

(1 citation statement)

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“…Mutation plays a crucial role in determining the pathogenicity of viruses as it directly affects their capacity to cause disease in a host organism. Compared to other organisms, viruses exhibit notably high mutation rates, leading to rapid evolution, which is a key factor in shaping their ability to cause disease ( Suleman et al, 2023b ; Aziz et al, 2023 ). To identify the newly emerged mutations in the NSP6 protein, the retrieved sequence was submitted to the GISAID database which is designed for sharing and analyzing genomic data of influenza viruses and other emerging infectious diseases.…”

Section: Resultsmentioning

confidence: 99%

Elucidating the binding mechanism of SARS-CoV-2 NSP6-TBK1 and structure-based designing of phytocompounds inhibitors for instigating the host immune response

Suleman,

Ishaq,

Khan

et al. 2024

Front. Chem.

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SARS-CoV-2, also referred to as severe acute respiratory syndrome coronavirus 2, is the virus responsible for causing COVID-19, an infectious disease that emerged in Wuhan, China, in December 2019. Among its crucial functions, NSP6 plays a vital role in evading the human immune system by directly interacting with a receptor called TANK-binding kinase (TBK1), leading to the suppression of IFNβ production. Consequently, in the present study we used the structural and biophysical approaches to analyze the effect of newly emerged mutations on the binding of NSP6 and TBK1. Among the identified mutations, four (F35G, L37F, L125F, and I162T) were found to significantly destabilize the structure of NSP6. Furthermore, the molecular docking analysis highlighted that the mutant NSP6 displayed its highest binding affinity with TBK1, exhibiting docking scores of −1436.2 for the wildtype and −1723.2, −1788.6, −1510.2, and −1551.7 for the F35G, L37F, L125F, and I162T mutants, respectively. This suggests the potential for an enhanced immune system evasion capability of NSP6. Particularly, the F35G mutation exhibited the strongest binding affinity, supported by a calculated binding free energy of −172.19 kcal/mol. To disrupt the binding between NSP6 and TBK1, we conducted virtual drug screening to develop a novel inhibitor derived from natural products. From this screening, we identified the top 5 hit compounds as the most promising candidates with a docking score of −6.59 kcal/mol, −6.52 kcal/mol, −6.32 kcal/mol, −6.22 kcal/mol, and −6.21 kcal/mol. The molecular dynamic simulation of top 3 hits further verified the dynamic stability of drugs-NSP6 complexes. In conclusion, this study provides valuable insight into the higher infectivity of the SARS-CoV-2 new variants and a strong rationale for the development of novel drugs against NSP6.

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Section: Resultsmentioning

confidence: 99%