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

Muhammad Suleman; Iqra Ishaq; Haji Khan; Safir Ullah Khan; Rehana Masood; Norah A Albekairi; Abdulrahman Alshammari; Sergio Crovella

doi:10.3389/fchem.2023.1346796

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

Front Chem. 2024 Jan 16:11:1346796. doi: 10.3389/fchem.2023.1346796. eCollection 2023.

Authors

Affiliations

¹ Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar.
² Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
³ Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
⁴ Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan.
⁵ Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.

^# Contributed equally.

Abstract

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.

Keywords: MD simulation; NSP6; SARS-CoV-2; TBK1; molecular docking.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Qatar University grant No. QUPD‐CAS‐23‐24‐491.