Structure Prediction of SPAK C-terminal Domain and Analysis of its Binding to RFXV/I Motifs by Homology Modelling, Docking and Molecular Dynamics Simulation Studies

Title:Structure Prediction of SPAK C-terminal Domain and Analysis of its Binding to RFXV/I Motifs by Homology Modelling, Docking and Molecular Dynamics Simulation Studies

Volume: 17 Issue: 5

Author(s): Mubarak A. Alamri*, Ahmed D. Alafnan, Obaid Afzal, Alhumaidi B. Alabbas and Safar M. Alqahtani

Affiliation:

• Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj- 11942,Saudi Arabia

Keywords: Docking, homology modelling, molecular dynamic simulation, OSR1, SPAK, WNK.

Abstract:

Background: The STE20/SPS1-related proline/alanine-rich kinase (SPAK) is a component of WNK-SPAK/OSR1 signaling pathway that plays an essential role in blood pressure regulation. The function of SPAK is mediated by its highly conserved C-terminal domain (CTD) that interacts with RFXV/I motifs of upstream activators, WNK kinases, and downstream substrate, cation- chloride cotransporters.

Objective: To determine and validate the three-dimensional structure of the CTD of SPAK and to study and analyze its interaction with the RFXV/I motifs.

Methods: A homology model of SPAK CTD was generated and validated through multiple approaches. The model was based on utilizing the OSR1 protein kinase as a template. This model was subjected to a 100 ns molecular dynamic (MD) simulation to evaluate its dynamic stability. The final equilibrated model was used to dock the RFQV-peptide derived from WNK4 into the primary pocket that was determined based on the homology sequence between human SPAK and OSR1 CTDs. The mechanism of interaction, conformational rearrangement and dynamic stability of the binding of RFQV-peptide to SPAK CTD were characterized by molecular docking and molecular dynamic simulation.

Results: The MD simulation suggested that the binding of RFQV induces a large conformational change due to the distribution of salt bridge within the loop regions. These results may help in understanding the relationship between the structure and function of SPAK CTD and to support the drug design of potential SPAK kinase inhibitors as antihypertensive agents.

Conclusion: This study provides deep insight into the SPAK CTD structure and function relationship.

Cite this article as:

Alamri A. Mubarak *, Alafnan D. Ahmed , Afzal Obaid , Alabbas B. Alhumaidi and Alqahtani M. Safar , Structure Prediction of SPAK C-terminal Domain and Analysis of its Binding to RFXV/I Motifs by Homology Modelling, Docking and Molecular Dynamics Simulation Studies, Current Computer-Aided Drug Design 2021; 17 (5) . https://dx.doi.org/10.2174/1573409916666200712140941