Mutation-induced structural and dynamic perturbations at the IL-17A–IL-17RA interface: Therapeutic insights from multi-replicate molecular dynamics simulations

The interaction between Interleukin-17A (IL-17A) and its receptor IL-17RA plays a key role in pro-inflammatory signal transduction and is implicated in the pathogenesis of inflammatory autoimmune diseases. Blocking this protein-protein interaction is a major approach to developing therapeutic agents to inhibit IL-17A-induced signaling. Predicting the consequences of mutations on structure and function in proteins can be accomplished by using computational methods, which are relatively inexpensive and rapid compared with experimental methods. Here, we used a multidimensional in silico approach to gain insight into the functional and thermodynamic consequences of targeted mutation of hotspot residues of IL-17A. The focus of our analysis was on the residues in the two chains that are equivalent to hotspot residues of the related cytokine, IL-17F, at positions 55 and 67 of chain B and 85 and 86 of chain A. Comprehensive analysis of the conformational dynamics, interaction profiles, and structural transitions of the four mutant variant systems (R55V, W67V, Y85I, and H86S) and the wild-type system was performed based on molecular dynamics (MD) simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations. A total of 3 μs simulations were performed: three 200 ns replicates for each of the wild-type and mutant complexes. Results from principal component analysis (PCA) and free energy landscape (FEL) analyses indicate conformational destabilization of the mutant systems. These findings help to elucidate the mechanisms of molecular interactions involved in the dynamics of cytokine–receptor interaction. Changes in these important PSN network parameters resulted in differences in hub connectivity and distribution of the links between the systems, which suggests allosteric perturbations and remodeling of the system in the interaction between IL-17A and IL-17RA when compared to the wild-type systems. The multiple-replica MD simulation protocol provided insight into how mutations affected the structure, contact networks, dynamics, and binding affinity of the IL-17A/IL-17RA complex, shedding light on the IL-17A downstream signaling cascades. Overall, this study provides a fundamental framework for designing therapeutic strategies to regulate IL-17A-mediated inflammatory diseases.