Investigating the molecular mechanism of selective inhibition of JAK1/TYK2 by SOCS1/SOCS3 using molecular dynamics...

Aberrant activation of the Janus kinase/Signal Transducer and Activator of Transcription (JAK/STAT) signaling pathway is associated with various pathological conditions. Suppressor of Cytokine Signaling (SOCS) proteins are able to inhibit this pathway by competitively binding to the STAT binding sites on JAK kinases (blocking the binding of STATs to JAK kinases). However, the mechanism of selective inhibition of JAK kinases by SOCSs remains poorly understood. Here, we performed microsecond-scale molecular dynamics (MD) simulations combined with molecular mechanics/generalized born surface area (MM/GBSA) binding free energy calculations, covariance analysis, and principal component analysis (PCA) to systematically compare the binding characteristics of six distinct JAK/SOCS complexes. The MM/GBSA results showed that the binding affinity of SOCS1/SOCS3 to JAK1/TYK2 is significantly stronger than that of SOCS2 to JAK1/TYK2. Correspondingly, PCA and covariance analysis revealed that SOCS2 and JAK1/TYK2 moved toward the opposite directions during the simulation. All these indicate that SOCS1/SOCS3 binds more stably to JAK1/TYK2 than SOCS2, implying that SOCS1/SOCS3 has a better inhibitory effect on JAK1/TYK2. Furthermore, the results of energy decomposition residues and hydrogen bond analysis illustrated that the strong binding ability of SOCS1/SOCS3 to JAK1/TYK2 is based on the presence of "Y", "QR", and "FF" motifs (missing in the SOCS2) in its KIR region and BC loop, which are able to form stable hydrogen bond networks and Met-aromatic interactions with the GQM motifs of JAK1/TYK2. This might be the fundamental reason why SOCS1/SOCS3 has a significantly stronger selective inhibitory effect on JAK1/TYK2 than SOCS2. Our work elucidates the dynamic structural basis of JAK/SOCS binding selectivity at the atomic level, providing new insights into the mechanism of JAK kinase selectivity and laying the foundation for the development of structure-based JAK1/TYK2-targeted cancer therapy drugs.