Asymmetric and Dynamic Binding of Suramin Attenuates CXCL3 Chemokine-Mediated Cellular Transmigration

The growth-related oncogenic chemokine CXCL3 is an established biomarker of cervical cancer promoting metastatic cell migration and proliferation. Such activities are an outcome of the interaction of CXCL3 with its cognate GPCR receptor and ECM-associated glycosaminoglycans (GAGs) such as heparin. A heparin-analogous negatively charged polysulfonated drug, suramin, has displayed promising binding potential to chemokines on the surface overlapping with the known heparin binding site. Therefore, the flexible, symmetric, bivalent molecule─suramin─has been investigated for its binding potency against the oncogenic chemokine CXCL3. An integrated study comprising NMR, ITC, docking, consecutive molecular dynamics, PCA-free energy landscape analysis, DCCM, and correlative motion studies has been performed to understand the characteristics of CXCL3–suramin interactions and their underlying molecular mechanisms. The results suggested that the initial binding, led by the charged centers of suramin’s sulfonates and the positively charged Lys side chains from the helical interface of the dimeric CXCL3, has been found to be further stabilized by van der Waals interactions. Suramin anchors stably to the chain B helix at residues P57, Q60, I61, K64, K65, and K68 by one arm, while the other arm dynamically samples chain A residues (I61, K64, K65) and transiently accesses the interhelical groove resulting in an asymmetric, hemi-anchored, and dynamic binding pattern. Suramin binding fragments the apo three-basin energy landscape into five-basin conformationally separated bound-state minima and rewires the intersubunit dynamic coupling without disrupting the overall secondary structure of CXCL3. ITC analysis of single and triple Lys mutants corroborates the significance of K64 and reinstates the primary role of these Lys residues in the interaction, as observed from MMPBSA analysis. Considering the similar nature of suramin and heparin binding to CXCL3, suramin’s overlapping binding site with GAGs on CXCL3, and the fuzzy nature of one arm of suramin along with the redistribution of the conformational landscape upon suramin binding establishes suramin’s repurposing potential to target CXCL3-mediated cellular pathways assisting cancer cell migration.