Revealing the atomistic details behind the binding of B7-1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study

Background: CD28 and CTLA-4 are homologous T-cell receptors that bind with B7-1 and produce two opposing immunological signals required for T-cell activation and inactivation, respectively. It has been clinically proven that specific blockade of these key protein-protein interactions at the synapse can offer immunotherapeutic benefits for cancers and autoimmune treatments. Hence, there is a growing interest towards developing anti-CD28 and anti-CTLA-4 small molecule inhibitors. To achieve this goal, it is important to understand unique molecular level fingerprint interactions that stabilize CTLA-4/B7-1 and CD28/B7-1 complexes. However, until recently, the structure of the human CD28/B7-1 complex has not been resolved experimentally, which remains a significant setback in achieving specific inhibitors against CTLA-4 or CD28. Methods: Here, we employed a combination of advanced molecular modelling and extensive molecular dynamics (MD) simulations to model the CD28/B7-1 complex and characterize the key interactions that stabilize the complex. Results: Ensemble protein-protein docking and MD-based binding-free energy calculations were used to obtain a comprehensive structural model of the CD28/B7-1 complex, which was validated with various mutation-based experimental data from literature. Our CD28/B7-1 model has much weaker binding affinity than the CTLA-4/B7-1 complex, which is in agreement with the results from our binding assay experiments and previous studies. Conclusions: Per-residue energy decomposition of the binding affinities of the two complexes revealed the unique fingerprint hot-spot sites in CTLA-4/B7-1 and CD28/B7-1 complexes. General significance: The results presented in this work will, on a long-run, be useful to develop new generation of specific CD28 and CTLA-4 inhibitors for targeted immunotherapy.