Interactions of domain antibody (dAbκ11) with Mycobacterium tuberculosis Ac₂SGL in complex with CD1b

Tuberculosis (TB) is the main cause of mortality among all infectious diseases. The presentation of lipids by CD1b molecules and the interactions of the CD1b-lipid complexes with the immune receptors are important for the understanding of the immune response to Mycobacterium tuberculosis (Mtb), and to develop TB control methods. A specific domain antibody (dAbk11) recognizing the complex of CD1b with Mtb sulphoglycolipid (Ac₂SGL) had been previously developed. In order to study the interactions of dAbk11 with Ac₂SGL:CD1b, the conformation of Ac₂SGL within CD1b was first modelled. The orientation of dAbκ11 with Ac₂SGL:CD1b was then predicted by a docking experiment and the complex was sampled using molecular dynamics simulation. Data showed that dAbκ11 Tyr32 O_H plays a decisive role in interacting with Ac₂SGL alkyl tail H_O17. The binding free energy calculation showed that Ac₂SGL establish strong hydrophobic interactions with dAbκ11. The model also predicted a higher affinity for the natural sulfoglycolipid (Ac₂SGL) than the synthetic analogue (SGL12), which was supported by the ELISA data. These results shed light on the likely mechanism of interactions between Ac₂SGL:CD1b and dAbκ11, thus making possible to envision the strategies for dAbκ11 optimization for possible future applications.