The human immune system is very powerful and whose one function is to detect and eliminate foreign, pathogenic compounds that enter the body. The conventional major histocompatibility complexes (MHC) are able to bind peptides and present them to the T-cell lymphocytes thereby allowing the cell to communicate whether it is healthy or has been compromised. A different category of T-cell known as natural killer T (NKT) cells play an important role in bridging the innate and the adaptive immune systems, where NK cells and conventional T-cells exist, respectively. The innate immune response of these specific NKT cells has been associated with tumor rejection activities with the adaptive immune response being associated with protection against primarily bacterial infections, but also with viral and parasitic attacks.
These NKT cells are also unique in that their T-cell receptor (TCR) proteins recognize foreign glycolipid antigens, not peptides, presented by MHC-I like Cluster of Differentiation 1 (CD1) molecules. The marine-sponge derived glycolipid α-galactosylceramide (α-GalCer) has so far been the most potent iNKT stimulatory ligand when presented by the CD1d protein. It is more than unusual that an α-glycolipid derived from a marine sponge could yield such a massive immune response in humans, since it is doubtful that humans have evolved with a defense mechanism against a possible invasion of marine sponges. Currently, the glycosphingolipids from the alpha-proteobacteria Sphingomonas are considered the natural foreign ligands for the system since they were found to activate iNKT cells but to a lesser degree than α-GalCer.
The massive immune response cascade that follows after CD1d presentation of a glycolipid to iNKT cells has yielded a search for a better ligand with either comparable activity as α-GalCer but with less of its pharmaceutical hindrances or a ligand that can control the immune response. To date, superficial structure-activity relationships have been defined wherein modifications to either the sphingosine chain or acyl chain of the lipid can lead to a bias in the immune response, and modifications to the galactose sugar have led to null activity.
Herein, this scientific project entailed the use of computational means to determine how the TCR protein of iNKT cells can differentiate so selectively between glycolipids presented by the CD1d protein in order to be able to design a better ligand for the system. Molecular dynamics simulations using AMBER found the crystallized CD1d/α-GalCer/TCR tertiary complex to be stable and relatively rigid in explicit solvent. A combination of high-level docking with AUTODOCK and simulation showed that modifications to the 2´- and 3´- positions of the galactose sugar are indeed not tolerated, whereas, modifications to the 4´- position were semi-tolerated. The simulations of CD1d/glycolipid binary complexes showed that glycolipids incapable of stimulating iNKT cells changed the direction of the CD1d residues that interact with TCR away from optimum orientation. Lastly, the evidence of a non-glycolipid ligand activating iNKT cells led to an undertaking of a virtual screening program to find a replacement for the galactose sugar yielding a library of viable aromatic-based lipid ligands.