KSEF RDE: Inhibition of the mammalian glycoprotein YKL-40: Identification of the physiological ligand

YKL--]40 is a mammalian glycoprotein that has been implicated as a biomarker associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Though the association of YKL--]40 with physical maladies is well--]known, both the function and conclusive identification of the physiological ligand of this lectin remains elusive. Speculation as to its function varies from both inhibiting and antagonizing collagen fibril formation as a result of injury or disease, as well as inferring drug resistance and increasing cell migration leading to progression of cancer, and protection from chitin--] containing pathogens. Understanding the mechanism and affinity for which YKL--]40 binds known ligands will lead to identification of therapeutic molecules as alternative binding ligands for inactivation. In vitro binding affinity studies have identified insoluble chitin as a preferred ligand; however, the presence of chitin in the human body has not yet been documented. It is likely that a closely related oligosaccharide plays the role of the physiological ligand due to their presence in the extracellular matrix. Using molecular modeling, we will address the question of which of the proposed physiological ligands is more likely based on relative binding affinity to chitin. Glucose, along with the glycosaminoglycans hyaluronic acid, heparin sulfate, and chondroitin sulfate, will be evaluated using thermodynamic integration to measure the relative change in binding free energy by alchemically transforming the chitin ligand known from the crystal structure into the target ligand. To gain insight into the binding affinity of potential protein ligands such as Type I collagen, we will employ advanced sampling free energy methods to arrive at absolute binding free energies of chitin and Type I collagen. These techniques will provide us with a quantitative measure of ligand preference for YKL--]40, which will serve as the basis for experimental therapeutic drug development. Key words: chitinase, glycosoaminoglycans, carbohydrates, glioma, inflammatory disease Areas of expertise: Molecular modeling, glycoside hydrolases, free energy, protein--]ligand interactions, structure--]function relationships