The rational design of acid ceramidase inhibitors

Abstract

Literature indicates a positive correlation between acid ceramidase expression and the severity of several forms of cancer, including melanoma. Furthermore, acid ceramidase inhibitors such as carmofur, the lead molecule in this study, have been shown to reduce malignant cell proliferation. Acid ceramidase is thus a potential target for the treatment of melanoma using in silico drug design techniques. This project aimed to probe the acid ceramidase enzyme and identify possible interactions that can result in the elucidation of a database of potential drugs that can be used to inhibit its action. PDB crystallographic deposition 2ZXC2 describing the holo- acid ceramidase:endogenous ceramide small molecule complex in situ was used as a template. The apo- form of the protein was modelled and a 3D model of carmofur was docked into it. Conformational analysis was performed, and the optimal conformer was used to generate a consensus pharmacophore with the bioactive ceramide molecule. This pharmacophore was used to query an online molecular database and a list of hit molecules was generated. These molecules were screened for Lipinski Rule compliance and ranked based on their affinity. Following virtual screening, de novo drug design was performed. Seed structures were generated based on the interactions elicited by carmofur in the Acid ceramidase enzyme. These were inserted into the target enzyme and “grown” in order to fully explore the available space within the protein. Non-viable seeds, such as seeds which “bump” when grown, were discarded. Resultant ligands were screened for Lipinski rule compliance. In total, 163 molecules were obtained from Virtual Screening following Lipinski Rule compliance screening. In addition, 4 potential lead molecules were obtained through de novo drug design. These molecules were suggested for optimisation. The molecules generated are likely to be orally bioactive due to Lipinski Rule compliance, thus are more viable candidates for drug development.