Sphingomyelin Synthase Protein Structure Design, Discovery Of Small Molecule Inhibitors And Activity Evaluation

Sphingomyelin synthase (SMS) is an important enzyme in lipid metabolism and the last key enzyme in the sphingomyelin (SM) biosynthesis pathway. SMS utilizes ceramide and phosphatidylcholine (PC) as its substrates to produce SM and diacylglycerol (DAG). Ceramide and DAG are two important second messengers in signal conduction and cell apoptosis. Recent research has found that SMS is highly related with atherosclerosis. Many studies have indicated that inhibition of SMS can effectively reduce the symptom of atherosclerosis. Till now no selective SMS inhibitor is found. SMS is a good and potential drug target for antiatherosclerosis.To find the first generation SMS inhibitors, we chose human SMS1 (hSMSl) as the target to simulate its 3D structure. Highly 3D Structural topology was chosen as the key strategy to select template proteins for homology modeling. From the PDB database, we got Escherichia coli GlpG (PDB code 2IC8) as the template. Modeller in Discovery Studio 2.0 was used to build the models. For modeling the important extracellular Loop 2, we chose highly homogeneous protein 1BWO as the template protein particularly. The molecular dynamics optimized SMS structure could explain the mechanism of the binding of the two natural ligands (PC and SM). This SMS structure was used to virtual screen the SPECS database. We used gold programming and then glide programming, to validate the hits. Considering the structural diversity, we manually selected the 93 highly score compounds from more than two hundred hits.In our SMS assay experiments, we tested the SMS activities of 93 compounds, and found two active leads, compound 34 and compound 72. After structural similarity searching of the compound 34, we got compounds 104,105 and 107. The results of SMS inhibitory assay in synthesized compounds showed that the compounds 104 and 105 were inhibitory active. Compound 72 gotten from SPECS database was proved as a mixture of some active components with unknown structure. From which, we have separated two active components. Besides, we found an active SMS agonist. Moreover, we designed seventeen analogous of natural substrates by structural modification and found four active compounds. Preliminary structural-activity relationship was gotten.MS-209 was considered as a SMS inhibitor in the literature. But the results of our SMS assay results showed that MS-209 was not a SMS inhibitor.