Delineating Cell Plasticity Regulating Proteins With Computational Chemical Biology

Cell is the basic unit of life activity.Protein is the important performer of cell activity and plasticity.The regulating of cell plasticity at the molecular level is reflected as dynamic protein-protein interaction network.The coordinated linking of the networks and the physical and chemical nature of the interactions determine cell plasticity.To understand the highly dynamic and complex molecular processes that control cell function,synthetic small molecules that can manipulate intracellular macromolecules reversely and specifically are of great need.Computer-aided drug design can greatly reduce the cost of discovering active small molecules,to the affordable level of a common biology laboratory.Structure-based virtual screening is a group of commonly used methods in computer-aided drug design,which screens small molecule libraries in a database through calculating the binding of a small molecule to a protein with molecular docking,based on the resolved protein structure.A large number of protein complexes exist in mitosis.Small molecule inhibitors of protein-protein interactions can suppress the assembly of these complexes with high specificity,providing great help for the research of mitosis,and have the prospect of becoming anti-cancer drugs with low side effects.BUBR1 is an important protein of spindle assembly checkpoint(SAC).The TPR domain of BUBR1 binds to KNL1,and is important for its kinetochore localization and the function of SAC.Based on the crystal structure of BUBR1 TPR domain,two small molecule binding pockets were selected and used for virtual screening with Clean Leads library in ZINC database and NCI library.CENP-T-W-S-X is a heterotetrameric protein complex,which localizes to the inner kinetochore and links the outer kinetochore to the centromere.The core of CENP-T-W-S-X complex is structurally similar to the nucleosome and can wrap DNA.The homology model of human CENP-T-W-S-X complex was generated and optimized based on the crystal structure of chicken CENP-T-W-S-X complex as a template.The model was analyzed and used for choosing a binding pocket.The pocket is localized to the CENP-S-X dimer at the interface with CENP-T-W dimer.The crystal structures of human CENP-S-X were compared with the model,and one of the structures was chosen for virtual screening with MolPort library.After exploring the relationship between small molecule structure and the result of molecular docking during the virtual screening for BUBR1 TPR domain,a novel method combining structure-based virtual screening and similarity searching was developed and used for the virtual screening targeting CENP-S-X dimer and targeting LKB1 kinase.This method can dramatically increase the efficiency of virtual screening and can save at least 2/3 of computational resources.Another novel method was also developed to visualize the result of virtual screening.With the help of the software Cytoscape and the plugin ChemViz2,a chemical similarity network can be generated with the structure and score of each small molecule visualized on the network.This network can be used for either choosing small molecules or analyzing the course of virtual screening.Methods for protein structure preparation,homology modeling,binding pocket identification,downloading from ZINC database are also discussed.We are currently working on the cell biological phenotype analysis and biochemistry experiments,to verify the activity and selectivity of the selected small molecules.Atrophic gastritis is a process of chronic inflammation during the function degradation of the stomach mucosa,leading to loss of gastric glandular structures.The consequences of prolonged atrophic gastritis includes hypochlorhydria,achlorhydria,megaloblastic anemia,iron deficiency anaemia,intestinal metaplasia and gastric cancer.The discovery of novel targets or biomarkers of atrophic gastritis will greatly facilitate the research,therapy and diagnosis of the disease.A novel method combining 2D difference gel electrophoresis,mass spectrum,and functional association network was developed,which can be used for predicting novel targets or biomarkers based on only a dozen of gel spots.Either Cytoscape or GeneMANIA can be used for generating functional association networks.A strategy of choosing different data sets to deal with the uncertainty in mass spectrum identification is also discussed.Further clinical related,prospective experimental validation and retrospective pathological and epidemiological analysis will further improve the efficiency of diagnosis and treatment in precision medicine.