Me2Explorer: An Integrated Software For Chemical Space Analysis

Biologically Relevant Spectrum and Three-Dimensional Biologically Relevant Spectrum are two molecular descriptors proposed by our laboratory,which can be used in the virtual screening,QSAR analysis and prediction of physicochemical property,ADME/T property and potential biological activity.Due to the large amount of calculation,BRS and BRS-3D online network computing services are currently unable to be provided.Based on RDKit,this thesis develops an integrated software,Me2 Explorer,for chemical spatial visualization analysis,which provides localized computing services for BRS and BRS-3D.Me2 Explorer includes a total of 7 functional modules,including molecular spreadsheet module,molecular structure viewer module,compound property analysis module,compound similarity analysis module,compound maximum common substructure analysis module,chemical space visualization analysis module and the physicochemical property prediction module.(1)Molecular spreadsheet module.The molecule spreadsheet is the basis of the other6 functional modules,mainly used to display the relevant information of all molecules in the read-in file,including SMILES expressions,pre-calculated physicochemical property,etc.(2)Molecular structure viewer module.Click the SMILES expression of the compound in the molecular table to view the structure of the corresponding molecule in the structure box in real time.In addition,the structure of all read molecules can be viewed through the "Structure" function.Clicking on a specific compound in this function can further display the relevant information of the corresponding compound.(3)Analysis of molecule physicochemical property.Me2 Explorer provides a variety of methods for calculation and visual analysis of physicochemical property,which is convenient for users to enter the property distribution of molecules and to screen drug-like properties.(4)Molecular similarity analysis.Me2 Explorer software provides functions for similarity calculation and similarity cloud graph analysis.It can calculate the similarity between the target compound and all compounds in the Specs database,and present the results as a compound similarity cloud graph.The software also provides a threedimensional similarity analysis method,which realizes the comparison of the shape similarity between compounds,and is suitable for quickly screening out molecules with a three-dimensional shape similarity to the active compound.(5)The maximum common substructure analysis.Me2 Explorer supports the largest common substructure analysis function of compounds,and can visually display the common part between two molecular structures.(6)Visual analysis of chemical space.Me2 Explorer software also supports the visualization of compound space based on two-dimensional molecular descriptors and three-dimensional molecular descriptors.Among them,the former provides three optional molecular descriptors,BRS,MACCS fingerprints,and Morgan fingerprints.The multidimensional representation vector is performed by principal component analysis or tDistributed Stochastic Neighbor Embedding.Reduce the dimensionality so as to realize the function of chemical space visualization.The latter can show the distribution of different molecules in chemical space from the perspective of the three-dimensional characteristics of molecules.(7)Prediction of physicochemical property.Me2 Explorer has built-in a variety of BRS-based physicochemical property prediction models,which can achieve rapid prediction of various physical and chemical properties such as the lipid-water partition coefficient and blood-brain barrier permeability of the compound.In summary,Me2 Explorer supports localized calculations of BRS and BRS-3D,and provides a variety of methods for molecular similarity evaluation,physicochemical property evaluation,and chemical spatial visualization.At present,the above functions have been tested for multiple rounds,and they can be used normally and stably.In addition,Me2 Explorer software reserves an interface to facilitate the subsequent expansion of other analysis functions.