Virtual Screening On B-Raf(V600E) Kinase ?B Inhibitors

Objective:B-Raf?V600E?kinase is currently one of the most attractive antitumor targets.Types of its inhibitors have ?,?A and ?B,and the ?B inhibitor becomes development hot spot because it has the advantages of specific inhibition and low toxicity.In recent years,a number of ? B inhibitors were synthesized,and Zelboraf?PLX4032?has been successfully listed.ft is still very necessary to develop a variety of novel ? B inhibitors because the drugs in use are easy to produce drug resistance.To provide an important research foundation for the development of novel anticancer drugs,this paper,by using computer aided drug design?CADD?technology,screens many kinds of lead compounds of B-Raf?V600E?kinase ? B inhibitors,which synthesise easyly and have different skeleton,from NCI2000 non-commercial database and ZINC commercial database.Methods:First of all,the studies on pharmacophore modeling and 3D-QSAR modeling are carried out for the selected B-Raf?V600E?kinase ? B inhibitors.Secondly,a combination of the best pharmacophore model,molecular docking method and the best 3D-QSAR model is used to screen the NCI2000 non-commercial database for obtaining B-Raf?V600E?kinase ? B inhibitors.And a combination of the best pharmacophore model,molecular docking method?binding free energy?AGbind?calculation and the best 3D-QSAR model is used to screen the ZINC commercial database for obtaining B-Raf?V600E?kinase ?B inhibitors.Finally,the biological activities of the best B-Raf?V600E?kinase ? B inhibitors hit compounds screened from ZINC commercial database are tested.Results:The pharmacophore model of B-Raf?V600E?kinase ?B inhibitor is established by GALAHAD and determined that the best model was Model 10.Characteristic elements of the Model 10 include three acceptor atoms?AA?,two donor atoms?DA?and two hydrophobes?HY?.The results that 3D-QSAR model is built on the basis of both ligand and receptor are:CoMFA model based on the common skeleton alignment:q2?r2cv?=0.585,r2ncv=0.966,r2pred=0.544,and CoMSIA model based on the common skeleton alignment:q2?r2cv?=0.539,r2ncv=0.732,r2pred=0.707;CoMFA model based on the pharmacophore alignment:q2?r2cv?=0.442,r2 ncv=1,r2 pred=0.425,and CoMSIA model based on the pharmacophore alignment:q2?r2cv?=0.406,r2ncv=0.996,r2pred=0.408;CoMFA model based on the docking alignment:q2?r2cv?=0.542,r2 ncv=0.987,r2pred=0.001,and CoMSIA model based on the docking alignment:q2?r2cv?=0.308,r2ncv=0.919;r2pred=0.081;By virtual screening of NCI2000 non-commercial database,we obtain 10 best hit compounds that the pICso prediction values of CoMFA and CoMSIA models are all greater than 8.60.At the same time,by virtual screening of ZINC commercial database,we obtain 5 hit compounds that have the lowest AGbind.The biological activities of 5 best hit compounds screened from ZINC commercial database are tested.The results are as follows:when the concentration is 1000 ?M,three hit compounds have an inhibition rate of 98%,and two have an inhibition rate of 97%.Conclusion:Model₁0 will be utilized to the subsequent construction of CoMFA and CoMSIA models and research of virtual screening.CoMFA and CoMSIA models based on the common skeleton alignment and pharmacophore alignment have good robustness and predictive ability.Analysing the three-dimensional isopotential map of CoMFA and CoMSIA models based on the pharmacophore alignment shows that increasing the volume of the group on the pyrimidine ring and reducing the electronegativity of the group on the benzene ring can improve the activity of compounds.Amino?-NH2?and imino group?-NH?in the molecule are hydrogen bond donor groups,carbonyl?>C=O?and sulfonyl?-SO2-?are hydrogen bond receptor groups,which play an important role in the activity of compounds.The nitrogen atoms in the pyridine ring are adverse to the activity of the compounds.The best hit compounds that obtained through the virtual screening of NCI2000 non-commercial database and ZINC commercial database have high activity and a big difference in structure.It is demonstrated by the activity experiment that our virtual screening method is feasible.At the same time,the above 5 compounds can be as having novel structure B-Raf kinase?V600E?IIB inhibitors,and provide an important basis of research that develops the B-Raf?V600E?kinase IIB inhibitors having new framework.