Classification of blocker and non-blocker of hERG potassium ion channel using a support vector machine

The human ether-a-go-go related gene （hERG） channel is responsible for the repolarization during the action potential, and blockage of that may result in severe cardiotoxicity and sudden death. In this study, a dataset containing 1969 compounds was compiled from literature and FDA-approved drugs. Using a support vector machine （SVM）, two groups of computational models were built to distinguish whether a compound is a blocker or non-blocker of hERG potassium ion channel. These mod- els fit generally satisfactory. The 100 models built with MACCS fingerprints （Model Group A） showed an average accuracy of 90% and an average matthews correlation coefficient （MCC） value of 0.77 on the test sets. The 100 models built with selected MOE descriptors （Model Group B） showed an average accuracy of 89% and an average MCC value of 0.74 on the test sets. Molecular hydrophobicity and lipophilicity were found to be very important factors which lead to block the hERG potassium ion channel. Some other molecular properties such as electrostatic properties, features based on van der Waals surface area, the number of rigid bonds and molecular surface rugosity also played important roles in blocking bERG potassium ion channel.

Regulation of cardiac hERG potassium channel by protein tyrosine phosphatase non-receptor type 12, 11 and 6

Background Long QT syndrome(LQTS)is a potentially fatal cardiac ion channel disease.Mutations in the gene encoding cardiac hERG potassium channel are the second most common causes of LQTS.Cardiac hERG potassium channel conducts the rapidly activating delayed rectifier potassium current(Ikr),which is one of the crucial currents in rapid repolarization phase of action potential in human cardiomyocytes.Function of hERG potassium channel is regulated by a variety of signaling pathways,in which phosphorylation and dephosphorylation of tyrosine proteins plays a major role.Previous research has found that non-receptor protein tyrosine phosphatase(PTPN)can interact with hERG potassium channel in cardiac cells.The aims of the present study were to investigate the regulatory effect of protein tyrosine phosphatase non-receptor type 12,11 and 6(PTPN12,PTPN11 and PTPN6)on cardiac hERG potassium channels.Methods HEK-293 cells were transfected with pcDNA3.0-hERG by Lipofectamine 2000 and selected by G418.HEK-293/hERG cells stably expressing hERG protein were then transfected with pcDNA3.1-PTPN12-RFP,pcDNA3.1-PTPN11-EGFP and pcDNA3.1-PTPN6-EGFP,respectively.Forty-eight hours after transfection,immunofluorescence assay and western blot were performed to detect the expression of hERG channel proteins and PTPN proteins.hERG channel currents in hERG alone-expressing group,PTPN12-,PTPN11-and PTPN6-overexpressing groups,as well as inhibitor groups were recorded by patch clamp technique.Results The maximum pulse current densities of PTPN12-,PTPN11-and PTPN6-overexpressing groups were all decreased when compared with hERG alone-expressing group(P<0.05).However,the maximum pulse current densities of inhibitor groups were all increased when compared with PTPN12-,PTPN11-and PTPN6-overexpressing groups,respectively(P<0.05).Conclusions Overexpression of PTPN12,PTPN11 and PTPN6 reduced the current density of hERG potassium channel,while this effect could be reversed by tyrosine phosphatase inhibitors.These results suggested that PTPN12,PTPN11 and PTPN6 negatively regulated hERG potassium channel currents by catalyzing the dephosphorylation process of hERG potassium channels.[S Chin J Cardiol 2021;22(1):38-49]