Study On Drug Pockets And Regulation Mechanism Of Human Kinase Complexes

Kinases regulate cell cycle,transcription,and other biological processes by phosphorylating other proteins.Aberrant kinase activity will cause some diseases related to cell cycle and transcription,such as cancer,AIDS.On the one hand,more than 90%of the kinase inhibitors target the conserved catalytic pocket,which have more drug side effects.Recent studies have shown that the sequence,structure,kinetics and network characteristics of pocket can help identify specific non-catalytic pocket and its allosteric mechanisms to promote specific drug development and reduce drug side effects.On the other hand,research on the pathogenic mechanism of kinase complexes at the molecular level is relatively scarce,which limits the further study on the pathogenic mechanism of kinase complexes.Aiming at the problem of drug pockets and regulatory mechanism of human kinase complexes,some methods such as the topology-based pocket class analysis,force topology network analysis,sequence conservation analysis,dynamic network correlation analysis,and molecular dynamics simulations are used to study the specificity of the non-catalytic pockets of human kinases,the non-catalytic TL pocket of cyclin-dependent kinase(CDK)and short peptide inhibitor screening,and the mechanism of CDK9/Cyclin T/Tat complex on the transcription-dependent HIV latency.The main contents and conclusion are summarized as follows:(1)Aiming at the problem of specific drug target discovery,a method based on rigid body topology and interaction network for systematic idenfication and quantitative analysis of kinase pocket specificity has been developed.This method first systematically identified 1985 pockets of 168 human kinases.Then,the specific drug pockets(targets)were determined by systematic clustering using the spetial location and structural topology information of the pockets.Finally,the key residues and allosteric mechanism of the pockets were revealed by sequence conservation analysis and residue-residue interaction network analysis.The results showed that 14 types of specific pocekts were identified.The key residues and allosteric mechanism of the specific pocekts were revealed by sequence conservation analysis and residue-residue interaction network analysis.The sequence,structure,key residues,allosteric mechanism of these specific pockets can promote the design,screening,and optimization of human kinase specific drugs,thereby reducing the side effects of drugs.(2)Aiming at the difficulty of accurately describing pocket information,the HKPocket,a human kinase pocket database,was established based on rigid body topology and interaction network.The information of 2936 pockets of 255 human kinase proteins were studied.The results showed that 91 types of pockets(1717 pockets)were identified.The sequence,structure,key residues,and druggability of these pockets were obtained by a method that developed by our research group to identify and quantitatively analyze the specificity of kinase pockets.HKPocket consists of seven modules,namely Home,Search,Visualization,Download,Links,Tutorial,and Contacts.The user can enter the information page of the given pocket through the search box.This work will help drug design,screening and optimization.(3)Aiming at the problem of specific drug screening,the non-catalytic TL pockets of CDKs were studied to screening potential specific inhibitors for the treatment of malaria by sequence conservation analysis and dynamic network correlation analysis.First,the TL pockets of human CDK2 protein and Plasmodium falciparum Pfmrk protein were compared using sequence conservation analysis,and the results showed that the two pockets have high specificity.Then,the effects of six short peptides targeting the TL pocket on the interaction of CDK2/Cyclin E and Pfmrk/Cyclin H interface were studied using dynamic network correlation analysis,so as to quantify the effects of the six short peptides on the activities of CDK2 and Pfmrk kinases.The results show that FAALA and RAALW peptides can inhibit the Pfmrk activity without affecting the CDK2 activity,and are potential specific inhibitors for the treatment of malaria.(4)Aiming at the lack of further research on the mechanism of HIV latency at the molecular level,the molecular dynamics simulations firstly were performed for the CDK9/Cyclin T/Tat complex structure in its native,P10S,W11R,and K12N mutant states.The interaction of CDK9/Cyclin T interfaces and the kinetics of CDK9's ATP pockets when CDK9/Cyclin T/Tat complex is in the four states are analyzed by interface angle calculation and dynamic network correlation analysis.The results show that,compared with the native state,the interaction of CDK9/Cyclin T interface in the P10S and W11R states becomes weaker,and the side chain orientation of residue K48 in the ATP pocket is similar to the inactive state;while the interaction of CDK9/Cyclin T interface in the K12N state becomes stronger,and the side chain orientation of residue K48 in the ATP pocket is similar to the active state.These simulation results are consistent with the experimental observations of HIV latency.Therefore,this study may help to better understand the mechanism of Tat for the transcription-dependent HIV latency.