Molecular Modeling And Drug Design Based On HIV-1 Related Proteins

Acquired Immune Deficiency Syndrome（AIDS）is the global infectious disease,whose causitive agent is Human Immunodeficiency Virus（HIV）,threating the health of human body.The drug design based on related proteins of HIV-1 has become a research hotspot in anti-AIDS drug development.HIV-1 related proteins include reverse transcriptase（RT）,integrase（IN）and protease（PR）etc.,playing important roles in viral life cycle.Therefore,the study on the interactions between drugs and the three enzymes is of great significance for anti-AIDS drug development.In this paper,the three key proteins were adopted to explore the following four scientific issues using computer aided drug design（CADD）method: molecular recognition between saquinavir（SQV）and HIV-1 protease（PR）;functional movement of HIV-1 reverse transcriptase（RT）;the validation of both vitual screening platform and molecular recognition of HIV-1 integrase（IN）inhibitors;the expression and purification of HIV-1 IN in the Escherichia coli.（1）Molecular recognition mechanism between SQV and PR was investigated via molecular dynamics（MD）simulation.Meanwhile,the hydrogen bonds of SQV with PR and the contribution of key residues of SQV to the recognition both were calculated.The results show that the computed value of B-factor has an obviouscorrelation with the experimental one,and hydrogen bonds formed by SQV and Asp25’,Asp25 may be the driving force to its recognition.In addition,Gly49’,Gly27’,Pro81 and Asp29’ residues all contribute a lot to the binding with SQV.（2）The motion characteristics of each functional region in RT was analyzed using the coarse-grained model,with the complex models being generated by molecular docking method.The results show that opening-closing movement of finger and RNase H regions is the major functional motion of RT,which favors the enzyme to exert its biological function.It is aloso found that the trans double bond is the preferential conformation of NAD compounds during the recognition with RT.（3）The effectiveness of PFV IN-DNA system as a new vitual screening platform of IN inhibitors was discussed through protein sequence alignment,vitual screening and bingding free energy calculation.Firstly,the recognition between IN and NRD compound with high activity was explored by MD simulation and conformation analysis.Simulation results indicate that the 40.8% sequence similarity between HIV-1 IN and PFV IN,high efficiency of virtual screening,and the good correlation between calculated binding free energy and experimented p IC50 values,all confirmed that PFV IN-DNA is a potential reliable template for virtual screening of HIV-1 IN inhibitors.Then,molecular recognition suggests that DTG could be divided into hydrophobic and hydrophilic parts.Mg²⁺ ions,water molecules and conserved residues all interacted with the hydrophilic partition,while the bases in viral DNA and residues like Tyr212,Pro214 interacted with the hydrophobic one.Finally,the reduction of motion amplitude in the IN-DNA system may be one of the inhibition mechanism of IN inhibitors after the conformational motion analysis.（4）The recombinant plasmid of p ET28a-IN with F185K/ C280 S double mutation was transferred into E.coli cells,then the expressed IN protein was purified and separated using SDS-PAGE.The results show that IN protein mainly stays in liquid supernatant of cell lysate after affinity chromatography,which suggests that the reliable preparation and purification of HIV-1 IN was established.