Screening Novel HIV-1 Protease Inhibitors Based On The Substrate Envelope Hypothesis

The aspartic proteinase encoded by human immunedeficiency virus type I (HIV-1), which is one of the key enzymes during the HIV-1 duplication, is a significant target enzyme in the anti-HIV/AIDS drug research. During HIV-1 replication, gag and gag-pol gene products are translated into precursor polyproteins and these polyproteins are cleaved and processed by HIV-1 protease into a serial of structural proteins (p17, p24, p7, p6, p2 and p1) and essential functional proteins (protease, reverse transcriptase, RNase H and integrase). All of these proteins are necessary to the HIV-1 provirus particles to produce mature infectious particles. HIV-1 protease inhibitors principally target HIV-1 protease and inhibit its activities to make HIV-1 produce immature and non-infectious particles in the infectious cell, then HIV can not assemble itself normally and will be inhibited. Therefore, the design of HIV-1 protease inhibitors was and will always be the hotspot in the area of anti-AIDS durg research. Now, there are 10 HIV-1 protease inhibitors going on the market authorized by American Food and Drug Administration. They are saquinavir (SQV), ritonavir (RTV), indinavir (IDV), nelfinavir (NFV), amprenavir (APV), 1opinavir (LPV), atazanavir (ATV), fosamprenavir, tipranavir (TPV) and Darunavir (DRV). Most of these inhibitors are pseudo-peptides drugs with great disadvantage, low bioavailability, heavy adverse reaction, and so on. In these drawbacks, the influence from HIV-1 protease mutation is especially worst, because the virus can emerge resistance and mutli-drug cross resistance, and then the marketed inhibitors can not inhibit HIV-1 effectively. A great many personnel and financial were threw into the anti-AIDS drug research, and how to develope a high performance, anti-drug resistance nonpeptidic inhibitor is the hotspot and difficulty in the research area of HIV-1 protease inhibitors.From the first HIV-1 protease crystal structure which was resolved in 1989, there are over 350 HIV-1 protease and protease-ligand complex structures included in protein data bank (PDB). These structures contain much information about the interaction between HIV-1 protease and its inhibitors, and these interaction informations serve as good foundation of the drug design based on HIV-1 protease structure and substrate structure. In face of drug resistance and multidrut cross resistance resulted from HIV-1 protease mutations, Chellappan et al concluded three pathways to combat mutation resistance in their fight work towards HIV. One approach is to seek inhibitors that bind wild-type HIV-1 protease so tightly that the losses in affinity produced by mutated protease can be tolerated. Another approach is to devise inhibitors with asymmetric, flexible chemical groups that can adapt conformationally to form stable interactions with both wild-type and mutant protease. The third approach is to design inhibitors based on substrate envelope hypothesis to inhibit HIV-1 while the inhibition activities can retain with no or low influence from protease mutation. Darunavir is the first anti-drug-resistance HIV-1 protease inhibitor, which was developed to enhance the binding affinity of the ligand to the protease. The substrate envelope hypothesis which was applied to design anti-HIV-1 drugs is based on the potential relationship between the van der waals surface of drugs and the location of HIV-1 protease mutations.These approachs are indeedly feasible ways to research and develop high performance, anti-drug resistance nonpeptidic HIV-1 protease inhibitors.This work was based on the substrate envelope hypothesis. In order to enhance the binding affinity of ligand, the active conformation and the cross-reaction information of anti-resistance HIV-1 protease inhibitor darunavir were used to constructed a novel pharmacophore model. With the utilization of hybrid method taking advantage of the synergistic effects of structure-based and ligand-based drug design techniques, such as pharmacophore model-based database searching, molecular docking and molecular dynamics simulation, a new HIV-1 protease inhibitor with novel structure was found in the Traditional Chinese Medicine Database.Objective: Based on the Substrate Envelope Hypothesis and With the utilization of hybrid method taking advantage of the synergistic effects of structure-based and ligand-based drug design techniques, a compound of novel structure that not only bind well with the HIV-1 protease, but also fit well within the substrate envelope, was found in the Traditional Chinese Medicine Database.Methods: Based on the Substrate Envelope Hypothesis and the available HIV-1 protease inhibitor darunavir, a new pharmacophore model of HIV-1 protease inhibitors was constructed, and applied to the Traditional Chinese Medicine Database searching. This method has higher direction.Through molecular docking, post-screening compounds were investigated further in their binding conditions with HIV-1 protease and their consistences with substrate envelope, and three compounds were selected as the candidate. They are anomonicin, cannabidiolic acid and desacetylbufotalin. Molecular dynamics simulation was applied to simulate these three compounds complexes with HIV-1 protease in explicit water, the structure stability of the complexes during the dynamics simulation was investigated and their potential energies and binding free energies were calculated. Through final evaluation of the screening results, compound anomonicin was worthy of further research.Results: Based on the active conformation and the cross-reaction information of anti-resistance HIV-1 protease inhibitor darunavir, a novel pharmacophore model was constructed. Through the Traditional Chinese Medicine Database searching based on the constructed pharmacophore model, 113 compounds were screened. With the use of molecular docking 3 compounds was selected, and compound anomonicin was worthy of further research by final evaluation of the screening results.Conclusion:1 Based on the substrate hypothesis and improving the binding affinity between drugs and receptor, anti-drug-resistance inhibitor Darunavir was selected as the templates to directly construct pharmacophore model, and the constructed model was applied to screening databases. This design method is more reasonable and has even higher direction.2 Through theory research and analysis, compound anomonicin was worthy of further research.3 Databases screening method was applied to screening the Traditional Chinese Medicine Database which was made up with compounds from traditional Chinese medicine. The screening compounds which generally possess novel structure, were expected to have the ability to breakthrough the single structure limitation of existing polypeptide drugs.