Virtual Screening Of HIV RNase H Inhibitors And Dual Inhibitors Against RNase H And Integrase From Traditional Chinese Medicines Chemical Components Database

Human immunodeficiency virus (HIV) is the pathogen which provokesthe acquired immunodeficiency syndrome (AIDS). AIDS is an infectiousdisease which terribly damages human immune system. Since1981when thefirst AIDS was discovered, over200countries and districts have discoveredAIDS cases, which have caused huge damage.The replication circle of HIV has several stages, and some criticalenzymes are used as targets for drug design. Till now, five inhibitors on themarket are widely applied in clinical therapy, that is nucleoside reversetranscriptase inhibitors, non-nucleoside reverse transcriptase inhibitors,protease inhibitors, integrase inhibitors and fusion inhibitors. Although thesedrugs play an important large role in anti-AIDS therapy, drug resistance strainsemerged and have kept growing. Therefore, there’s an urgent demand fordeveloping new anti-HIV drugs. At present, the research on anti-HIV agentshas been carried out in two ways: one is basing on known targets, the other isbasing on new targets or new mechanism.HIV-1Ribonuclease H (RNase H), which is one of catalytic domains ofthe reverse transcriptase (RT) with unique enzyme function, can be used as anindependent target for drug design. Till now, there are no inhibitors of RNaseH on the market. Most of RNase H inhibitors are chemical synthetic inhibitors,such as diketo acid, naphthyl hydrazone, pyrimidinol carboxylic acid andnitro-furan, etc. Only a few RNase H inhibitors come from components oftraditional Chinese medicines (TCM), such as emodin, galloyl, etc.Clinical practices have demostrated that drugs against one target ofcomplex disease hardly have good effects, and multi-targets drugs havebecome a hot spot for anti-HIV drug design. Besides, HIV-1RNase H and HIV-1integrase (IN) share strikingly structural similarity, and multi-targetsdrugs against RNase H and IN should be paid attention. Structure homology ofHIV-1IN and virtual screening of HIV IN inhibitors were performed inour laboratory, which set a basis for discovering dual inhibitors againstRNase H/IN.Our country has plentiful natural resources of TCM, and using TCMto treat AIDS is distinctive. Rich clinical practice and experiment data inprescriptions, single Chinese herbs, effective components anti HIV andtreat AIDS are accumulated. We investigated and sorted out the anti-AIDSTCM prescriptions which appeared in clinical or laboratory studies at homeand abroad and calculated the frequencies of usage of single Chinese herbsfrom the anti-AIDS TCM prescriptions. Then we collected the chemicalcomponents of the frequently used single Chinese herbs and other anti-HIVchemical components from other single Chinese herbs. Based on these, webuild a database named anti-HIV traditional Chinese medicines componentsdatabase (anti-HIVTCMCD) which mainly focuses on the information abouttheir structures and activities. This research makes full use of the structures ofHIV-1RNase H and its inhibitors in the biological information database andchemical information database, and we use molecular simulation andcomputer-aided drug design methods to build pharmacophore model anddocking pocket. Based on pharmacophore model and docking pocket wescreened TCMD which we have purchased and anti-HIVTCMCD which wasbuilt by ourselves, and we discovered some new RNase H inhibitors, then wedocked these inhibitors into IN catalytic domain using the IN docking model,and discovered some dual inhibitors against RNase H and IN, and revealed themechanism on molecular level. Our work will make a contribution to thedevelopment of anti-HIV drugs and multi-targets drugs from traditionalChinese medicine.Objective: To investigate the characteristics and laws of anti-AIDS TCMprescriptions, through collecting the anti-AIDS TCM prescriptions whichappeared in clinical or laboratory studies at home and abroad; build anti-HIVTCMCD; to screen new RNase H inhibitors, IN inhibitors and RNaseH/IN dual inhibitors from TCMD and anti-HIVTCMCD by molecularsimulation and computer-aided drug design, based on known crystal structuresof RNase H and its inhibitors, and set a foundation for the development ofnatural anti-HIV drugs and anti-HIV multi-targets drugs.Methods:1We calculated the frequencies of usage of single Chinese herbs fromanti-AIDS TCM prescriptions which appeared in clinical or laboratorystudies at home and abroad, and then investigated the characteristics andlaws of anti-AIDS TCM prescriptions.2Use molecular simulation software to build Anti-HIVTCMCD.3Use molecular simulation and pharmacophore recognition method tobuild a new pharmacophore model and protein active site model forHIV-1RNase H, based on the available HIV-1RNase H and itsinhibitors.4Screened TCMD and anti-HIVTCMCD for new potential RNase Hinhibitors, IN inhibitors and RNase H/IN dual inhibitors, based onpharmacophore model and molecular docking technique.5Use molecular docking to explore the binding modes of inhibitors toenzyme, reveal their mechanisms on molecular level, and explicit how tomodify the structure of inhibitors.6Use quantitative structure-activity relationship research methods to builda quantitative structure-activity relationship model for RNase H.Results:1We collected149anti-AIDS TCM prescriptions which appeared inclinical or laboratory studies at home and abroad, and selected77anti-AIDS TCM prescriptions. Among them,44prescriptions haveantiviral activity, and33prescriptions can strengthen the immune systemand relieve the symptoms. Then we calculated the frequencies of usage ofsingle Chinese herbs. The top ten frequently used single Chinese herbsare Glycyrrhizae, Leguminosae, Scutellaria baicalensis, Panax ginseng, Lonicera japonica, Savia miltiorrhiza, Radix bupleuri, Angelica,Hedyotis diffusa and Viola philippica car. All of these single Chineseherbs had been found to exhibit anti-HIV activities except Panax ginsengand Angelica.2Build anti-HIVTCMCD from chemical components collected from thefrequently used single Chinese herbs in anti-AIDS TCM prescriptionsand chemical components which have anti-HIV activities. Now we havecollect components from Leguminosae (98), Scutellaria baicalensis (80),Glycyrrhizae (258), Lonicera japonica (155), and the databse have591chemical components.3Based on the crystal structure of HIV-1RNase H and three pyrimidinolcarboxylic acid inhibitors, a4-feature pharmacophore model for RNase Hinhibitors and RNase H protein active site model were built throughmolecular simulation and pharmacophore recognition method. Thepharmacophore model has three hydrogen bond acceptors and onearomatic center.4Three inhibitors were docked into RNase H protein active site model, andthe results showed that the scoring fit with the activity, so it suggestedthat the docking pocket is a rational model.5We screened the TCMD by a series of computational simulation methods,such as pharmacophore modeling, docking, and obtained new potentialinhibitors of multiple structures. Among them, the flavonoids account forthe largest proportion and fit best to the RNase H active site. Then wedocked the potential inhibitors into the HIV-1IN catalytic domain anddiscovered some potential dual inhibitors against both HIV-1RNase Hand IN, such as flavones, terpenoids, alkaloids, etc. The flavonoids alsooccupy the largest proportion, but this class has different binding modesto HIV-1RNase H and IN. The highest-scored inhibitor terpenoids T-1can inhibit hepatitis B virus, and is a potential dual inhibitor, which isworthwhile for further study.6Through screening the anti-HIVTCMCD based on RNase H protein active site model, some potential inhibitors were obtained. Among them,baicalein and baicalin had been proven to inhibit HIV-1RT, and thisresearch revealed how baicalein and baicalin inhibit RNase H of reversetranscriptaseon on molecular level. Then we screened TCMCD using INprotein active site model, and obtained some dual inhibitors againstRNase H/IN. Baicalein from Scutellaria baicalensis had showninhibitory activities against both HIV-1reverse transcriptase and INactivity in vitro, and this research revealed that baicalein binds toHIV-1RNase H region in reverse transcriptase and the hydrophobicregion of HIV-1IN on molecular level.7A2D-QSAR model was built through2D quantitative structure-activityrelationships research (QSAR), and the model showed hydrogen bondacceptor atoms had the most impact on the inhibitory activity.Conclusion:1Through calculating the frequencies of usage of single Chinese herbs, wediscovered that anti-AIDS traditional Chinese medical prescriptions aremainly composed of single Chinese herbs which have anti-HIV activities.2Docking results of three inhibitors into RNase H protein active site modelverified the rationality of the RNase H protein active site model.3The potential RNase H inhibitors, IN inhibitors and RNase H/IN dualinhibitors obtained from TCMD and anti-HIVTCMCD demonstrated thatthese inhibitors may be the main components of anti-HIV TCM foranti-HIV activity, and this research revealed their targets and mechanismson molecular level.4Terpenoids T-1obtained from TCMD which can inhibit hepatitisB virusis a potential dual inhibitor against both HIV-1RNase H and IN, which isworthwhile for further study.5Baicalein and baicalin obtained from HIVTCMCD were proven to haveinhibitory activities, which verified the rationality of the pharmacophoremodel used in virtual screening and the target protein active site model.6New RNase H inhibitors, IN inhibitors and RNase H/IN dual inhibitors screened from TCMD and anti-HIVTCMCD include flavones, terpenoids,alkaloids, etc. Among them, the flavonoids account for the largestproportion and fit best to the target. Therefore, flavonoids may be themain components of anti-HIV TCM for anti-HIV activity. These resultswill set a foundation for the development of new anti-HIV drugs andanti-HIV multi-targets drugs, new anti-HIV TCM prescriptions andmodernization of anti-HIV TCM.