Molecular Design,Synthesis And 3D-QSAR Research Of 6-Naphthoyl Substituted HEPT Analogs And 6-Arylcarbonyl,6-(α-Cyanoarylmethyl) Substituted S-DABO Analogs As Nonnucleoside HIV-1 Reverse Transcriptase Inhibitors

Acquired immune deficiency syndrome (AIDS) is one of the infectious diseases, which is caused by human immunodeficiency virus (HIV). The virally encoded HIV-1 reverse transcriptase (RT) provides an important target for the development of anti-AIDS drugs. In the 20 years research on HIV reverse transcriptase inhibitors has achieved great success. Among the 22 FDA-approved anti-HIV drugs, 14 drugs belong to HIV RT inhibitors. Especially, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have gained a definitive and important place for their unique antiviral potency, high specificity and low toxicity. Along with the developments of molecular modeling, computer aided drug design (CADD), and X-ray crystal technique, NNRTIs were developed rapidly. In particular, HEPTs and DABOs were the most representative classes of NNRTIs and showed good prospect, which attracted us to stick to their further structural modification with the aim to find more potent NNRTIs.Recently, our group had successfully designed and synthesized a series of 6-naphthylmethyl and 6-naphthylthio substituted HEPT and DABO analogues as high potent HIV-1 inhibitors. Inspired by these promising results, we continued our work on the research of novel NNRTIs. However, few modifications of the aryl methylic carbon bound to C-6 of the pyrimidine ring have been reported so far. Therefore, there is still a need to focus on modifying the methene to exploit new NNRTIs.In this paper, we further studied the binding model of HEPTs against HIV-1 RT by using automated molecular docking method. Based on the docking results and our previous research in this field, we postulate that the replacement of the methene at position C-6 of HEPTs with a carbonyl group as an electron withdrawing substituent may be more beneficial to improve the anti-HIV activity. The previous studies of the structure-activity relationships (SAR) of HEPT based on the Hopkins postulation analogs indicated that the replacement of the phenyl moiety with a naphthyl group of C-6 position would be favorable for their anti-HIV-1 activities through a putative Ï€-stacking interaction between the ligand and the Tyr188 or Tyr181 of RT. On the other hand, the introduction of various substitutents to the N-1 position, such asalkyloxymethyl, substituted allyl, substituted 2-propyl, and so on, maybe more benefit to make hydrophobic interaction with the RT. Based on the above analysis, a series of 6-(1-naphthoyl) substituted novel HEPTs were designed.Since the structurally similarity of them, DABOs and HEPTs share similar chemical requirements for anti-HIV activity, thus, the structure-activity relationship (SAR) conclusions of HEPTs could further guide the new designs of 5-DABO analogues. Based on the Hopkins postulation and the docking results, we also designed a series of 6-arylcarbonyl substituted 5-DABO analogues. In addition, in order to decrease the rigidity of the title molecules, a cyano group was introduced to the aryl methylic carbon at C-6 position of the pyrimidine ring. So a new series of 6-(α-cyanoarylmethyl) or 6-arylcarbonyl substituted S-DABOs were designed, which were expected to be novel and potent inhibitors of NNRTIs, through a putative Ï€-stacking interaction between the electron-deficient aryl ring of the ligand and the electron-rich benzene ring of Tyr188 or Tyr181 of the RT.The synthesis of the two series of novel HEPT and DABO derivatives was carried out successfully. The required 5-alkyl-6-chIoro-2,4-dimethoxypyrimidines were synthesized from the corresponding trichloropyrimidines prepared by reaction of the appropriate barbituric acid derivatives with POCl₃. The resulting 5-alkyl-2,4,6-trichloropyrimidines were reacted with NaOMe to afford the 5-alkyl-6-chloro-2,4-dimethoxypyrimidines. And then reacted with 1-naphthylacetonitrile to afford the 5-alkyl-6-(l-naphthoyl)-2,4-pyrimidinediones, which were subjected to N-\ alkylation with various halids in the presence of K₂CO₃ in anhydrous DMF to afford the desirable HEPT target compounds.The 2-thiobarbituric acid derivatives were prepared by condensation of thiourea with the appropriate diethyl malonates in the presence of sodium methoxide in methanol at refluxing temperature. Subsequent S-alkylation with various alkyl halides in the presence of sodium hydroxide gave the corresponding 5-alkyl-2-alkylthiobarbituric acids respectively. Treatment with p-toluenesulfonyl chloride afforded the disulfonates, which were reacted with various aryl acetonitriles and then hydrolysis afforded 6-(α-cyanoarylmethyl) substituted title compounds. Besides, the 6-(α-cyanoarylmethyl) substituted S-DABOs were successfully oxidized to 6-arylcarbonyl substituted S-DABOs by passing air through the reaction mixture in the presence of 60% NaH in anhydrous DMF at room temperature.More than 200 intermediates and final products were synthesized in this paper,among which, all the title compounds are new compounds and have not been reported in literatures. The structures of all these compounds were confirmed by spectroscopic methods or X-ray analysis.The novel HEPTs and S-DABO analogues were evaluated for their cytotoxicity and anti-HIV activity in MT-4 cells in comparison with HEPT and DDL The results were expressed as CC₅₀ (cytotoxicity), IC₅₀ (inhibitory concentration ) and SI (selectivity, given by the CC50/IC50 ratio). In general, it was found that most of the title compounds of HEPTs showed more potent anti-HIV-1 activities than the reference compounds HEPT and DDL Among which, fifteen compounds were proved to be approximately 10 to 50-fold more active than HEPT and DDL In particular, compound 1 -benzyloxymethyl-5-isopropyl-6-(1-naphthoyl)-2,4-pyrimidinedione(JL-043) displayed the most potent anti-HIV-1 activity. 6-Arylcarbonyl substituted S-DABO analogues showed striking low cytotoxicity. Most 6-(α-cyanoarylmethyl) substituted S-DABOs showed anti-HIV-1 activity that was more potent than that of DDI in MT-4 cells. Particularly, compounds JL-055 and JL-057 proved to be highly effective in inhibiting HIV-1 replication at nanomolar concentrations (IC₅₀ = 0.002 -0.09 μM), which were improved about 55 and 2500-fold than DDI and about 2 and 125-fold than nevirapine, respectively. More importantly, they also had high specificities and selectivity (SI = 1551, 4657). In addition, we have chosen two representative compounds to evaluate their anti-HIV-1 activity in human peripheral blood mononuclear cells (PBMCs). As a result, two compounds showed good anti-HIV-1 activity in human PBMCs.Finally, the 3D-QSAR between activity and quantum parameters or other descriptors were studies by the methods of and CoMFA and CoMSIA. Based on the 3D-QSAR model, the further SAR of the newly synthesized title compounds were explored in the aspects of steric, electrical and hydrophobic fields. The conclusions summarized from these results will serve as the guide for designing new HEPT and S-DABO analogs as HIV-1 NNRTIs. Our research will provide further enrichment for the basic theory of searching HIV-1 NNRTIs.