Structure-based Design, Synthesis And Biological Evaluation Of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors

Acquired immune deficiency syndrome (AIDS) mainly caused by human immunodeficiency virus type-1 (HIV-1), continues to be a major leading pandemic disease worldwide. The reverse transcriptase (RT) of HIV-1 is one of the crucial enzymes in the replication of the virus, being responsible for the conversion of the viral genomic RNA into proviral DNA. Due to its special and important role in the HIV-1 life-cycle, RT has been identified as a prime target for anti-HIV drug discovery. HIV-1 RT inhibitors are classified as nucleos(t)ide RT inhibitors (N(t)RTIs) and non-nucleoside RT inhibitors (NNRTIs) based on their mechanism of action and structures. NNRTIs bind to a nonactive site, a flexible allosteric pocket (known as NNIBP, namely NNRTIs binding pocket), at about 10A distance from the enzymatic catalytic site. Compared with other inhibitors, NNRTIs have gained an indispensable place in AIDS chemotherapy, owing to their unique antiviral potency, relatively low toxicity and high selectivity. Currently, five NNRTIs have been approved for clinical use by US FDA, namely nevirapine, delavirdine, efavirenz, etravirine and most recently rilpivirine. However, its use in the first line treatment is usually hampered by potential drug interactions, a high rate of adverse effects as well as inevitable emergence of HIV-1 resistant strains. Consequently, there still remains continuous need to discover novel NNRTIs with improved antiviral efficacy, good pharmacokinetic (PK) and reduced drug resistance mutation profiles.In continuation of our efforts toward study of arylazolylthioacetanilide platform, two series of novel compounds (series Ⅱa and Ⅱb, totally 48 compounds) were firstly design. In series a, pyrimidinylthioacetanilides were designed based on bioisosterism principle, synthesized, and evaluated for their biological activity as NNRTIs. Most of the tested compounds were proved to be effective in inhibiting HIV-1 (ⅢB) replication with EC50 ranging from 0.15 μM to 24.2 μM, thereinto compound IIa-6 and IIa-15 were the most active lead with favorable inhibitory activity against HIV-1 (IIIB) (0.18 μM, SI=132 and EC50= 0.15μ, SI= 684), which were superior to DLV and similar to NVP. Besides, compound IIa-6 displayed moderate inhibition against the double-mutated HIV-1 strain (K103N/Y181C) (EC50=3.9μM). In series Ⅱb, we employed a scaffold hopping strategy to explore the chemically diversed space of binding site and imidazopyridinylthioacetanilide scaffolds were built to yield the optimal pharmacophore moieties in order to generate novel NNRTIs. Some of the new compounds proved able to inhibit HIV-1 replication in the low micromolar range. In particular, compound IIb-24 and IIb-40 displayed the most potent anti-HIV-1 activity (EC50=0.75μM and EC50=0.21μ), which were more effectively than DDC (EC50 = 1.4μ) and similarly to NVP (EC50=0.20μM).On the base of the obtained SAR conclusions (especially the series Ⅱb), a series of novel imidazo[4,5-b]pyridin-2-ylthioacetanilides (series Ⅱc), were designed, synthesized and evaluated for their antiviral activities through combining bioisosteric replacement and structure-based drug design. Almost all of the title compounds displayed moderate to excellent activities against wild-type (WT) HIV-1 strain with EC50 values ranging from 0.059μM to 1.41 μn a cell-based antiviral assay. Thereinto, compounds Ⅱc-12 and Ⅱc-13 were the most active two analogues possessing an EC50 value of 0.059μM and 0.073 μM against wt HIV-1 respectively, which was much more effective than the control drug NVP (EC50= 0.26μ) and comparable to DLV (EC50=0.038 μM).In the third part of this thesis, DAPY NNRTIs were chosen as lead compounds due to their prominent role in anti-HIV drugs. Guided by crystal structures of HIV-1 RT/DAPY complex and molecular modeling studies, a series of novel DAPY derivatives were rationally designed (series Ⅲa), in which the positions of nitrogen atoms in the central pyrimidine ring were changed, and nitro, amino and other nitrogen-containing groups were introduced at the primary position and the two phenyl rings in the left and right wings and the NH linker were maintained. Among them,16 compounds significantly inhibited HIV-1 ⅢB replication with EC50 values lower than 66 nM. Particularly, compound Ⅲa-6 and Ⅲa-10 were the most potent inhibitor against WT HIV-1, with an EC50 value of 2.5 nM (SI= 13740) and 7.2 nM (SI= 1432). Otherwise, Ⅲa-6 maintained moderate inhibitory avtivity against K103N/Y181C HIV-1 strain with 0.33μM (SI= 107). Unexpectedly, compound Ⅲa-15 and Ⅲa-23 were found to show moderate anti-HIV-2 potency (EC50= 5.57 and 36 μM).Guided by promising anti-HIV results of series Ⅲa and the report of N-substituted benzyl/phenyl piperidine NNRTIs, series Ⅲb (totally 15 compounds) was designed to target the right wing of DAPYs. The structural optimizations fall into the following two aspects:(1) Nitrogen-containing aromatic ring or N-substituted benzyl/phenyl piperidine were introduced to right wing, supposing that the additional hydrogen bonds with surrounding residues could be formed by nitrogen atom. Meanwhile, the privileged group amino at central pyrimidine ring of series Ⅲa was maintained. (2) With continuous exploration of optimal group at 5-position of pyrimidine, guanidino, urea and thiourea groups were introdunced based the prelimirary conclusion from series Ⅲa that the contribution of hydrogen-bond donor is more favourable than that of hydrogen-bond aceptor at this site. The results indicate that introduction of N-substituted benzyl/phenyl piperidine is good for keeping/improving anti-HIV activity. The most potent compound is Ⅲb-20 with EC50 values of 2.6 nM (ⅢB) and 160 nM (RES056). To evaluate their potential as drug candidates, Ⅲb-17 and Ⅲb-20 were further assessed for their physicochemical and druglike properties. The representative compounds showed improved solubility at both pH 7.4 and pH 2.0 compared with TMC125.In the fourth part of thesis, a series of novel indolylarylsulfones (IASs) NNRTIs (series Ⅳa, totally 24 compounds) that targetting the second channel of RT were designed based on the crystal structures of RT/IASs complex and the analysis of pharmacophore models. The newly designed compounds retained the basic scafold and pharmacophores of IASs. Meanwhile, the N-substituted piperidine was introduced to molecular based on scaffold hopping strategy, which has been identified as preponderant group in DAPY NNRTIs targetting the first channel of RT. The anti-HIV results indicated all of the target compounds displayed moderate to excellent activities against WT HIV-1 strain with EC50 values ranging from 0.62 μM to 0.06 μM in a cell-based antiviral assay. Moreover, the most compounds can inhibit a variety of single mutant strains such as L100I, K103N, Y181C and E138K. Thereinto, compounds Ⅳa-8’ and Ⅳa-12 were the most active two analogues possessing an EC50 value of 0.006μM and 0.009 μM, SI value of 1005 and 1476 against WT HIV-1 respectively.In summary, taking the AATs, DAPYs and IASs as leads, totally 133 compounds (6 series) that belong to three categories of NNRTIs were rationally designed based on crystal structures of RT/inhibitors and pharmarcophore models. Moreover, computer-aided drug design technology was widely used to verify reasonability of design. The convenient synthetic approaches to target compounds were built or optimized. Lastly, biological evaluation results demonstrate several compounds owing high antiviral activity with EC50 ranging from micromole to nanonolar levels, and some of them also exhibit good performance against the serious resistant strains including the Y181C/K103N double mutant, which have great potential for further investigation. In addition, the structure-activity relationship (SAR) information of each series in the thesis were discussed in detail for further research.