6-(1-Benzyl-1H-pyrrol-2-yl)-2,4-dioxo-5-hexenoic Acids as Dual Inhibitors of Recombinant HIV-1 Integrase and Ribonuclease H, Synthesized by a Parallel Synthesis Approach

Abstract

The increasing efficiency of HAART has helped to transform HIV/AIDS into a chronic disease. Still, resistance and drug-drug interactions warrant the development of new anti-HIV agents. We previously discovered hit 6, active against HIV-1 replication and targeting RNase H in vitro. Because of its diketo-acid moiety, we speculated that this chemotype could serve to develop dual inhibitors of both RNase H and integrase. Here, we describe a new series of 1-benzyl-pyrrolyl diketohexenoic derivatives, 7a-y and 8a-y, synthesized following a parallel solution-phase approach. Those 50 analogues have been tested on recombinant enzymes (RNase H and integrase) and in cell-based assays. Approximately half (22) exibited inhibition of HIV replication. Compounds 7b, 7u, and 8g were the most active against the RNase H activity of reverse-transcriptase, with IC50 values of 3, 3, and 2.5 μM, respectively. Compound 8g was also the most potent integrase inhibitor with an IC50 value of 26 nM.

Identification of Highly Conserved Residues Involved in Inhibition of HIV-1 RNase H Function by Diketo Acid Derivatives

“…Starting from these results, in the present study we synthesized 6 new couples of diketo ester and DKA derivatives with various structural features, to be used as chemical tools in the characterization of RNase H binding modes. In agreement with previous studies (30,31), among the designed molecules all of the acids were more potent against IN, while three esters (RDS1759, RDS2291, and RDS2400) proved to selectively inhibit RNase H activity, compared to IN. Interestingly, a few DKA derivatives were also able to inhibit RDDP activity.…”

“…All of the DKAs inhibited RNase H activity, with the ester derivatives generally being more potent than their acid counterparts (Table 1). This effect was more evident for derivatives RDS1759, RDS2291, and RDS2400, which showed 50% inhibitory concentration (IC 50 ) values for RNase H activity of 7.3, 8.2, and 11.2 M, respectively, while being completely inactive as IN inhibitors at up to 100 M. Conversely, all of the acid derivatives were more potent than their ester counterparts as IN inhibitors, as reported previously (31). Interestingly, some derivatives, independent of their acid/ester structure, also inhibited RDDP activity.…”

“…Based on the interaction patterns predicted by docking calculations, we selectively mutated into Ala residues R448, N474, Q475, Y501, and R557 within the sole p66 subunit of HIV-1 RT. It is important to note that the N474, Q475, and Y501 residues are highly conserved, playing crucial roles as part of the RNase H primer grip (31). In fact, amino acid substitutions of these residues have been reported to reduce the HIV-1 replication rate drastically (41) and to affect RNase H enzymatic activity strongly (42).…”

“…Among them, 6-[1-(4-fluorophenyl)methyl-1H-pyrrol-2-yl)]-2,4-dioxo-5-hexenoic acid ethyl ester (RDS1643) was the first ligand proven to be able to inhibit both HIV-1 RNase H in biochemical assays and viral replication in cell culture (30). Recently, a new series of pyrrolyl DKAs that are active against both HIV-1 IN and RNase H has been reported (31), with acidic compounds being more effective with IN and ester counterparts being active with both enzymes, with no particular difference. Moreover, a recent study on RHI effects on and binding to prototype foamy virus (PFV) RT showed a putative RDS1643 binding region in the PFV RNase H active site and suggested, given the high level of structural similarity between PFV and HIV-1 RNase H domains, the possibility that RDS1643 could show similar interactions with the HIV-1 RNase H domain (32).…”

Structure–Activity Relationship of Pyrrolyl Diketo Acid Derivatives as Dual Inhibitors of HIV-1 Integrase and Reverse Transcriptase Ribonuclease H Domain

“…Synthetic Route to Pyrrolyl DKAs 6k,l and 7k,l a a Reagents and conditions: (i) NIS, acetone, -78 °C, 96 h; (ii) phenylboronic acid, Cs 2 CO 3 , P(t-But) 3 , Pd 2 (dba) 3 (Table 1). In general, as reported previously, 31 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 15 the NH 2 derivative improved its potency of inhibition (7d, IC 50 value of 2 µM; 7a, IC 50 value of 7. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42...…”