6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase

Abstract

3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design, synthesis and biological evaluation of an HPD subtype (4) featuring a cyclohexylmethyl group at the C-6 position. Antiviral testing showed that most analogues of 4 inhibited HIV-1 in the low nanomolar to submicromolar range, without cytotoxicity at concentrations up to 100 μM. Biochemically, these analogues dually inhibited both the polymerase (pol) and the RNase H functions of RT, but not INST. Co-crystal structure of 4a with RT revealed a nonnucleoside RT inhibitor (NNRTI) binding mode. Interestingly, chemotype 11, the synthetic precursor of 4 lacking the 3-OH group, did not inhibit RNase H while potently inhibiting pol. By virtue of the potent antiviral activity and biochemical RNase H inhibition, HPD subtype 4 could provide a viable platform for eventually achieving potent and selective RNase H inhibition through further medicinal chemistry.

Double-Winged 3-Hydroxypyrimidine-2,4-diones: Potent and Selective Inhibition against HIV-1 RNase H with Significant Antiviral Activity

“…Results were analyzed using “Prism” software (GraphPad Software, San Diego, CA) for nonlinear regression to fit dose-response data to logistic curve models. 28 …”

“…We have long been interested in developing potent and selective RNase H inhibitors. 23-28 Particularly interesting is our reported 25 HPD 29-30 subtype 8 designed to specifically inhibit RNase H. Potent and selective RNase H inhibition was indeed achieved with many analogues; however, none showed significant antiviral activity. 25 Interestingly, when 8 is docked into the RNase H active site, two distinct binding modes are observed (Figure 2A) with or without nucleic acid substrate.…”

Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H

“…Reactions were read at ex/em 504/531 nm in a PerkinElmer EnSpire Multilabel plate reader. Results were analyzed using Prism software (GraphPad Software, San Diego, CA) for nonlinear regression to fit dose-response data to logistic curve models [20, 41]. …”

“…Therefore, most reported RNase H inhibitors also tend to inhibit IN, making achievement of selective biochemical inhibition of HIV RNase H over IN challenging. We have long been interested in designing potent and selective RNase H inhibitors [12, 13, 15, 18–20] particularly with the HID ( 2 ) [12, 13] and 3-hydroxypyrimidine-2,4-dione (HPD) ( 8 ) [18–20] chemotypes. Hybridization of these two scaffolds led to the design of chemotype 9 (Figure 1B) which is similar to the N -hydroxyurea reported as an inhibitor type of flap endonuclease-1 [21].…”

Design, synthesis, and biologic evaluation of novel galloyl derivatives as HIV‐1 RNase H inhibitors

“…HIV‐1 RT is a well‐established target that plays a key role in viral replication by converting the viral genomic single‐stranded RNA into double‐stranded DNA (Menéndez‐Arias, ; Menéndez‐Arias, Sebastian‐Martin, & Alvarez, ). The viral RT possesses two distinct enzymatic functions: a DNA polymerase activity that synthesizes the proviral DNA and a ribonuclease H (RNase H) activity that selectively degrades the RNA strand in RNA/DNA replication intermediates (Tang et al., ). All currently approved antiretroviral drugs targeting the RT are DNA polymerase inhibitors.…”