3-Hydroxypyrimidine-2,4-diones as Selective Active Site Inhibitors of HIV Reverse Transcriptase-Associated RNase H: Design, Synthesis, and Biochemical Evaluations

Abstract

Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains an unvalidated antiviral target. A major challenge of specifically targeting HIV RNase H arises from the general lack of selectivity over RT polymerase (pol) and integrase (IN) strand transfer (ST) inhibitions. We report herein the synthesis and biochemical evaluations of three novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes carefully designed to achieve selective RNase H inhibition. Biochemical studies showed the two subtypes with an N-1 methyl group (9 and 10) inhibited RNase H in low micromolar range without siginificantly inhibiting RT polymerase, whereas the N-1 unsubstituted subtype 11 inhibited RNase H in submicromolar range and RT polymerase in low micromolar range. Subtype 11 also exhibited substantially reduced inhibition in the HIV-1 INST assay, and no significant cytotoxicity in the cell viability assay, suggesting that it may be amenable to further structure-activity-relationship (SAR) for identifying RNase H inhibitors with antiviral activity.

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

“…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].…”

A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase

“…These include acylhydrazones (5-7), diketo acids (8,9), ␣-hydroxytropolones (10), vinylogous ureas (11), naphthyridinones (12), pyridopyrimidinones (13,14), pyrimidinol carboxylic acids (15), hydroxypyridonecarboxylic acids (16), 3-hydroxypyrimidine-2,4-diones (17,18), and 2-hydroxyisoquinoline-1,3-diones (HIDs) (19). Notably, many 2-hydroxyisoquinoline-1,3-diones inhibit both RT polymerase and RNH functions of RT (19).…”

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

“…One such chemotype is the versatile HPD core (Figure 1) which was initially designed to dually inhibit RT pol and INST (subtype 1 ) [12]. Removal of the N-1 and C5 substituents and redesign of the C6 moiety led to subtype 2 which selectively inhibited the RNase H function of RT [8]. Introduction of a C-5 carboxamide moiety and replacement of the C-6 aryl with a small alkyl group resulted in subtype 3 , which potently inhibited both RNase H and INST [9].…”