Scaffold hopping and optimisation of 3’,4’-dihydroxyphenyl- containing thienopyrimidinones: synthesis of quinazolinone derivatives as novel allosteric inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H

Abstract

Bioisosteric replacement and scaffold hopping are powerful strategies in drug design useful for rationally modifying a hit compound towards novel lead therapeutic agents. Recently, we reported a series of thienopyrimidinones that compromise dynamics at the p66/p51 HIV-1 reverse transcriptase (RT)-associated Ribonuclease H (RNase H) dimer interface, thereby allosterically interrupting catalysis by altering the active site geometry. Although they exhibited good submicromolar activity, the isosteric replacement of the thiophene ring, a potential toxicophore, is warranted. Thus, in this article, the most active 2-(3,4-dihydroxyphenyl)-5,6-dimethylthieno[2,3-d]pyrimidin-4(3 H )-one 1 was selected as the hit scaffold and several isosteric substitutions of the thiophene ring were performed. A novel series of highly active RNase H allosteric quinazolinone inhibitors was thus obtained. To determine their target selectivity, they were tested against RT-associated RNA-dependent DNA polymerase (RDDP) and integrase (IN). Interestingly, none of the compounds were particularly active on (RDDP) but many displayed micromolar to submicromolar activity against IN.

Dihydroxyphenyl- and Heteroaromatic-Based Thienopyrimidinones to Tackle HIV-1 LEDGF/p75-Dependent IN Activity

“…Methods of investigation are shown in Figure 3. Recently, we also reported on the ability of some 3,4-catechol-thienopyrimidinone [30,31] and quinazolinone derivatives [32], originally designed to allosterically inhibit the HIV-1 RT-associated Ribonuclease H (RNase H) function, to hamper LEDGF/p75-dependent IN activity. Interestingly, with regard to thienopyrimidinones, we observed that the 2-(2,3dihydroxyphenyl)-6-methyl-5-propylthieno [2,3-d]pyrimidin-4(3H)-one (5), bearing a 2,3catecol moiety, displayed the best IN inhibitory activity [30].…”

“…The previously reported procedure was used for preparation and purification of wild type p66/p51 HIV-1 RT. Enzyme was stored in a 50% glycerol-containing buffer at −20 °C [ 32 , 46 ]. An 18-nt 3′-fluorescein-labeled RNA annealed to a complementary 18-nt 5′-dabsyl-labeled DNA was used to determine IC 50 values, following a previously described procedure [ 47 ].…”