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

Abstract

Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture. Current structure-activity-relationship (SAR) identified analogue 11d as a nanomolar inhibitor of RNase H (IC50 = 0.04 μM) with decent antiviral potency (EC50 = 7.4 μM) and no cytotoxicity (CC50 > 100 μM). In extended biochemical assays compound 11d did not inhibit RT polymerase (pol) while inhibiting integrase strand transfer (INST) with 53 fold lower potency (IC50 = 2.1 μM) than RNase H inhibition. Crystallographic and molecular modeling studies confirmed the RNase H active site binding mode.

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

“…RNase H active‐site inhibitors act by chelating the two divalent metal ions essential for the degradation of the RNA strand in RNA/DNA hybrids. Examples of compounds with such a mechanism of action are given in Figure and include N ‐hydroxylisoquinolinediones (HID; Billamboz et al., ; Kankanala et al., ; Vernekar et al., ), β‐thujaplicinol (Budihas et al., ), diketoacid derivatives (Tramontano et al., ), pyrimidinol carboxylic acids (Lansdon et al., ), naphthyridinones (Williams et al., ), pyridopyrimidinones (Beilhartz et al., ), hydroxypyrimidines (Tang et al., ), 3‐hydroxypyrimidine‐2,4‐diones (HPD; Tang et al., ; Vernekar et al., ; Wang et al., ,b; Wu et al., ), and hydroxypyridonecarboxylic acids (Kankanala et al., ). For reviews, see references (Yu, Liu, Zhan, & De Clercq, ; Wang, Gao, Menéndez‐Arias, Liu, & Zhan, ).…”

Cyanoacetyl urea in heterocyclic synthesis part V: Facile synthesis of poly-functionalized pyrimdines via different behaviors of its free urea amino group

“…In addition, its IR spectrum revealed the presence of C=O absorption peaks while its mass spectral data showed molecular ion peak at m/z = 218 (95%). Based on the previous data, the structure 1H-benzo [4,5]thiazolo [3,2-c] pyrimidine-1,3(2H)-dione (6) was established to this product (Scheme 1). Compound 6 is assumed to be formed via self cyclization involving the nucleophilic attack of benzothiazole NH on C=O group of the ureido residue with evolution of ammonia, a result in accordance with previous reports [7].…”

“…Among various pyrimidine derivatives, the synthesis of pyrimidine-2,4-diones remains an area of current interest due to the presence of such moiety in a large number of biologically important compounds [3][4][5]. Recently, we synthesized a superabsorbent which could be used to absorb urea from urine [6] as we are interested in utilizing biomass building block in organic synthesis.…”

Development of Resistance to 4’-Ethynyl-2-Fluoro-2’-Deoxyadenosine (EFdA) by WT and Nucleoside Reverse Transcriptase Inhibitor Resistant Human Immunodeficiency Virus Type 1

“…RT was expressed in JM-109 cells (Invitrogen) and purified by nickel affinity chromatography and Mono Q anion exchange chromatography. Steady state kinetic parameters, Km, for incorporation of EFdA-MP were determined using plate-based assays measuring an 18 nucleotide primer annealed to 100 nucleotide DNA template (Kankanala et al, 2017;Singh et al, 2012;Tang et al, 2019Tang et al, , 2017Vernekar et al, 2017;Wang et al, 2018). The reactions were carried out in RT buffer with 6 mM MgCl2, 40 nM Td100/Pd18, and 10 nM RT in a final volume of 20 μl for 30min at 37 °C, and arrested by 100 mM of EDTA.…”