Quinolinonyl Non-Diketo Acid Derivatives as Inhibitors of HIV-1 Ribonuclease H and Polymerase Functions of Reverse Transcriptase

Abstract

Novel anti-HIV agents are still needed to overcome resistance issues, in particular inhibitors acting against novel viral targets. The ribonuclease H (RNase H) function of the reverse transcriptase (RT) represents a validated and promising target, and no inhibitor has reached the clinical pipeline yet. Here, we present rationally designed non-diketo acid selective RNase H inhibitors (RHIs) based on the quinolinone scaffold starting from former dual integrase (IN)/RNase H quinolinonyl diketo acids. Several derivatives were synthesized and tested against RNase H and viral replication and found active at micromolar concentrations. Docking studies within the RNase H catalytic site, coupled with site-directed mutagenesis, and Mg 2+ titration experiments demonstrated that our compounds coordinate the Mg 2+ cofactor and interact with amino acids of the RNase H domain that are highly conserved among naïve and treatment-experienced patients. In general, the new inhibitors influenced also the polymerase activity of RT but were selective against RNase H vs the IN enzyme.

4,5-Dihydroxypyrimidine Methyl Carboxylates, Carboxylic Acids, and Carboxamides as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease

“…Against similar enzymes featuring two divalent metal ions at the active site, optimal inhibition of HIV-1 INST appears to strongly prefer carbox­amide functionality, whereas the carboxylic acid functionality is favored for inhibiting HIV-1 RNase H 44 and HCV NS5B . Although the ester functionality is typically undesired, analogs of certain chemotypes have been reported to potently inhibit HIV RNase H, congruent with the observation herein (Table ). (2) With all three subtypes, the SAR seems to prefer an aryl or arylmethyl group at R 1 over a methyl group (e.g., 13l / 13c vs 13a ; 14l / 14c vs 14a ; 15r / 15h vs 15c ).…”

“…42 As for ester derivatives, partial NS5B inhibitory activity was observed with the methyl ester of acid subtype 10. 43 Similarly, both quinolinone carboxylic acids and ester derivatives were active inhibiting HIV-1 RNase H. 45 However, the methyl ester of another HIV-1 RNase H inhibitor type, DHP carboxylic acid 12 (Figure 3A), was only marginally active. 44 Esterification of the prototypical diketoacid INST inhibitor also led to complete loss of activity.…”

Inhibiting HCMV pUL89-C Endonuclease with Metal-Binding Compounds

“…As for ester derivatives, partial NS5B inhibitory activity was observed with the methyl ester of acid subtype (39a). 65 Moreover, though quinolinone carboxylic acids and ester derivatives demonstrated inhibitory activity against HIV-1 RNase H, 68 the methyl ester of DHP carboxylic acid 41b (Figure 7), showed mediocre inhibition of HIV-1 RNase H. 67 Similarly, ester analogues of the prototypical diketoacid were inactive against HIV-1 INST. 69 Inspired by SAR observations of DHP core and similarity of metal dependent catalytic mechanism of pUL89-C to integrase/ RNase H-like viral metalloenzymatic functions, three DHP subtypes were explored as inhibitors of HCMV pUL89-C (Figure 7): methyl carboxylate (41), carboxylic acid (39), and carboxamide (40) (see Table 5).…”

NNRTI and Liver Damage: Evidence of Their Association and the Mechanisms Involved

“…clinical use [9]. Combination therapy is still the gold standard for treatment of HIV infection, and regimens are tailored to the individual in order to minimize toxicity/intolerance and diminish the risk of developing resistance [10].…”

“…Of the four enzymatic activities found in HIV-1 proteins (protease, reverse transcriptase polymerase, reverse transcriptase RNase H, and integrase), only RNase H has no approved therapeutical agents directed against it. Actually, many RHIs have been reported in the literature as effective inhibitors in enzyme assay; however, their high levels of toxicity or lack of selective inhibition have hampered their development for clinical use [ 9 ]. Combination therapy is still the gold standard for treatment of HIV infection, and regimens are tailored to the individual in order to minimize toxicity/intolerance and diminish the risk of developing resistance [ 10 ].…”