Salicylhydrazine-Containing Inhibitors of HIV-1 Integrase:  Implication for a Selective Chelation in the Integrase Active Site

ABSTRACT HIV/AIDS continues to be a menace to public health. Several drugs currently on the market have successfully improved the ability to manage the viral burden in infected patients. However, new drugs are needed to combat the rapid emergence of mutated forms of the virus that are resistant to existing therapies. Currently, approved drugs target three of the four major enzyme activities encoded by the virus that are critical to the HIV life cycle. Although a number of inhibitors of HIV RNase H activity have been reported, few inhibit by directly engaging the RNase H active site. Here, we describe structures of naphthyridinone-containing inhibitors bound to the RNase H active site. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain. In addition, one of the naphthyridinone-based compounds was found to bind at a second site close to the polymerase active site and non-nucleoside/nucleotide inhibitor sites in a metal-independent manner. Further characterization, using fluorescence-based thermal denaturation and a crystal structure of the isolated RNase H domain reveals that this compound can also bind the RNase H site and retains the metal-dependent binding mode of this class of molecules. These structures provide a means for structurally guided design of novel RNase H inhibitors.

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Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02635-18 ◽

2019 ◽

Vol 63 (6) ◽

Cited By ~ 4

Author(s):

Shin-ichiro Hattori ◽

Hironori Hayashi ◽

Haydar Bulut ◽

Kalapala Venkateswara Rao ◽

Prasanth R. Nyalapatla ◽

...

Keyword(s):

Antiviral Activity ◽

Protease Inhibitors ◽

Active Site ◽

Fluorine Atom ◽

Halogen Bond ◽

The Novel ◽

Wild Type ◽

Flap Region ◽

Hiv 1

ABSTRACTWe generated two novel nonpeptidic HIV-1 protease inhibitors (PIs), GRL-001-15 and GRL-003-15, which contain unique crown-like tetrahydropyranofuran (Crn-THF) and P2′-cyclopropyl-aminobenzothiazole (Cp-Abt) moieties as P2 and P2′ ligands, respectively. GRL-001-15 and GRL-003-15 havemeta-monofluorophenyl andpara-monofluorophenyl at the P1 site, respectively, exert highly potent activity against wild-type HIV-1 with 50% effective concentrations (EC50s) of 57 and 50 pM, respectively, and have favorable cytotoxicity profiles with 50% cytotoxic concentrations (CC50s) of 38 and 11 μM, respectively. The activity of GRL-001-15 against multi-PI-resistant HIV-1 variants was generally greater than that of GRL-003-15. The EC50of GRL-001-15 against an HIV-1 variant that was highly resistant to multiple PIs, including darunavir (DRV) (HIV-1DRVRP30), was 0.17 nM, and that of GRL-003-15 was 3.3 nM, while DRV was much less active, with an EC50of 216 nM. The emergence of HIV-1 variants resistant to GRL-001-15 and GRL-003-15 was significantly delayed compared to that of variants resistant to selected PIs, including DRV. Structural analyses of wild-type protease (PRWT) complexed with the novel PIs revealed that GRL-001-15’smeta-fluorine atom forms halogen bond interactions (2.9 and 3.0 Å) with Gly49 and Ile50, respectively, of the protease flap region and with Pro81′ (2.7 and 3.2 Å), which is located close to the protease active site, and that two fluorine atoms of GRL-142-13 form multiple halogen bond interactions with Gly49, Ile50, Pro81′, Ile82′, and Arg8′. In contrast, GRL-003-15 forms halogen bond interactions with Pro81′ alone, suggesting that the reduced antiviral activity of GRL-003-15 is due to the loss of the interactions with the flap region.

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Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease

Journal of the American Chemical Society ◽

10.1021/ja504096m ◽

2014 ◽

Vol 136 (34) ◽

pp. 11956-11963 ◽

Cited By ~ 50

Author(s):

Debra A. Ragland ◽

Ellen A. Nalivaika ◽

Madhavi N. L. Nalam ◽

Kristina L. Prachanronarong ◽

Hong Cao ◽

...

Keyword(s):

Drug Resistance ◽

Active Site ◽

Structural Ensemble ◽

Hiv 1

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Lipopeptides as Dimerization Inhibitors of HIV-1 Protease

Biological Chemistry ◽

10.1515/bc.1999.076 ◽

1999 ◽

Vol 380 (5) ◽

pp. 593-596 ◽

Cited By ~ 33

Author(s):

H. J. Schramm ◽

E. De Rosny ◽

M. Reboud-Ravaux ◽

J. Büttner ◽

A. Dick ◽

...

Keyword(s):

Active Site ◽

Structural Features ◽

Hiv Protease ◽

Blocking Group ◽

Aids Therapy ◽

Inhibitory Power ◽

Natural Amino Acids ◽

Enzyme Test ◽

Hiv 1 ◽

Dimerization Inhibitors

Abstract In AIDS therapy, attempts have been made to inhibit the virus-encoded enzymes, e.g. HIV-1 protease, using active site-directed inhibitors. This approach is questionable, however, due to virus mutations and the high toxicity of the drugs. An alternative method to inhibit the dimeric HIV protease is the targeting of the interface region of the protease subunits in order to prevent subunit dimerization and enzyme activity. This approach should be less prone to inactivation by mutation. A list of improved ‘dimerization inhibitors’ of HIV-1 protease is presented. The main structural features are a short ‘interface’ peptide segment, including non-natural amino acids, and an aliphatic N-terminal blocking group. The high inhibitory power of some of the lipopeptides [e.g. palmitoyl-Tyr-Glu-Leu-OH, palmitoyl-Tyr-Glu-(L-thyronine)-OH, palmitoyl-Tyr-Glu-(L-biphenyl-alanine)-OH] with low nanomolar Ki valuesin the enzyme test suggests that mimetics with good bio-availability can be derived for AIDS therapy.

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Two Coselected Distal Mutations in HIV-1 Reverse Transcriptase (RT) Alter Susceptibility to Nonnucleoside RT Inhibitors and Nucleoside Analogs

Journal of Virology ◽

10.1128/jvi.00224-19 ◽

2019 ◽

Vol 93 (11) ◽

Author(s):

Paul L. Boyer ◽

Kevin Melody ◽

Steven J. Smith ◽

Linda L. Dunn ◽

Chris Kline ◽

...

Keyword(s):

Nucleic Acid ◽

Reverse Transcriptase ◽

Active Site ◽

Nucleoside Analogs ◽

Transcriptase Inhibitor ◽

Drug Resistant ◽

Resistance Mutations ◽

Hydrophobic Region ◽

Nnrti Resistance ◽

Hiv 1

ABSTRACTTwo mutations, G112D and M230I, were selected in the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) by a novel nonnucleoside reverse transcriptase inhibitor (NNRTI). G112D is located near the HIV-1 polymerase active site; M230I is located near the hydrophobic region where NNRTIs bind. Thus, M230I could directly interfere with NNRTI binding but G112D could not. Biochemical and virological assays were performed to analyze the effects of these mutations individually and in combination. M230I alone caused a reduction in susceptibility to NNRTIs, while G112D alone did not. The G112D/M230I double mutant was less susceptible to NNRTIs than was M230I alone. In contrast, both mutations affected the ability of RT to incorporate nucleoside analogs. We suggest that the mutations interact with each other via the bound nucleic acid substrate; the nucleic acid forms part of the polymerase active site, which is near G112D. The positioning of the nucleic acid is influenced by its interactions with the “primer grip” region and could be influenced by the M230I mutation.IMPORTANCEAlthough antiretroviral therapy (ART) is highly successful, drug-resistant variants can arise that blunt the efficacy of ART. New inhibitors that are broadly effective against known drug-resistant variants are needed, although such compounds might select for novel resistance mutations that affect the sensitivity of the virus to other compounds. Compound 13 selects for resistance mutations that differ from traditional NNRTI resistance mutations. These mutations cause increased sensitivity to NRTIs, such as AZT.

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