HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2′ Ligands To Optimize Hydrogen Bonding in the Substrate Envelope

ABSTRACTWe identified GRL-1388 and -1398, potent nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran (Tp-THF). GRL-1388 was as potent as darunavir (DRV) against various drug-resistant HIV-1 laboratory strains with 50% effective concentration (EC50s) of 2.6 to 32.6 nM. GRL-1398 was significantly more potent against such variants than DRV with EC50s of 0.1 to 5.7 nM. GRL-1388 and -1398 were also potent against multiple-PI-resistant clinical HIV-1 variants (CLHIV-1MDR) with EC50s ranging from 2.7 to 21.3 nM and from 0.3 to 4.8 nM, respectively. A highly DRV-resistant HIV-1 variant selectedin vitroremained susceptible to GRL-1398 with the EC50of 21.9 nM, while the EC50of DRV was 214.1 nM. When HIV-1NL4-3was selected with GRL-1398, four amino acid substitutions—leucine to phenylalanine at a position 10 (L10F), A28S, L33F, and M46I—emerged, ultimately enabling the virus to replicate in the presence of >1.0 μM the compound beyond 57 weeks of selection. When a mixture of 10 differentCLHIV-1MDRstrains was selected, the emergence of resistant variants was more substantially delayed with GRL-1398 than with GRL-1388 and DRV. Modeling analyses revealed that GRL-1398 had greater overall hydrogen bonding and hydrophobic interactions than GRL-1388 and DRV and that GRL-1388 and -1398 had hydrogen bonding interactions with the main chain of the active-site amino acids (Asp29 and Asp30) of protease. The present findings warrant that GRL-1398 be further developed as a potential drug for treating individuals with HIV-1 infection.

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Using substrate envelope to develop better HIV‐1 protease inhibitors.

The FASEB Journal ◽

10.1096/fasebj.2020.34.s1.09010 ◽

2020 ◽

Vol 34 (S1) ◽

pp. 1-1

Author(s):

Evelyn Kerr ◽

Meera Bhakta ◽

Jesi Hunter ◽

John Hernandez ◽

Carolyn Stelluti

Keyword(s):

Protease Inhibitors ◽

Hiv 1 ◽

Substrate Envelope

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Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance

Journal of Virology ◽

10.1128/jvi.02531-09 ◽

2010 ◽

Vol 84 (10) ◽

pp. 5368-5378 ◽

Cited By ~ 70

Author(s):

Madhavi N. L. Nalam ◽

Akbar Ali ◽

Michael D. Altman ◽

G. S. Kiran Kumar Reddy ◽

Sripriya Chellappan ◽

...

Keyword(s):

Drug Resistance ◽

Protease Inhibitors ◽

Active Site ◽

Crystallographic Analysis ◽

Van Der Waals Interactions ◽

Drug Resistant ◽

Design Strategies ◽

Resistance Mutations ◽

Hiv 1 ◽

Substrate Envelope

ABSTRACT Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type protease ranging from 58 nM to 0.8 pM was chosen for crystallographic analysis. The inhibitor-protease complexes revealed that tightly binding inhibitors (at the picomolar level of affinity) appear to “lock” into the protease active site by forming hydrogen bonds to particular active-site residues. Both this hydrogen bonding pattern and subtle variations in protein-ligand van der Waals interactions distinguish nanomolar from picomolar inhibitors. In general, inhibitors that fit within the substrate envelope, regardless of whether they are picomolar or nanomolar, have flatter profiles with respect to drug-resistant protease variants than inhibitors that protrude beyond the substrate envelope; this provides a strong rationale for incorporating substrate-envelope constraints into structure-based design strategies to develop new HIV-1 protease inhibitors.

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Faculty Opinions recommendation of Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718102534.793484449 ◽

2013 ◽

Author(s):

Jürgen Bajorath

Keyword(s):

Drug Resistance ◽

Protease Inhibitors ◽

Hiv 1 ◽

Substrate Envelope

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C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir

Journal of Virology ◽

10.1128/jvi.01829-15 ◽

2015 ◽

Vol 90 (5) ◽

pp. 2180-2194 ◽

Cited By ~ 11

Author(s):

Manabu Aoki ◽

Hironori Hayashi ◽

Ravikiran S. Yedidi ◽

Cuthbert D. Martyr ◽

Yuki Takamatsu ◽

...

Keyword(s):

Hydrogen Bonding ◽

Oxygen Atom ◽

Protease Inhibitors ◽

Multidrug Resistant ◽

Carbonyl Oxygen ◽

Carbonyl Oxygen Atom ◽

Strong Hydrogen Bond ◽

Wild Type ◽

Genetic Barrier ◽

Hiv 1

ABSTRACTWe identified three nonpeptidic HIV-1 protease inhibitors (PIs), GRL-015, -085, and -097, containing tetrahydropyrano-tetrahydrofuran (Tp-THF) with a C-5 hydroxyl. The three compounds were potent against a wild-type laboratory HIV-1 strain (HIV-1WT), with 50% effective concentrations (EC50s) of 3.0 to 49 nM, and exhibited minimal cytotoxicity, with 50% cytotoxic concentrations (CC50) for GRL-015, -085, and -097 of 80, >100, and >100 μM, respectively. All the three compounds potently inhibited the replication of highly PI-resistant HIV-1 variants selected with each of the currently available PIs and recombinant clinical HIV-1 isolates obtained from patients harboring multidrug-resistant HIV-1 variants (HIVMDR). Importantly, darunavir (DRV) was >1,000 times less active against a highly DRV-resistant HIV-1 variant (HIV-1DRVRP51); the three compounds remained active against HIV-1DRVRP51with only a 6.8- to 68-fold reduction. Moreover, the emergence of HIV-1 variants resistant to the three compounds was considerably delayed compared to the case of DRV. In particular, HIV-1 variants resistant to GRL-085 and -097 did not emerge even when two different highly DRV-resistant HIV-1 variants were used as a starting population. In the structural analyses, Tp-THF of GRL-015, -085, and -097 showed strong hydrogen bond interactions with the backbone atoms of active-site amino acid residues (Asp29 and Asp30) of HIV-1 protease. A strong hydrogen bonding formation between the hydroxyl moiety of Tp-THF and a carbonyl oxygen atom of Gly48 was newly identified. The present findings indicate that the three compounds warrant further study as possible therapeutic agents for treating individuals harboring wild-type HIV and/or HIVMDR.IMPORTANCEDarunavir (DRV) inhibits the replication of most existing multidrug-resistant HIV-1 strains and has a high genetic barrier. However, the emergence of highly DRV-resistant HIV-1 strains (HIVDRVR) has recently been observedin vivoandin vitro. Here, we identified three novel HIV-1 protease inhibitors (PIs) containing a tetrahydropyrano-tetrahydrofuran (Tp-THF) moiety with a C-5 hydroxyl (GRL-015, -085, and -097) which potently suppress the replication of HIVDRVR. Moreover, the emergence of HIV-1 strains resistant to the three compounds was considerably delayed compared to the case of DRV. The C-5 hydroxyl formed a strong hydrogen bonding interaction with the carbonyl oxygen atom of Gly48 of protease as examined in the structural analyses. Interestingly, a compound with Tp-THF lacking the hydroxyl moiety substantially decreased activity against HIVDRVR. The three novel compounds should be further developed as potential drugs for treating individuals harboring wild-type and multi-PI-resistant HIV variants as well as HIVDRVR.

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