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Miglioli F, Joel S, Tegoni M, Neira-Pelén P, Günther S, Carcelli M, Fisicaro E, Brancale A, Fernández-García Y, Rogolino D. Inhibitory interactions of the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold with Bunyavirales cap-snatching endonucleases expose relevant drug design features. Eur J Med Chem 2024; 272:116467. [PMID: 38735150 DOI: 10.1016/j.ejmech.2024.116467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
The World Health Organization (WHO) identifies several bunyaviruses as significant threats to global public health security. Developing effective therapies against these viruses is crucial to combat future outbreaks and mitigate their impact on patient outcomes. Here, we report the synthesis of some isoindol-1-one derivatives and explore their inhibitory properties over an indispensable metal-dependent cap-snatching endonuclease (Cap-ENDO) shared among evolutionary divergent bunyaviruses. The compounds suppressed RNA hydrolysis by Cap-ENDOs, with IC50 values predominantly in the lower μM range. Molecular docking studies revealed the interactions with metal ions to be essential for the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold activity. Calorimetric analysis uncovered Mn2+ ions to have the highest affinity for sites within the targets, irrespective of aminoacidic variations influencing metal cofactor preferences. Interestingly, spectrophotometric findings unveiled sole dinuclear species formation between the scaffold and Mn2+. Moreover, the complexation of two Mn2+ ions within the viral enzymes appears to be favourable, as indicated by the binding of compound 11 to TOSV Cap-ENDO (Kd = 28 ± 3 μM). Additionally, the tendency of compound 11 to stabilize His+ more than His- Cap-ENDOs suggests exploitable differences in their catalytic pockets relevant to improving specificity. Collectively, our results underscore the isoindolinone scaffold's potential as a strategic starting point for the design of pan-antibunyavirus drugs.
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Affiliation(s)
- Francesca Miglioli
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Shindhuja Joel
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Matteo Tegoni
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Pedro Neira-Pelén
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Emilia Fisicaro
- Department of Food and Drug, University of Parma, Viale delle Scienze 27/A, 43124, Parma, Italy
| | - Andrea Brancale
- Department of Organic Chemistry, University of Chemistry and Technology, 16628, Prague, Czech Republic
| | - Yaiza Fernández-García
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany.
| | - Dominga Rogolino
- Department of Chemistry, Life Sciences, Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.
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2
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Muvvala S, Kumari K, Miriyala V, Mogili P, Chidara S, Maddirala SJ, Saxena A, Behera M. Microwave‐Assisted Reductive Amination of 2‐Carboxybenzaldehydes with Amines for the Synthesis of N‐Substituted Isoindolin‐1‐one. ChemistrySelect 2022. [DOI: 10.1002/slct.202202500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Subhashini Muvvala
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
- Department of Engineering Chemistry Andhra University Visakhapatnam Andhra Pradesh 530003 India
| | - Krishnaiah Kumari
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
| | - Venkatesh Miriyala
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
| | - Padma Mogili
- Department of Engineering Chemistry Andhra University Visakhapatnam Andhra Pradesh 530003 India
| | - Sridhar Chidara
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
| | - Shambabu Joseph Maddirala
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
| | - Abhishek Saxena
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
| | - Manoranjan Behera
- Chemistry services, Aragen Life Sciences, Survey Nos:125 (part) & 126, IDA Mallapur Hyderabad 500076 Telangana State India
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3
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Rogolino D, Naesens L, Bartoli J, Carcelli M, De Luca L, Pelosi G, Stokes RW, Van Berwaer R, Vittorio S, Stevaert A, Cohen SM. Exploration of the 2,3-dihydroisoindole pharmacophore for inhibition of the influenza virus PA endonuclease. Bioorg Chem 2021; 116:105388. [PMID: 34670331 DOI: 10.1016/j.bioorg.2021.105388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 09/25/2021] [Indexed: 11/19/2022]
Abstract
Seasonal influenza A and B viruses represent a global concern. Antiviral drugs are crucial to treat severe influenza in high-risk patients and prevent virus spread in case of a pandemic. The emergence of viruses showing drug resistance, in particular for the recently licensed polymerase inhibitor baloxavir marboxil, drives the need for developing alternative antivirals. The endonuclease activity residing in the N-terminal domain of the polymerase acidic protein (PAN) is crucial for viral RNA synthesis and a validated target for drug design. Its function can be impaired by molecules bearing a metal-binding pharmacophore (MBP) able to coordinate the two divalent metal ions in the active site. In the present work, the 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one scaffold is explored for the inhibition of influenza virus PA endonuclease. The structure-activity relationship was analysed by modifying the substituents on the lipophilic moiety linked to the MBP. The new compounds exhibited nanomolar inhibitory activity in a FRET-based enzymatic assay, and a few compounds (15-17, 21) offered inhibition in the micromolar range, in a cell-based influenza virus polymerase assay. When investigated against a panel of PA-mutant forms, compound 17 was shown to retain full activity against the baloxavir-resistant I38T mutant. This was corroborated by docking studies providing insight into the binding mode of this novel class of PA inhibitors.
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Affiliation(s)
- Dominga Rogolino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy.
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.
| | - Jennifer Bartoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, Polo Universitario SS. Annunziata, Università di Messina, Viale Palatucci 13, Messina I-98168, Italy
| | - Giorgio Pelosi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici) Parma Unit, 43124 Parma, Italy
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
| | - Ria Van Berwaer
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Serena Vittorio
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, Polo Universitario SS. Annunziata, Università di Messina, Viale Palatucci 13, Messina I-98168, Italy
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
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Espinoza-Culupú A, Vázquez-Ramírez R, Farfán-López M, Mendes E, Notomi Sato M, da Silva Junior PI, Borges MM. Acylpolyamine Mygalin as a TLR4 Antagonist Based on Molecular Docking and In Vitro Analyses. Biomolecules 2020; 10:E1624. [PMID: 33271940 PMCID: PMC7761503 DOI: 10.3390/biom10121624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023] Open
Abstract
Toll-like receptors (TLRs) are transmembrane proteins that are key regulators of innate and adaptive immune responses, particularly TLR4, and they have been identified as potential drug targets for the treatment of disease. Several low-molecular-weight compounds are being considered as new drug targets for various applications, including as immune modulators. Mygalin, a 417 Da synthetic bis-acylpolyamine, is an analog of spermidine that has microbicidal activity. In this study, we investigated the effect of mygalin on the innate immune response based on a virtual screening (VS) and molecular docking analysis. Bone marrow-derived macrophages and the cell lines J774A.1 and RAW 264.7 stimulated with lipopolysaccharide (LPS) were used to confirm the data obtained in silico. Virtual screening and molecular docking suggested that mygalin binds to TLR4 via the protein myeloid differentiation factor 2 (MD-2) and LPS. Macrophages stimulated by mygalin plus LPS showed suppressed gene expression of tumor necrosis factor (TNF-α), interleukine 6 (IL-6), cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS), as well as inhibition of signaling protein p65 of the nuclear factor κB (NF-κB), resulting in decreased production of nitric oxide (NO) and TNF-α. These results indicate that mygalin has anti-inflammatory potential, being an attractive option to be explored. In addition, we reinforce the importance of virtual screening analysis to assist in the discovery of new drugs.
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Affiliation(s)
- Abraham Espinoza-Culupú
- Interunits Graduate Program in Biotechnology, USP/IBu/IPT, São Paulo 01000-000, Brazil; (A.E.-C.); (P.I.d.S.J.)
- Bacteriology Laboratory, Butantan Institute, São Paulo 01000-000, Brazil;
| | - Ricardo Vázquez-Ramírez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 00-16, Mexico;
| | - Mariella Farfán-López
- Microbiology Molecular and Biotechnology Laboratory, Universidad Nacional Mayor de San Marcos, Lima District 15081, Peru;
| | - Elizabeth Mendes
- Bacteriology Laboratory, Butantan Institute, São Paulo 01000-000, Brazil;
| | - Maria Notomi Sato
- Laboratory of Dermatology and Immunodeficiencies, Medical School, University of São Paulo, São Paulo 01000-000, Brazil;
| | - Pedro Ismael da Silva Junior
- Interunits Graduate Program in Biotechnology, USP/IBu/IPT, São Paulo 01000-000, Brazil; (A.E.-C.); (P.I.d.S.J.)
- Laboratory for Applied Toxinology (LETA), Butantan Institute, São Paulo 01000-000, Brazil
| | - Monamaris Marques Borges
- Interunits Graduate Program in Biotechnology, USP/IBu/IPT, São Paulo 01000-000, Brazil; (A.E.-C.); (P.I.d.S.J.)
- Bacteriology Laboratory, Butantan Institute, São Paulo 01000-000, Brazil;
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Two Coselected Distal Mutations in HIV-1 Reverse Transcriptase (RT) Alter Susceptibility to Nonnucleoside RT Inhibitors and Nucleoside Analogs. J Virol 2019; 93:JVI.00224-19. [PMID: 30894467 PMCID: PMC6532099 DOI: 10.1128/jvi.00224-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
Although 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. Two 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. IMPORTANCE Although 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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6
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Peptide-guided functionalization and macrocyclization of bioactive peptidosulfonamides by Pd(II)-catalyzed late-stage C-H activation. Nat Commun 2018; 9:3383. [PMID: 30139997 PMCID: PMC6107497 DOI: 10.1038/s41467-018-05440-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/09/2018] [Indexed: 01/09/2023] Open
Abstract
Peptides and peptidomimetics are emerging as an important class of clinic therapeutics. Here we report a peptide-guided method for the functionalization and macrocyclization of bioactive peptidosulfonamides by Pd(II)-catalyzed late-stage C-H activation. In this protocol, peptides act as internal directing groups and enable site-selective olefination of benzylsulfonamides and cyclization of benzosulfonamides to yield benzosultam-peptidomimetics. Our results provide an unusual example of benzosulfonamide cyclization with olefins through a sequential C-H activation, which involves the generation of a reactive palladium-peptide complex. Furthermore, this protocol allows facile self-guided macrocyclization of sulfonamide-containing peptides by intramolecular olefination with acrylates and unactivated alkenes, affording bioactive peptidosulfonamide macrocycles of various sizes. Together, our results highlight the utility of peptides as internal directing groups in facilitating transition metal-catalyzed functionalization of peptidomimetics.
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Nam TK, Jang DO. Radical "On Water" Addition to the C═N Bond of Hydrazones: A Synthesis of Isoindolinone Derivatives. J Org Chem 2018; 83:7373-7379. [PMID: 29498284 DOI: 10.1021/acs.joc.7b03193] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A radical "on water" addition to the C═N bond of hydrazones has been described. Hydrazone, diphenylsilane, alkyl iodide, and triethylborane afforded the corresponding addition products "on water" in good yields. A significant solvent effect was observed from the water. The developed protocol can be applied to the synthesis of 3-substituted isoindolinone derivatives. Moreover, the process offers environmentally benign tin-free radical reaction conditions.
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Affiliation(s)
- Tae Kyu Nam
- Department of Chemistry , Yonsei University , Wonju 26493 , Republic of Korea
| | - Doo Ok Jang
- Department of Chemistry , Yonsei University , Wonju 26493 , Republic of Korea
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8
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Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase. J Virol 2018; 92:JVI.02203-17. [PMID: 29643235 DOI: 10.1128/jvi.02203-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/31/2018] [Indexed: 12/25/2022] Open
Abstract
We tested three compounds for their ability to inhibit the RNase H (RH) and polymerase activities of HIV-1 reverse transcriptase (RT). A high-resolution crystal structure (2.2 Å) of one of the compounds showed that it chelates the two magnesium ions at the RH active site; this prevents the RH active site from interacting with, and cleaving, the RNA strand of an RNA-DNA heteroduplex. The compounds were tested using a variety of substrates: all three compounds inhibited the polymerase-independent RH activity of HIV-1 RT. Time-of-addition experiments showed that the compounds were more potent if they were bound to RT before the nucleic acid substrate was added. The compounds significantly inhibited the site-specific cleavage required to generate the polypurine tract (PPT) RNA primer that initiates the second strand of viral DNA synthesis. The compounds also reduced the polymerase activity of RT; this ability was a result of the compounds binding to the RH active site. These compounds appear to be relatively specific; they do not inhibit either Escherichia coli RNase HI or human RNase H2. The compounds inhibit the replication of an HIV-1-based vector in a one-round assay, and their potencies were only modestly decreased by mutations that confer resistance to integrase strand transfer inhibitors (INSTIs), nucleoside analogs, or nonnucleoside RT inhibitors (NNRTIs), suggesting that their ability to block HIV replication is related to their ability to block RH cleavage. These compounds appear to be useful leads that can be used to develop more potent and specific compounds.IMPORTANCE Despite advances in HIV-1 treatment, drug resistance is still a problem. Of the four enzymatic activities found in HIV-1 proteins (protease, RT polymerase, RT RNase H, and integrase), only RNase H has no approved therapeutics directed against it. This new target could be used to design and develop new classes of inhibitors that would suppress the replication of the drug-resistant variants that have been selected by the current therapeutics.
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Malviya J, Singh RKP, Kala S, Sharma LK. Anodic Synthesis of New Benzofuran Derivatives Using Active Methylene Group at Platinum Electrode. RUSS J ELECTROCHEM+ 2018. [DOI: 10.1134/s1023193518030096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhao XZ, Smith SJ, Maskell DP, Métifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR. Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors. J Med Chem 2017; 60:7315-7332. [PMID: 28737946 PMCID: PMC5601359 DOI: 10.1021/acs.jmedchem.7b00596] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Indexed: 12/16/2022]
Abstract
Integrase mutations can reduce the effectiveness of the first-generation FDA-approved integrase strand transfer inhibitors (INSTIs), raltegravir (RAL) and elvitegravir (EVG). The second-generation agent, dolutegravir (DTG), has enjoyed considerable clinical success; however, resistance-causing mutations that diminish the efficacy of DTG have appeared. Our current findings support and extend the substrate envelope concept that broadly effective INSTIs can be designed by filling the envelope defined by the DNA substrates. Previously, we explored 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides as an INSTI scaffold, making a limited set of derivatives, and concluded that broadly effective INSTIs can be developed using this scaffold. Herein, we report an extended investigation of 6-substituents as well the first examples of 7-substituted analogues of this scaffold. While 7-substituents are not well-tolerated, we have identified novel substituents at the 6-position that are highly effective, with the best compound (6p) retaining better efficacy against a broad panel of known INSTI resistant mutants than any analogues we have previously described.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical
Biology Laboratory and HIV Dynamics and Replication Program, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland 21702, United States
| | - Steven J. Smith
- Chemical
Biology Laboratory and HIV Dynamics and Replication Program, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland 21702, United States
| | - Daniel P. Maskell
- Chromatin
Structure and Mobile DNA, The Francis Crick
Institute, London NW1 1AT, United Kingdom
| | - Mathieu Métifiot
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Valerie E. Pye
- Chromatin
Structure and Mobile DNA, The Francis Crick
Institute, London NW1 1AT, United Kingdom
| | - Katherine Fesen
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christophe Marchand
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yves Pommier
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Peter Cherepanov
- Chromatin
Structure and Mobile DNA, The Francis Crick
Institute, London NW1 1AT, United Kingdom
- Imperial
College London, St-Mary’s
Campus, Norfolk Place, London W2 1PG, United Kingdom
| | - Stephen H. Hughes
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Terrence R. Burke
- Chemical
Biology Laboratory and HIV Dynamics and Replication Program, Center
for Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland 21702, United States
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11
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Zhao XZ, Metifiot M, Smith SJ, Maddali K, Marchand C, Hughes SH, Pommier Y, Burke TR. 6,7-Dihydroxyisoindolin-1-one and 7,8-Dihydroxy-3,4-Dihydroisoquinolin- 1(2H)-one Based HIV-1 Integrase Inhibitors. Curr Top Med Chem 2016; 16:435-40. [PMID: 26268341 DOI: 10.2174/1568026615666150813150058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/22/2022]
Abstract
Integrase (IN) is an essential viral enzyme required for HIV-1 replication, which has been targeted by anti-AIDS therapeutics. Integrase strand transfer inhibitors (INSTIs) represent a new class of antiretroviral agents developed for the treatment of HIV-1 infections. Important structural features that are shared by many INSTIs include a coplanar arrangement of three heteroatoms that chelate two catalytic Mg(2+) ions in the IN active site and a linked halophenyl ring that binds in the hydrophobic pocket formed by the complex of IN with viral DNA. We recently reported bicyclic 6,7-dihydroxyoxoisoindolin-1-one-based IN inhibitors. In the current study, we modified these inhibitors in three ways. First, we increased the spacer length between the metalchelating triad and the halophenyl group. Second, we replaced the indoline [5,6] bicycle with a fused dihydroxyisoquinolinones [6,6] ring system. Finally, we prepared bis-6,7-dihydroxyisoindolin-1-one-4-sulfonamides as dimeric HIV-1 IN inhibitors. These new analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA.
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12
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Métifiot M, Johnson BC, Kiselev E, Marler L, Zhao XZ, Burke TR, Marchand C, Hughes SH, Pommier Y. Selectivity for strand-transfer over 3'-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme-DNA interactions in the active site. Nucleic Acids Res 2016; 44:6896-906. [PMID: 27369381 PMCID: PMC5001616 DOI: 10.1093/nar/gkw592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 06/21/2016] [Indexed: 12/23/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are highly effective against HIV infections. Co-crystal structures of the prototype foamy virus intasome have shown that all three FDA-approved drugs, raltegravir (RAL), elvitegravir and dolutegravir (DTG), act as interfacial inhibitors during the strand transfer (ST) integration step. However, these structures give only a partial sense for the limited inhibition of the 3′-processing reaction by INSTIs and how INSTIs can be modified to overcome drug resistance, notably against the G140S-Q148H double mutation. Based on biochemical experiments with modified oligonucleotides, we demonstrate that both the viral DNA +1 and −1 bases, which flank the 3′-processing site, play a critical role for 3′-processing efficiency and inhibition by RAL and DTG. In addition, the G140S-Q148H (SH) mutant integrase, which has a reduced 3′-processing activity, becomes more active and more resistant to inhibition of 3′-processing by RAL and DTG in the absence of the −1 and +1 bases. Molecular modeling of HIV-1 integrase, together with biochemical data, indicate that the conserved residue Q146 in the flexible loop of HIV-1 integrase is critical for productive viral DNA binding through specific contacts with the virus DNA ends in the 3′-processing and ST reactions. The potency of integrase inhibitors against 3′-processing and their ability to overcome resistance is discussed.
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Affiliation(s)
- Mathieu Métifiot
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Barry C Johnson
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Laura Marler
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
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13
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Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR. HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases. ACS Chem Biol 2016; 11:1074-81. [PMID: 26808478 PMCID: PMC4836387 DOI: 10.1021/acschembio.5b00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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HIV
integrase (IN) strand transfer inhibitors (INSTIs) are among
the newest anti-AIDS drugs; however, mutant forms of IN can confer
resistance. We developed noncytotoxic naphthyridine-containing INSTIs
that retain low nanomolar IC50 values against HIV-1 variants
harboring all of the major INSTI-resistant mutations. We found by
analyzing crystal structures of inhibitors bound to the IN from the
prototype foamy virus (PFV) that the most successful inhibitors show
striking mimicry of the bound viral DNA prior to 3′-processing
and the bound host DNA prior to strand transfer. Using this concept
of “bi-substrate mimicry,” we developed a new broadly
effective inhibitor that not only mimics aspects of both the bound
target and viral DNA but also more completely fills the space they
would normally occupy. Maximizing shape complementarity and recapitulating
structural components encompassing both of the IN DNA substrates could
serve as a guiding principle for the development of new INSTIs.
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Affiliation(s)
| | | | - Daniel P. Maskell
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
| | - Mathieu Metifiot
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Valerie E. Pye
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
| | - Katherine Fesen
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christophe Marchand
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yves Pommier
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Peter Cherepanov
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
- Imperial College London, St-Mary’s
Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Stephen H. Hughes
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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14
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Smith SJ, Pauly GT, Akram A, Melody K, Rai G, Maloney DJ, Ambrose Z, Thomas CJ, Schneider JT, Hughes SH. Rilpivirine analogs potently inhibit drug-resistant HIV-1 mutants. Retrovirology 2016; 13:11. [PMID: 26880034 PMCID: PMC4754833 DOI: 10.1186/s12977-016-0244-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are a class of antiretroviral compounds that bind in an allosteric binding pocket in HIV-1 RT, located about 10 Å from the polymerase active site. Binding of an NNRTI causes structural changes that perturb the alignment of the primer terminus and polymerase active site, preventing viral DNA synthesis. Rilpivirine (RPV) is the most recent NNRTI approved by the FDA, but like all other HIV-1 drugs, suboptimal treatment can lead to the development of resistance. To generate better compounds that could be added to the current HIV-1 drug armamentarium, we have developed several RPV analogs to combat viral variants that are resistant to the available NNRTIs. Results Using a single-round infection assay, we identified several RPV analogs that potently inhibited a broad panel of NNRTI resistant mutants. Additionally, we determined that several resistant mutants selected by either RPV or Doravirine (DOR) caused only a small increase in susceptibility to the most promising RPV analogs. Conclusions The antiviral data suggested that there are RPV analogs that could be candidates for further development as NNRTIs, and one of the most promising compounds was modeled in the NNRTI binding pocket. This model can be used to explain why this compound is broadly effective against the panel of NNRTI resistance mutants. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0244-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven J Smith
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Gary T Pauly
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Aamir Akram
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Kevin Melody
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Ganesha Rai
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - David J Maloney
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - Zandrea Ambrose
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA. .,Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Drive, Bethesda, MD, 3370, USA.
| | - Joel T Schneider
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
| | - Stephen H Hughes
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD, USA.
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15
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Abstract
The catalytic site of the HIV integrase is contained within an RNase H-like fold, and numerous drugs have been developed that bind to this site and inhibit its activity. Herpes simplex virus (HSV) encodes two proteins with potential RNase H-like folds, the infected cell protein 8 (ICP8) DNA-binding protein, which is necessary for viral DNA replication and exhibits recombinase activity in vitro, and the viral terminase, which is essential for viral DNA cleavage and packaging. Therefore, we hypothesized that HIV integrase inhibitors might also inhibit HSV replication by targeting ICP8 and/or the terminase. To test this, we evaluated the effect of 118-D-24, a potent HIV integrase inhibitor, on HSV replication. We found that 118-D-24 inhibited HSV-1 replication in cell culture at submillimolar concentrations. To identify more potent inhibitors of HSV replication, we screened a panel of integrase inhibitors, and one compound with greater anti-HSV-1 activity, XZ45, was chosen for further analysis. XZ45 significantly inhibited HSV-1 and HSV-2 replication in different cell types, with 50% inhibitory concentrations that were approximately 1 µM, but exhibited low cytotoxicity, with a 50% cytotoxic concentration greater than 500 µM. XZ45 blocked HSV viral DNA replication and late gene expression. XZ45 also inhibited viral recombination in infected cells and ICP8 recombinase activity in vitro. Furthermore, XZ45 inhibited human cytomegalovirus replication and induction of Kaposi’s sarcoma herpesvirus from latent infection. Our results argue that inhibitors of enzymes with RNase H-like folds may represent a general antiviral strategy, which is useful not only against HIV but also against herpesviruses. The herpesviruses cause considerable morbidity and mortality. Nucleoside analogs have served as effective antiviral agents against the herpesviruses, but resistance can arise through viral mutation. Second-line anti-herpes drugs have limitations in terms of pharmacokinetic properties and/or toxicity, so there is a great need for additional drugs for treatment of herpesviral infections. This study showed that the HIV integrase inhibitors also block herpesviral infection, raising the important potential of a new class of anti-herpes drugs and the prospect of drugs that combat both HIV and the herpesviruses.
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16
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Reddy KK, Singh SK. Combined ligand and structure-based approaches on HIV-1 integrase strand transfer inhibitors. Chem Biol Interact 2014; 218:71-81. [DOI: 10.1016/j.cbi.2014.04.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/11/2014] [Accepted: 04/16/2014] [Indexed: 11/25/2022]
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17
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Zhao XZ, Smith SJ, Métifiot M, Marchand C, Boyer PL, Pommier Y, Hughes SH, Burke TR. 4-amino-1-hydroxy-2-oxo-1,8-naphthyridine-containing compounds having high potency against raltegravir-resistant integrase mutants of HIV-1. J Med Chem 2014; 57:5190-202. [PMID: 24901667 PMCID: PMC4216207 DOI: 10.1021/jm5001908] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
There
are currently three HIV-1 integrase (IN) strand transfer
inhibitors (INSTIs) approved by the FDA for the treatment of AIDS.
However, the emergence of drug-resistant mutants emphasizes the need
to develop additional agents that have improved efficacies against
the existent resistant mutants. As reported herein, we modified our
recently disclosed 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides
IN inhibitors to develop compounds that have improved efficacies against
recombinant IN in biochemical assays. These new compounds show single-digit
nanomolar antiviral potencies against HIV vectors that carry wild-type
(WT) IN in a single round replication assay and have improved potency
against vectors harboring the major forms of drug resistant IN mutants.
These compounds also have low toxicity for cultured cells, which in
several cases, results in selectivity indices (CC50/EC50) of greater than 10000. The compounds have the potential,
with additional structural modifications, to yield clinical agents
that are effective against the known strains of resistant viruses.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, and ‡HIV Drug Resistance Program, Center for Cancer Research, NCI at Frederick, National Institutes of Health , Building 376, Boyles Street, P.O. Box B, Frederick, Maryland 21702, United States
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18
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Lewis acid-catalyzed cascade radical addition/cyclization for the synthesis of 3-substituted isoindolin-1-one derivatives. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Zhao XZ, Smith SJ, Métifiot M, Johnson BC, Marchand C, Pommier Y, Hughes SH, Burke TR. Bicyclic 1-hydroxy-2-oxo-1,2-dihydropyridine-3-carboxamide-containing HIV-1 integrase inhibitors having high antiviral potency against cells harboring raltegravir-resistant integrase mutants. J Med Chem 2014; 57:1573-82. [PMID: 24471816 PMCID: PMC3983366 DOI: 10.1021/jm401902n] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Integrase
(IN) inhibitors are the newest class of antiretroviral
agents developed for the treatment of HIV-1 infections. Merck’s
Raltegravir (RAL) (October 2007) and Gilead’s Elvitegravir
(EVG) (August 2012), which act as IN strand transfer inhibitors (INSTIs),
were the first anti-IN drugs to be approved by the FDA. However, the
virus develops resistance to both RAL and EVG, and there is extensive
cross-resistance to these two drugs. New “2nd-generation”
INSTIs are needed that will have greater efficacy against RAL- and
EVG-resistant strains of IN. The FDA has recently approved the first
second generation INSTI, GSK’s Dolutegravir (DTG) (August 2013).
Our current article describes the design, synthesis, and evaluation
of a series of 1,8-dihydroxy-2-oxo-1,2-dihydroquinoline-3-carboxamides,
1,4-dihydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides,
and 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides.
This resulted in the identification of noncytotoxic inhibitors that
exhibited single digit nanomolar EC50 values against HIV-1
vectors harboring wild-type IN in cell-based assays. Importantly,
some of these new inhibitors retain greater antiviral efficacy compared
to that of RAL when tested against a panel of IN mutants that included
Y143R, N155H, G140S/Q148H, G118R, and E138K/Q148K.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health , Frederick, Maryland 21702, United States
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20
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Esposito F, Tramontano E. Past and future. Current drugs targeting HIV-1 integrase and reverse transcriptase-associated ribonuclease H activity: single and dual active site inhibitors. Antivir Chem Chemother 2014; 23:129-44. [PMID: 24150519 DOI: 10.3851/imp2690] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2013] [Indexed: 02/07/2023] Open
Abstract
Catalytic HIV type-1 (HIV-1) integrase (IN) and ribonuclease H (RNase H) domains belong to the polynucleotidyl transferase superfamily and are characterized by highly conserved motifs that coordinate two divalent Mg(2+) cations and are attractive targets for new antiviral agents. Several structural features of both domains are now available. Drugs targeting the HIV-1 IN are currently approved for anti-HIV therapy, while no drug targeting the HIV-1 RNase H function is yet available. This review describes HIV-1 IN and the RNase H function and structures, compounds targeting their active sites and dual inhibition as a new approach for drug development.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
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21
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Bhatt H, Patel P, Pannecouque C. Discovery of HIV-1 Integrase Inhibitors: Pharmacophore Mapping, Virtual Screening, Molecular Docking, Synthesis, and Biological Evaluation. Chem Biol Drug Des 2013; 83:154-66. [DOI: 10.1111/cbdd.12207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/18/2013] [Accepted: 08/12/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Hardik Bhatt
- Department of Pharmaceutical Chemistry; Institute of Pharmacy; Nirma University; Ahmedabad 382 481 India
| | - Paresh Patel
- Department of Pharmaceutical Chemistry; L.J. Institute of Pharmacy; L.J. Campus, S.G. Highway Ahmedabad 382 210 India
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22
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Xuan S, Wang M, Kang H, Kirchmair J, Tan L, Yan A. Support Vector Machine (SVM) Models for Predicting Inhibitors of the 3′ Processing Step of HIV-1 Integrase. Mol Inform 2013; 32:811-26. [DOI: 10.1002/minf.201300107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/26/2013] [Indexed: 01/24/2023]
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23
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Johnson BC, Métifiot M, Ferris A, Pommier Y, Hughes SH. A homology model of HIV-1 integrase and analysis of mutations designed to test the model. J Mol Biol 2013; 425:2133-46. [PMID: 23542006 DOI: 10.1016/j.jmb.2013.03.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 01/26/2023]
Abstract
Although there are structures of the different domains of human immunodeficiency virus type 1 (HIV-1) integrase (IN), there is no structure of the entire protein. The recently determined crystal structures of the prototype foamy virus (PFV) IN tetramer, in complexes with viral DNA, led to the generation of models of full-length HIV-1 IN. These models were generated, in part, by superimposing the structures of the domains of HIV-1 IN onto the structure of full-length PFV IN. We developed a model for HIV-1 IN-based solely on its sequence alignment with PFV IN-that differs in several ways from the previous models. Specifically, in our model, the junction between the catalytic core domain and C-terminal domain adopts a helix-loop-helix motif that is similar to the corresponding segment of PFV IN and differs from the crystal structures of these two HIV-1 IN domains. The alignment of residues in the C-terminal domain also differs from the previous models. Our model can be used to explain the phenotype of previously published HIV-1 IN mutants. We made additional mutants, and the behavior of these new mutants provides additional support for the model.
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Affiliation(s)
- Barry C Johnson
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, P.O. Box B, Frederick, MD 21702, USA.
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24
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Métifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao X, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y. Activities, crystal structures, and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase. ACS Chem Biol 2013; 8:209-17. [PMID: 23075516 PMCID: PMC3548936 DOI: 10.1021/cb300471n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
On the basis of a series of lactam and phthalimide derivatives that inhibit HIV-1 integrase, we developed a new molecule, XZ-259, with biochemical and antiviral activities comparable to raltegravir. We determined the crystal structures of XZ-259 and four other derivatives in complex with the prototype foamy virus intasome. The compounds bind at the integrase-Mg(2+)-DNA interface of the integrase active site. In biochemical and antiviral assays, XZ-259 inhibits raltegravir-resistant HIV-1 integrases harboring the Y143R mutation. Molecular modeling is also presented suggesting that XZ-259 can bind in the HIV-1 intasome with its dimethyl sulfonamide group adopting two opposite orientations. Molecular dynamics analyses of the HIV-1 intasome highlight the importance of the viral DNA in drug potency.
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Affiliation(s)
| | | | - Barry C. Johnson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Stephen Hare
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Steven J. Smith
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - XueZhi Zhao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Terrence R. Burke
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Stephen H. Hughes
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Peter Cherepanov
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892 (KM, MM, CM, YP). Division of Infectious Diseases, Imperial College London, London, UK (SH, PC). HIV Drug Resistance Program (SS, BJ, SHH) and Chemical Biology Laboratory (XZ, TB), Molecular Discovery Program, Center for Cancer Research, Frederick National Laboratory, National Institutes of Health, Frederick, MD 21702
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25
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Mamidyala SK, Cooper MA. Probing the reactivity of o-phthalaldehydic acid/methyl ester: synthesis of N-isoindolinones and 3-arylaminophthalides. Chem Commun (Camb) 2013; 49:8407-9. [DOI: 10.1039/c3cc43838d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Zhao XZ, Maddali K, Smith SJ, Métifiot M, Johnson BC, Marchand C, Hughes SH, Pommier Y, Burke TR. 6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 integrase inhibitors. Bioorg Med Chem Lett 2012; 22:7309-13. [PMID: 23149229 PMCID: PMC3523327 DOI: 10.1016/j.bmcl.2012.10.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 12/22/2022]
Abstract
Although an extensive body of scientific and patent literature exists describing the development of HIV-1 integrase (IN) inhibitors, Merck's raltegravir and Gilead's elvitegravir remain the only IN inhibitors FDA-approved for the treatment of AIDS. The emergence of raltegravir-resistant strains of HIV-1 containing mutated forms of IN underlies the need for continued efforts to enhance the efficacy of IN inhibitors against resistant mutants. We have previously described bicyclic 6,7-dihydroxyoxoisoindolin-1-ones that show good IN inhibitory potency. This report describes the effects of introducing substituents into the 4- and 5-positions of the parent 6,7-dihydroxyoxoisoindolin-1-one platform. We have developed several sulfonamide-containing analogs that enhance potency in cell-based HIV assays by more than two orders-of-magnitude and we describe several compounds that are more potent than raltegravir against the clinically relevant Y143R IN mutant.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702, United States
| | - Kasthuraiah Maddali
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Steven J. Smith
- HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702, United States
| | - Mathieu Métifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Barry C. Johnson
- HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702, United States
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Stephen H. Hughes
- HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702, United States
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Terrence R. Burke
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702, United States
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27
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Viral enzymes containing magnesium: Metal binding as a successful strategy in drug design. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Zhao XZ, Maddali K, Metifiot M, Smith SJ, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR. Bicyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors. Chem Biol Drug Des 2011; 79:157-65. [PMID: 22107736 DOI: 10.1111/j.1747-0285.2011.01270.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
HIV-1 integrase (IN) is a validated therapeutic target for the treatment of AIDS. However, the emergence of resistance to raltegravir, the sole marketed FDA-approved IN inhibitor, emphasizes the need to develop second-generation inhibitors that retain efficacy against clinically relevant IN mutants. We report herein bicyclic hydroxy-1H-pyrrolopyridine-triones as a new family of HIV-1 integrase inhibitors that were efficiently prepared using a key 'Pummerer cyclization deprotonation cycloaddition' cascade of imidosulfoxides. In in vitro HIV-1 integrase assays, the analogs showed low micromolar inhibitory potencies with selectivity for strand transfer reactions as compared with 3'-processing inhibition. A representative inhibitor (5e) retained most of its inhibitory potency against the three major raltegravir-resistant IN mutant enzymes, G140S/Q148H, Y143R, and N155H. In antiviral assays employing viral vectors coding these IN mutants, compound 5e was approximately 200- and 20-fold less affected than raltegravir against the G140S/Q148H and Y143R mutations, respectively. Against the N155H mutation, 5e was approximately 10-fold less affected than raltegravir. Thus, our new compounds represent a novel structural class that may be further developed to overcome resistance to raltegravir, particularly in the case of the G140S/Q148H mutations.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA
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Abstract
With the U.S. Food and Drug Administration approval of raltegravir (RAL; MK-0518; Merck & Co.), HIV-1 integrase (IN) is the newest therapeutic target for AIDS and HIV infections. Recent structural analyses show that IN strand transfer inhibitors (INSTIs) share a common binding mode in the enzyme active site. While RAL represents a therapeutic breakthrough, the emergence of IN resistance mutations imposes the development of new INSTIs. We report here the biochemical and antiviral activities of MK-0536, a new IN inhibitor. We demonstrate that, like RAL, MK-0536 is highly potent against recombinant IN and viral replication. It is also effective against INs that carry the three main RAL resistance mutations (Y143R, N155H, and to a lesser extent G140S-Q148H) and against the G118R mutant. Modeling of IN developed from recent prototype foamy virus structures is presented to account for the differences in the drug activities of MK-0536 and RAL against the IN mutants.
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Hare S, Smith SJ, Métifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P. Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572). Mol Pharmacol 2011; 80:565-72. [PMID: 21719464 DOI: 10.1124/mol.111.073189] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Raltegravir (RAL) and related HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) efficiently block viral replication in vitro and suppress viremia in patients. These small molecules bind to the IN active site, causing it to disengage from the deoxyadenosine at the 3' end of viral DNA. The emergence of viral strains that are highly resistant to RAL underscores the pressing need to develop INSTIs with improved resistance profiles. Herein, we show that the candidate second-generation drug dolutegravir (DTG, S/GSK1349572) effectively inhibits a panel of HIV-1 IN variants resistant to first-generation INSTIs. To elucidate the structural basis for the increased potency of DTG against RAL-resistant INs, we determined crystal structures of wild-type and mutant prototype foamy virus intasomes bound to this compound. The overall IN binding mode of DTG is strikingly similar to that of the tricyclic hydroxypyrrole MK-2048. Both second-generation INSTIs occupy almost the same physical space within the IN active site and make contacts with the β4-α2 loop of the catalytic core domain. The extended linker region connecting the metal chelating core and the halobenzyl group of DTG allows it to enter farther into the pocket vacated by the displaced viral DNA base and to make more intimate contacts with viral DNA, compared with those made by RAL and other INSTIs. In addition, our structures suggest that DTG has the ability to subtly readjust its position and conformation in response to structural changes in the active sites of RAL-resistant INs.
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Affiliation(s)
- Stephen Hare
- Division of Infectious Diseases, Imperial College London, London, United Kingdom
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Fan X, Zhang FH, Al-Safi RI, Zeng LF, Shabaik Y, Debnath B, Sanchez TW, Odde S, Neamati N, Long YQ. Design of HIV-1 integrase inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75: a scaffold hopping approach using salicylate and catechol groups. Bioorg Med Chem 2011; 19:4935-52. [PMID: 21778063 DOI: 10.1016/j.bmc.2011.06.058] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 06/18/2011] [Accepted: 06/20/2011] [Indexed: 12/31/2022]
Abstract
HIV-1 integrase (IN) is a validated therapeutic target for antiviral drug design. However, the emergence of viral strains resistant to clinically studied IN inhibitors demands the discovery of novel inhibitors that are structurally as well mechanistically different. Herein, we describe the design and discovery of novel IN inhibitors targeting the catalytic domain as well as its interaction with LEDGF/p75, which is essential for the HIV-1 integration as an IN cofactor. By merging the pharmacophores of salicylate and catechol, the 2,3-dihydroxybenzamide (5a) was identified as a new scaffold to inhibit the strand transfer reaction efficiently. Further structural modifications on the 2,3-dihydroxybenzamide scaffold revealed that the heteroaromatic functionality attached on the carboxamide portion and the piperidin-1-ylsulfonyl substituted at the phenyl ring are beneficial for the activity, resulting in a low micromolar IN inhibitor (5p, IC(50)=5 μM) with more than 40-fold selectivity for the strand transfer over the 3'-processing reaction. More significantly, this active scaffold remarkably inhibited the interaction between IN and LEDGF/p75 cofactor. The prototype example, N-(cyclohexylmethyl)-2,3-dihydroxy-5-(piperidin-1-ylsulfonyl) benzamide (5u) inhibited the IN-LEDGF/p75 interaction with an IC(50) value of 8 μM. Using molecular modeling, the mechanism of action was hypothesized to involve the chelation of the divalent metal ions inside the IN active site. Furthermore, the inhibitor of IN-LEDGF/p75 interaction was properly bound to the LEDGF/p75 binding site on IN. This work provides a new and efficient approach to evolve novel HIV-1 IN inhibitors from rational integration and optimization of previously reported inhibitors.
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Affiliation(s)
- Xing Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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32
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Pendri A, Meanwell NA, Peese KM, Walker MA. New first and second generation inhibitors of human immunodeficiency virus-1 integrase. Expert Opin Ther Pat 2011; 21:1173-89. [DOI: 10.1517/13543776.2011.586631] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zhao XZ, Maddali K, Metifiot M, Smith SJ, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR. Development of tricyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors. Bioorg Med Chem Lett 2011; 21:2986-90. [PMID: 21493066 PMCID: PMC3085635 DOI: 10.1016/j.bmcl.2011.03.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 11/20/2022]
Abstract
New tricyclic HIV-1 integrase (IN) inhibitors were prepared that combined structural features of bicyclic pyrimidinones with recently disclosed 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones. This combination resulted in the introduction of a nitrogen into the aryl ring and the addition of a fused third ring to our previously described inhibitors. The resulting analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays, with good selectivity for strand transfer relative to 3'-processing.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Molecular Discovery Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Kasthuraiah Maddali
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mathieu Metifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Steven J. Smith
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - B. Christie Vu
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Stephen H. Hughes
- HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular Discovery Program, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
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Pharmacophore modeling of some novel indole β-diketo acid and coumarin-based derivatives as HIV integrase inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9520-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Gao XG, Yang CW, Zhang ZZ, Zeng CC, Song XQ, Hu LM, Zhong RG, She YB. Electrochemical oxidation of substituted catechols in the presence of pyrazol-5-ones: characterization of products and reaction mechanism. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Ramkumar K, Serrao E, Odde S, Neamati N. HIV-1 integrase inhibitors: 2007-2008 update. Med Res Rev 2010; 30:890-954. [DOI: 10.1002/med.20194] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Marchand C, Maddali K, Métifiot M, Pommier Y. HIV-1 IN inhibitors: 2010 update and perspectives. Curr Top Med Chem 2010; 9:1016-37. [PMID: 19747122 DOI: 10.2174/156802609789630910] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 06/13/2009] [Indexed: 12/29/2022]
Abstract
Integrase (IN) is the newest validated target against AIDS and retroviral infections. The remarkable activity of raltegravir (Isentress((R))) led to its rapid approval by the FDA in 2007 as the first IN inhibitor. Several other IN strand transfer inhibitors (STIs) are in development with the primary goal to overcome resistance due to the rapid occurrence of IN mutations in raltegravir-treated patients. Thus, many scientists and drug companies are actively pursuing clinically useful IN inhibitors. The objective of this review is to provide an update on the IN inhibitors reported in the last two years, including second generation STI, recently developed hydroxylated aromatics, natural products, peptide, antibody and oligonucleotide inhibitors. Additionally, the targeting of IN cofactors such as LEDGF and Vpr will be discussed as novel strategies for the treatment of AIDS.
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Affiliation(s)
- Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Andrake MD, Ramcharan J, Merkel G, Zhao XZ, Burke TR, Skalka AM. Comparison of metal-dependent catalysis by HIV-1 and ASV integrase proteins using a new and rapid, moderate throughput assay for joining activity in solution. AIDS Res Ther 2009; 6:14. [PMID: 19563676 PMCID: PMC2717984 DOI: 10.1186/1742-6405-6-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Accepted: 06/29/2009] [Indexed: 01/06/2023] Open
Abstract
Background HIV-1 integrase (IN) is an attractive target for the development of drugs to treat AIDS, and inhibitors of this viral enzyme are already in the clinic. Nevertheless, there is a continuing need to devise new approaches to block the activity of this viral protein because of the emergence of resistant strains. To facilitate the biochemical analysis of wild-type IN and its derivatives, and to measure the potency of prospective inhibitory compounds, a rapid, moderate throughput solution assay was developed for IN-catalyzed joining of viral and target DNAs, based on the detection of a fluorescent tag. Results A detailed, step-by-step description of the new joining assay is provided. The reactions are run in solution, the products captured on streptavidin beads, and activity is measured by release of a fluorescent tag. The procedure can be scaled up for the analysis of numerous samples, and is substantially more rapid and sensitive than the standard radioactive gel methods. The new assay is validated and its utility demonstrated via a detailed comparison of the Mg++- and Mn++-dependent activities of the IN proteins from human immunodeficiency virus type 1 (HIV-1) and the avian sarcoma virus (ASV). The results confirm that ASV IN is considerably more active than HIV-1 IN, but with both enzymes the initial rates of joining, and the product yields, are higher in the presence of Mn++ than Mg++. Although the pH optima for these two enzymes are similar with Mn++, they differ significantly in the presence of Mg++, which is likely due to differences in the molecular environment of the binding region of this physiologically relevant divalent cation. This interpretation is strengthened by the observation that a compound that can inhibit HIV-1 IN in the presence of either metal cofactors is only effective against ASV in the presence of Mn++. Conclusion A simplified, assay for measuring the joining activity of retroviral IN in solution is described, which offers several advantages over previous methods and the standard radioactive gel analyses. Based on comparisons of signal to background ratios, the assay is 10–30 times more sensitive than gel analysis, allows more rapid and accurate biochemical analyses of IN catalytic activity, and moderate throughput screening of inhibitory compounds. The assay is validated, and its utility demonstrated in a comparison of the metal-dependent activities of HIV-1 and ASV IN proteins.
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Zhao XZ, Maddali K, Marchand C, Pommier Y, Burke TR. Diketoacid-genre HIV-1 integrase inhibitors containing enantiomeric arylamide functionality. Bioorg Med Chem 2009; 17:5318-24. [PMID: 19527935 DOI: 10.1016/j.bmc.2009.05.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 04/29/2009] [Accepted: 05/01/2009] [Indexed: 11/30/2022]
Abstract
Using our recently disclosed 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one and 4,5-dihydroxy-1H-isoindole-1,3(2H)-dione integrase inhibitors, we report differential effects on inhibitory potency induced by introduction of an alpha-chiral center into a key aryl substituent. We show that introduction of the chiral center is uniformly deleterious to binding, with the (R)-enantiomer being more deleterious than the (S)-enantiomer. A greater enantiomeric difference in potency is shown by inhibitors that have restricted rotation of the aryl ring, with the larger difference being due to poorer potency of the (R)-enantiomer rather than higher potency of the (S)-enantiomer. The potency difference for enantiomers based on the isoindoline-1,3-dione ring system is less than for those derived from the isoindol-1-one ring system. Our findings provide useful information that should aid in understanding molecular binding interactions of DKA-derived IN inhibitors.
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Affiliation(s)
- Xue Zhi Zhao
- Laboratory of Medicinal, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, United States
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Zhao XZ, Maddali K, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR. Examination of halogen substituent effects on HIV-1 integrase inhibitors derived from 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-ones and 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones. Bioorg Med Chem Lett 2009; 19:2714-7. [PMID: 19364649 DOI: 10.1016/j.bmcl.2009.03.122] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 10/21/2022]
Abstract
Using 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one and 4,5-dihydroxy-1H-isoindole-1,3(2H)-dione based HIV-1 integrase inhibitors as display platforms, we undertook a thorough examination of the effects of modifying the halogen substituents on a key benzyl ring that is hypothesized to bind in a hydrophobic pocket of the integrase.DNA complex. Data from this study suggest that in general dihalo-substituted analogues have higher potency than monohalo-substituted compounds, but that further addition of halogens is not beneficial.
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Affiliation(s)
- Xue Zhi Zhao
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, MD 21702, United States
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