1
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Grandgenett DP, Engelman AN. Brief Histories of Retroviral Integration Research and Associated International Conferences. Viruses 2024; 16:604. [PMID: 38675945 PMCID: PMC11054761 DOI: 10.3390/v16040604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The field of retroviral integration research has a long history that started with the provirus hypothesis and subsequent discoveries of the retroviral reverse transcriptase and integrase enzymes. Because both enzymes are essential for retroviral replication, they became valued targets in the effort to discover effective compounds to inhibit HIV-1 replication. In 2007, the first integrase strand transfer inhibitor was licensed for clinical use, and subsequently approved second-generation integrase inhibitors are now commonly co-formulated with reverse transcriptase inhibitors to treat people living with HIV. International meetings specifically focused on integrase and retroviral integration research first convened in 1995, and this paper is part of the Viruses Special Issue on the 7th International Conference on Retroviral Integration, which was held in Boulder Colorado in the summer of 2023. Herein, we overview key historical developments in the field, especially as they pertain to the development of the strand transfer inhibitor drug class. Starting from the mid-1990s, research advancements are presented through the lens of the international conferences. Our overview highlights the impact that regularly scheduled, subject-specific international meetings can have on community-building and, as a result, on field-specific collaborations and scientific advancements.
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Affiliation(s)
- Duane P. Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO 63104, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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2
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Kang JX, Zhao GK, Yang XM, Huang MX, Hui WQ, Zeng R, Ouyang Q. Recent advances on dual inhibitors targeting HIV reverse transcriptase associated polymerase and ribonuclease H. Eur J Med Chem 2023; 250:115196. [PMID: 36787657 DOI: 10.1016/j.ejmech.2023.115196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Reverse transcriptase (RT) plays an indispensable role in the replication of human immunodeficiency virus (HIV) through its associated polymerase and ribonuclease H (RNase H) activities during the viral RNA genome transformation into proviral DNA. Due to the fact that HIV is a highly mutagenic virus and easily resistant to single-target RT inhibitors, dual inhibitors targeting HIV RT associated polymerase and RNase H have been developed. These dual inhibitors have the advantages of increasing efficacy, reducing drug resistance, drug-drug interactions, and cytotoxicity, as well as improving patient compliance. In this review, we summarize recent advances in polymerase/RNase H dual inhibitors focusing on drug design strategies, and structure-activity relationships and share new insights into developing anti-HIV drugs.
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Affiliation(s)
- Jia-Xiong Kang
- Department of Pharmacy, Armed Police Forces Hospital of Sichuan, 614000, Leshan, China
| | - Guang-Kuan Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Xiu-Ming Yang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Mou-Xin Huang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Wen-Qi Hui
- Department of Pharmacy, Xi'an Fifth Hospital, Xian, 710082, Shaanxi, China
| | - Rong Zeng
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Qin Ouyang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China.
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3
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Yuldasheva GA, Argirova R, Ilin AI. Molecular Modeling of the Anti-HIV Activity Mechanism of Iodine-Containing Drugs Armenicum and FS-1. ACS OMEGA 2023; 8:8617-8624. [PMID: 36910923 PMCID: PMC9996613 DOI: 10.1021/acsomega.2c07720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Drugs Armenicum and FS-1 are a solution of ionic nanostructured complexes of α-dextrin. In the active centers of these drugs, located inside the dextrin helix, molecular iodine has such an electronic form that minimizes toxic effects in the human body, so these drugs can be used for parenteral and oral administration. On the human lymphoblastoid cell line MT-2, the effect of the antiviral action of FS-1 against HIV-1 was established. Literature data on the results of treatment of people with HIV infection with Armenicum are presented. The mechanism of anti-HIV action of drugs Armenicum and FS-1 was proposed by the molecular modeling method. Using the DFT/B3PW91/6-31G** approach, it was shown that LiI(Cl)I2 active center drugs of Armenicum and FS-1 can be segregated from the dextrin helix and can form a complex with the ACT nucleotide triplet, which is part of a specific fragment of viral DNA that binds to the active center of integrase. The formation of this complex is a key moment in the mechanism of anti-HIV drug action. Molecular iodine and lithium halide, which are part of the active complexes, inhibit the active center of the catalytic domain of the integrase. A new nucleoprotein complex is created that destroys the nucleoprotein preintegration complex (PIC) and inhibits the HIV DNA and the active center of the catalytic domain, while a new N-I bond appears in the viral DNA in the cytosine pyrimidine cycle.
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Affiliation(s)
| | - Radka Argirova
- Clinical
Laboratory Tokuda Hospital, Street 51B Nikola I. Vaptsarov Boulevard, Lozenets, Sofia 1407, Bulgaria
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4
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Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses 2021; 13:v13020205. [PMID: 33572956 PMCID: PMC7912079 DOI: 10.3390/v13020205] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are currently recommended for the first line treatment of human immunodeficiency virus type one (HIV-1) infection. The first-generation INSTIs are effective but can select for resistant viruses. Recent advances have led to several potent second-generation INSTIs that are effective against both wild-type (WT) HIV-1 integrase and many of the first-generation INSTI-resistant mutants. The emergence of resistance to these new second-generation INSTIs has been minimal, which has resulted in alternative treatment strategies for HIV-1 patients. Moreover, because of their high antiviral potencies and, in some cases, their bioavailability profiles, INSTIs will probably have prominent roles in pre-exposure prophylaxis (PrEP). Herein, we review the current state of the clinically relevant INSTIs and discuss the future outlook for this class of antiretrovirals.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (D.O.P.); (D.L.)
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (X.Z.Z.); (T.R.B.J.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
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5
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Jóźwik IK, Passos DO, Lyumkis D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. Trends Pharmacol Sci 2020; 41:611-626. [PMID: 32624197 PMCID: PMC7429322 DOI: 10.1016/j.tips.2020.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Integrase (IN) strand transfer inhibitors (INSTIs) are recent compounds in the antiretroviral arsenal used against HIV. INSTIs work by blocking retroviral integration; an essential step in the viral lifecycle that is catalyzed by the virally encoded IN protein within a nucleoprotein assembly called an intasome. Recent structures of lentiviral intasomes from simian immunodeficiency virus (SIV) and HIV have clarified the INSTI binding modes within the intasome active sites and helped elucidate an important mechanism of viral resistance. The structures provide an accurate depiction of interactions of intasomes and INSTIs to be leveraged for structure-based drug design. Here, we review these recent structural findings and contrast with earlier studies on prototype foamy virus intasomes. We also present and discuss examples of the latest chemical compounds that show promising inhibitory potential as INSTI candidates.
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Affiliation(s)
- Ilona K Jóźwik
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dario O Passos
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA; The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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6
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Engelman AN. Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition. J Biol Chem 2019; 294:15137-15157. [PMID: 31467082 DOI: 10.1074/jbc.rev119.006901] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral inhibitors that are used to manage HIV infection/AIDS predominantly target three enzymes required for virus replication: reverse transcriptase, protease, and integrase. Although integrase inhibitors were the last among this group to be approved for treating people living with HIV, they have since risen to the forefront of treatment options. Integrase strand transfer inhibitors (INSTIs) are now recommended components of frontline and drug-switch antiretroviral therapy formulations. Integrase catalyzes two successive magnesium-dependent polynucleotidyl transferase reactions, 3' processing and strand transfer, and INSTIs tightly bind the divalent metal ions and viral DNA end after 3' processing, displacing from the integrase active site the DNA 3'-hydroxyl group that is required for strand transfer activity. Although second-generation INSTIs present higher barriers to the development of viral drug resistance than first-generation compounds, the mechanisms underlying these superior barrier profiles are incompletely understood. A separate class of HIV-1 integrase inhibitors, the allosteric integrase inhibitors (ALLINIs), engage integrase distal from the enzyme active site, namely at the binding site for the cellular cofactor lens epithelium-derived growth factor (LEDGF)/p75 that helps to guide integration into host genes. ALLINIs inhibit HIV-1 replication by inducing integrase hypermultimerization, which precludes integrase binding to genomic RNA and perturbs the morphogenesis of new viral particles. Although not yet approved for human use, ALLINIs provide important probes that can be used to investigate the link between HIV-1 integrase and viral particle morphogenesis. Herein, I review the mechanisms of retroviral integration as well as the promises and challenges of using integrase inhibitors for HIV/AIDS management.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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7
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Noshi T, Kitano M, Taniguchi K, Yamamoto A, Omoto S, Baba K, Hashimoto T, Ishida K, Kushima Y, Hattori K, Kawai M, Yoshida R, Kobayashi M, Yoshinaga T, Sato A, Okamatsu M, Sakoda Y, Kida H, Shishido T, Naito A. In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Antiviral Res 2018; 160:109-117. [PMID: 30316915 DOI: 10.1016/j.antiviral.2018.10.008] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/02/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Cap-dependent endonuclease (CEN) resides in the PA subunit of the influenza virus and mediates the critical "cap-snatching" step of viral RNA transcription, which is considered to be a promising anti-influenza target. Here, we describe in vitro characterization of a novel CEN inhibitor, baloxavir acid (BXA), the active form of baloxavir marboxil (BXM). BXA inhibits viral RNA transcription via selective inhibition of CEN activity in enzymatic assays, and inhibits viral replication in infected cells without cytotoxicity in cytopathic effect assays. The antiviral activity of BXA is also confirmed in yield reduction assays with seasonal type A and B viruses, including neuraminidase inhibitor-resistant strains. Furthermore, BXA shows broad potency against various subtypes of influenza A viruses (H1N2, H5N1, H5N2, H5N6, H7N9 and H9N2). Additionally, serial passages of the viruses in the presence of BXA result in isolation of PA/I38T variants with reduced BXA susceptibility. Phenotypic and genotypic analyses with reverse genetics demonstrate the mechanism of BXA action via CEN inhibition in infected cells. These results reveal the in vitro characteristics of BXA and support clinical use of BXM to treat influenza.
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Affiliation(s)
| | | | - Keiichi Taniguchi
- Shionogi & Co., Ltd., Osaka, Japan; Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | | | | | | | | | | | | | | | | | | | | | | | - Akihiko Sato
- Shionogi & Co., Ltd., Osaka, Japan; Research Center for Zoonosis Control, Hokkaido University, Japan
| | - Masatoshi Okamatsu
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Yoshihiro Sakoda
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Hiroshi Kida
- Research Center for Zoonosis Control, Hokkaido University, Japan
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8
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Pommier Y, Pilon A, Bajaj K, Mazumder A, Neamati N. HIV-1 Integrase as a Target for Antiviral Drugs. ACTA ACUST UNITED AC 2017. [DOI: 10.1177/095632029700800601] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Y Pommier
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Building 37, Room 5C25, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - Aa Pilon
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Building 37, Room 5C25, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - K Bajaj
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Building 37, Room 5C25, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - A Mazumder
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Building 37, Room 5C25, National Institutes of Health, Bethesda, MD 20892-4255, USA
| | - N Neamati
- Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, Building 37, Room 5C25, National Institutes of Health, Bethesda, MD 20892-4255, USA
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9
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Liu GN, Luo RH, Zhou Y, Zhang XJ, Li J, Yang LM, Zheng YT, Liu H. Synthesis and Anti-HIV-1 Activity Evaluation for Novel 3a,6a-Dihydro-1H-pyrrolo[3,4-c]pyrazole-4,6-dione Derivatives. Molecules 2016; 21:molecules21091198. [PMID: 27617994 PMCID: PMC6274355 DOI: 10.3390/molecules21091198] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
The search for new molecular constructs that resemble the critical two-metal binding pharmacophore and the halo-substituted phenyl functionality required for HIV-1 integrase (IN) inhibition represents a vibrant area of research within drug discovery. As reported herein, we have modified our recently disclosed 1-[2-(4-fluorophenyl)ethyl]-pyrrole-2,5-dione scaffolds to design 35 novel compounds with improved biological activities against HIV-1. These new compounds show single-digit micromolar antiviral potencies against HIV-1 and low toxicity. Among of them, compound 9g and 15i had potent anti-HIV-1 activities (EC50 < 5 μM) and excellent therapeutic index (TI, CC50/EC50 > 100). These two compounds have potential as lead compounds for further optimization into clinical anti-HIV-1 agents.
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Affiliation(s)
- Guan-Nan Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China.
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Yu Zhou
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Xing-Jie Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Jian Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Liu-Meng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Hong Liu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
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10
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Wang Y, Klock H, Yin H, Wolff K, Bieza K, Niswonger K, Matzen J, Gunderson D, Hale J, Lesley S, Kuhen K, Caldwell J, Brinker A. Homogeneous High-Throughput Screening Assays for HIV-1 Integrase 3β-Processing and Strand Transfer Activities. ACTA ACUST UNITED AC 2016; 10:456-62. [PMID: 16093555 DOI: 10.1177/1087057105275212] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
HIV-1 integrase (HIV-IN) is a well-validated antiviral drug target catalyzing a multistep reaction to incorporate the HIV-1 provirus into the genome of the host cell. Smallmolecule inhibitors of HIV-1 integrase that specifically target the strand transfer step have demonstrated efficacy in the suppression of virus propagation. However, only fewspecific strand transfer inhibitors have been identified to date, and the need to screen for novel compound scaffolds persists. Here, the authors describe 2 homogeneous time-resolved fluorescent resonance energy transfer-based assays for the measurement of HIV-1 integrase 3'-processing and strand transfer activities. Both assayswere optimized for high-throughput screening formats, and a diverse library containingmore than 1million compoundswas screened in 1536-well plates for HIV-IN strand transfer inhibitors. As a result, compounds were found that selectively affect the enzymatic strand transfer reaction over 3β processing. Moreover, several bioactivemoleculeswere identified that inhibited HIV-1 reporter virus infection in cellularmodel systems. In conclusion, the assays presented herein have proven their utility for the identification ofmechanistically interesting and biologically active inhibitors of HIV-1 integrase that hold potential for further development into potent antiviral drugs.
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Affiliation(s)
- Yu Wang
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
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Pescatori L, Métifiot M, Chung S, Masoaka T, Cuzzucoli Crucitti G, Messore A, Pupo G, Madia VN, Saccoliti F, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Pommier Y, Marchand C, Costi R, Di Santo R. N-Substituted Quinolinonyl Diketo Acid Derivatives as HIV Integrase Strand Transfer Inhibitors and Their Activity against RNase H Function of Reverse Transcriptase. J Med Chem 2015; 58:4610-23. [PMID: 25961960 DOI: 10.1021/acs.jmedchem.5b00159] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bifunctional quinolinonyl DKA derivatives were first described as nonselective inhibitors of 3'-processing (3'-P) and strand transfer (ST) functions of HIV-1 integrase (IN), while 7-aminosubstituted quinolinonyl derivatives were proven IN strand transfer inhibitors (INSTIs) that also displayed activity against ribonuclease H (RNase H). In this study, we describe the design, synthesis, and biological evaluation of new quinolinonyl diketo acid (DKA) derivatives characterized by variously substituted alkylating groups on the nitrogen atom of the quinolinone ring. Removal of the second DKA branch of bifunctional DKAs, and the amino group in position 7 of quinolinone ring combined with a fine-tuning of the substituents on the benzyl group in position 1 of the quinolinone, increased selectivity for IN ST activity. In vitro, the most potent compound was 11j (IC50 = 10 nM), while the most active compounds against HIV infected cells were ester derivatives 10j and 10l. In general, the activity against RNase H was negligible, with only a few compounds active at concentrations higher than 10 μM. The binding mode of the most potent IN inhibitor 11j within the IN catalytic core domain (CCD) is described as well as its binding mode within the RNase H catalytic site to rationalize its selectivity.
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Affiliation(s)
- Luca Pescatori
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Mathieu Métifiot
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Suhman Chung
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Takashi Masoaka
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Giuliana Cuzzucoli Crucitti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Antonella Messore
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Giovanni Pupo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Valentina Noemi Madia
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saccoliti
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Luigi Scipione
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Silvano Tortorella
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Francesco Saverio Di Leva
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Sandro Cosconati
- ⊥DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luciana Marinelli
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Stuart F J Le Grice
- §Resistance Mechanisms Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Yves Pommier
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Christophe Marchand
- ‡Laboratory of Molecular Pharmacology and Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5068, Bethesda, Maryland 20892-4255, United States
| | - Roberta Costi
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
| | - Roberto Di Santo
- †Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, P-le Aldo Moro 5, I-00185, Roma, Italy
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12
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Aromatic Medicinal Plants from Tajikistan (Central Asia). MEDICINES 2015; 2:28-46. [PMID: 28933380 PMCID: PMC5532974 DOI: 10.3390/medicines2010028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/13/2015] [Accepted: 02/09/2015] [Indexed: 12/03/2022]
Abstract
Tajikistan is a small country located in Central Asia. The mostly mountainous terrain with a continental, subtropical, and semiarid climate, is characterized by diverse flora. Many people in Tajikistan rely on medicinal plants as their traditional form of medicine to prevent and cure health disorders. Aromatic medicinal plants, in particular, have played an important role for the local people. In this review, we present a summary of the uses of 18 aromatic medicinal plants from Tajikistan and their compositions of secondary metabolites.
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13
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Synthesis and antitumor activities of novel α-aminophosphonate derivatives containing an alizarin moiety. Eur J Med Chem 2014; 83:116-28. [DOI: 10.1016/j.ejmech.2014.02.067] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/19/2014] [Accepted: 02/19/2014] [Indexed: 02/07/2023]
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14
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Bushman FD. Engineering the human genome: reflections on the beginning. Hum Gene Ther 2014; 25:395-400. [PMID: 24848314 DOI: 10.1089/hum.2014.2524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine , Philadelphia, PA 19104-6076
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15
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Duan F, Li X, Cai S, Xin G, Wang Y, Du D, He S, Huang B, Guo X, Zhao H, Zhang R, Ma L, Liu Y, Du Q, Wei Z, Xing Z, Liang Y, Wu X, Fan C, Ji C, Zeng D, Chen Q, He Y, Liu X, Huang W. Haloemodin as Novel Antibacterial Agent Inhibiting DNA Gyrase and Bacterial Topoisomerase I. J Med Chem 2014; 57:3707-14. [PMID: 24588790 DOI: 10.1021/jm401685f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Feixia Duan
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
- College
of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Xiaohong Li
- Department
of Biopharmaceutics, Key Laboratory of Drug Targeting and Drug Delivery
Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, No. 17, Section 3 Southern Renmin Road, Chengdu 610041, China
| | - Suping Cai
- Shenzhen
Eye Hospital, Jinan University, No. 18, Zetian Road, Futian District, Shenzhen 518040, China
| | - Guang Xin
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Yanyan Wang
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Dan Du
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Shiliang He
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Baozhan Huang
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Xiurong Guo
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Hang Zhao
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
- State
Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, Sichuan 610041, China
| | - Rui Zhang
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Limei Ma
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Yan Liu
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Qigen Du
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Zeliang Wei
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Zhihua Xing
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Yong Liang
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Xiaohua Wu
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Chengzhong Fan
- Department
of Nuclear Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan 610041, China
| | - Chengjie Ji
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Dequan Zeng
- State
Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, Sichuan 610041, China
| | - Qianming Chen
- State
Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University Chengdu, Sichuan 610041, China
| | - Yang He
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
| | - Xuyang Liu
- Shenzhen
Eye Hospital, Jinan University, No. 18, Zetian Road, Futian District, Shenzhen 518040, China
| | - Wen Huang
- Laboratory
of Ethnopharmacology, Institute for Nanobiomedical Technology and
Membrane Biology, Regenerative Medicine Research Center, West China
Hospital, West China Medical School, Sichuan University Keyuan 4 Road
No. 1, Gaopeng Avenue, Gaoxinqu, Chengdu, Sichuan 610041 China
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Li BJ, Chiang CC, Hsu LY. QSAR Studies of 3,3′-(Substituted-Benzylidene)-Bis-4-Hydroxycoumarin, Potential HIV-1 Integrase Inhibitor. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Biochemical screening assays to identify HIV-1 integrase inhibitors. Methods Mol Biol 2013; 1030:25-36. [PMID: 23821258 DOI: 10.1007/978-1-62703-484-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase is, in addition to reverse transcriptase and protease, an important enzymatic target for antiretroviral drug development. Integrase plays a critical role in the HIV-1 life cycle coordinating the integration of the reverse-transcribed viral DNA into the host genome. This integration step is the net result of two consecutive integrase-related processes. First, integrase removes a dinucleotide from the 3' viral DNA ends in a process called 3'-processing. Next, in a process called strand transfer, the viral DNA is integrated into the host genomic DNA. Early on, biochemical assays have played a critical role in understanding the function of HIV-1 integrase and the discovery of small-molecule inhibitors. In this chapter we describe two biochemical assays to identify inhibitors of the 3'-processing and strand transfer process of HIV-1 integrase.
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Van Loock M, Hombrouck A, Jacobs T, Winters B, Meersseman G, Van Acker K, Clayton RF, Malcolm BA. Reporter gene expression from LTR-circles as tool to identify HIV-1 integrase inhibitors. J Virol Methods 2012. [PMID: 23178583 DOI: 10.1016/j.jviromet.2012.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Early HIV-1 integrase inhibitors, such as compounds containing a β-diketo acid moiety, were identified by extensive high-throughput screening campaigns. Traditionally, in vitro biochemical assays, measuring the catalytic activities of integrase, have been used for this purpose. However, these assays are confounded by the absence of cellular processes or cofactors that play a role in the integration of HIV-1 DNA in the cellular genome. In contrast to regular cell-based virus inhibition assays, which targets all steps of the viral replication cycle, a novel cellular screening assays was developed to enable the specific identification of integrase inhibitors, employing a readout that is linked with the inhibition of integrase activity. Therefore, a HIV-1 lentiviral vector equipped with the enhanced green fluorescent protein (eGFP) reporter gene was used to detect expression from extrachromosomal viral DNA (1- or 2-long terminal repeat circles), formed when integration of vector DNA into the cellular genome is prevented by an integrase inhibitor. In this assay, eGFP expression from the low residual level of transcriptional activity of extrachromosomal DNA was measured via high-throughput flow cytometry. An algorithm for analysis of eGFP expression histograms enabled the specific identification of integrase inhibitors. This assay is amenable for high throughput screening to identify inhibitors of HIV-1 integrase.
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Affiliation(s)
- M Van Loock
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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19
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Esposito F, Corona A, Zinzula L, Kharlamova T, Tramontano E. New anthraquinone derivatives as inhibitors of the HIV-1 reverse transcriptase-associated ribonuclease H function. Chemotherapy 2012; 58:299-307. [PMID: 23128501 DOI: 10.1159/000343101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/31/2012] [Indexed: 02/02/2023]
Abstract
BACKGROUND The degradative activity of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), termed ribonuclease H (RNase H), which hydrolyzes the RNA component of the heteroduplex RNA:DNA replication intermediate, is an excellent target for drug discovery. Anthraquinones (AQs) and their derivatives, which are common secondary metabolites occurring in bacteria, fungi, lichens and a large number of families in higher plants, have been reported to have several biological activities including that of inhibiting HIV-1 RT activities in biochemical assays. METHODS We have assayed new AQ derivatives on HIV-1 RNase H activities in biochemical assays. RESULTS Six series of new AQ derivatives with various substituents at positions 1, 2, 3 and 4 of the AQ ring were tested, and new analogs able to inhibit HIV-1 RT-associated RNase H activity in the low micromolar range were found. CONCLUSIONS Our results demonstrate that AQ derivatives are promising anti-RNase H inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy.
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20
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Krishnan L, Engelman A. Retroviral integrase proteins and HIV-1 DNA integration. J Biol Chem 2012; 287:40858-66. [PMID: 23043109 DOI: 10.1074/jbc.r112.397760] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Retroviral integrases catalyze two reactions, 3'-processing of viral DNA ends, followed by integration of the processed ends into chromosomal DNA. X-ray crystal structures of integrase-DNA complexes from prototype foamy virus, a member of the Spumavirus genus of Retroviridae, have revealed the structural basis of integration and how clinically relevant integrase strand transfer inhibitors work. Underscoring the translational potential of targeting virus-host interactions, small molecules that bind at the host factor lens epithelium-derived growth factor/p75-binding site on HIV-1 integrase promote dimerization and inhibit integrase-viral DNA assembly and catalysis. Here, we review recent advances in our knowledge of HIV-1 DNA integration, as well as future research directions.
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Affiliation(s)
- Lavanya Krishnan
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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21
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Han YS, Quashie P, Mesplede T, Xu H, Mekhssian K, Fenwick C, Wainberg MA. A high-throughput assay for HIV-1 integrase 3'-processing activity using time-resolved fluorescence. J Virol Methods 2012; 184:34-40. [PMID: 22584270 DOI: 10.1016/j.jviromet.2012.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 04/26/2012] [Accepted: 05/03/2012] [Indexed: 01/08/2023]
Abstract
HIV-1 integrase (HIV-1 IN), a well-validated antiviral drug target, catalyzes multistep reactions to incorporate viral DNA into the genome of the host cell; these include both a 3'-processing (3'P) reaction and a strand transfer reaction. These enzymatic activities can be measured in vitro with short DNA oligonucleotides that mimic a single viral LTR DNA end and purified IN. A highly sensitive and reproducible time-resolved fluorescence (TRF)-based assay for HIV-1 IN 3'P activity is now reported. This assay was optimized with respect to time and concentrations of metal ions, substrate and enzyme. The assay has now been used successfully to measure HIV-1 IN 3'P activity and has been shown to detect the anti-IN activity of several known 3'P inhibition compounds accurately. This assay, which is amenable to high-throughput screening, will be useful for identification of additional HIV-1 IN 3'P inhibitors.
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Affiliation(s)
- Ying-Shan Han
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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22
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Van Loock M, Meersseman G, Van Acker K, Van Den Eynde C, Jochmans D, Van Schoubroeck B, Dams G, Heyndrickx L, Clayton RF. A novel high-throughput cellular screening assay for the discovery of HIV-1 integrase inhibitors. J Virol Methods 2011; 179:396-401. [PMID: 22172974 DOI: 10.1016/j.jviromet.2011.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/27/2022]
Abstract
The discovery of HIV-1 integrase inhibitors has been enabled by high-throughput screening and rational design of novel chemotypes. Traditionally, biochemical assays focusing on the strand transfer activity of integrase have been used to screen compound libraries for identification of novel inhibitors. In contrast, cellular screening assays enable a phenotypic or multi-target approach, and may result in identification of compounds inhibiting integrase in its natural context, the pre-integration complex. Furthermore, a cellular assay encompassing 3' processing, strand transfer and nuclear import may lead to the identification of compounds with novel mechanisms of action targeting cellular and viral factors. Therefore, a cellular screening assay was developed, which focused on integrase activity, where infection of MT4 cells with an HIV-1 based lentiviral vector was synchronized by temporary arrest at the reverse transcriptase step and subsequent release to enable integration. The assay was validated using a panel of antivirals and proved to be a robust cellular screening assay for the identification of novel integrase inhibitors.
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Esposito F, Kharlamova T, Distinto S, Zinzula L, Cheng YC, Dutschman G, Floris G, Markt P, Corona A, Tramontano E. Alizarine derivatives as new dual inhibitors of the HIV-1 reverse transcriptase-associated DNA polymerase and RNase H activities effective also on the RNase H activity of non-nucleoside resistant reverse transcriptases. FEBS J 2011; 278:1444-57. [PMID: 21348941 DOI: 10.1111/j.1742-4658.2011.08057.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HIV-1 reverse transcriptase (RT) has two associated activities, DNA polymerase and RNase H, both essential for viral replication and validated drug targets. Although all RT inhibitors approved for therapy target DNA polymerase activity, the search for new RT inhibitors that target the RNase H function and are possibly active on RTs resistant to the known non-nucleoside inhibitors (NNRTI) is a viable approach for anti-HIV drug development. In this study, several alizarine derivatives were synthesized and tested for both HIV-1 RT-associated activities. Alizarine analogues K-49 and KNA-53 showed IC(50) values for both RT-associated functions of ∼ 10 μm. When tested on the K103N RT, both derivatives inhibited the RT-associated functions equally, whereas when tested on the Y181C RT, KNA-53 inhibited the RNase H function and was inactive on the polymerase function. Mechanism of action studies showed that these derivatives do not intercalate into DNA and do not chelate the divalent cofactor Mg(2+) . Kinetic studies demonstrated that they are noncompetitive inhibitors, they do not bind to the RNase H active site or to the classical NNRTI binding pocket, even though efavirenz binding negatively influenced K-49/KNA-53 binding and vice versa. This behavior suggested that the alizarine derivatives binding site might be close to the NNRTI binding pocket. Docking experiments and molecular dynamic simulation confirmed the experimental data and the ability of these compounds to occupy a binding pocket close to the NNRTI site.
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Affiliation(s)
- Francesca Esposito
- Department of Applied Sciences in Biosystems, University of Cagliari, Cagliari, Italy
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Sharma H, Patil S, Sanchez TW, Neamati N, Schinazi RF, Buolamwini JK. Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorg Med Chem 2011; 19:2030-45. [PMID: 21371895 DOI: 10.1016/j.bmc.2011.01.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/16/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
HIV-1 integrase is one of the three most important enzymes required for viral replication and is therefore an attractive target for anti retroviral therapy. We herein report the design and synthesis of 3-keto salicylic acid chalcone derivatives as novel HIV-1 integrase inhibitors. The most active compound, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) was selectively active against integrase strand transfer, with an IC(50) of 3.7 μM. While most of the compounds exhibited strand transfer selectivity, a few were nonselective, such as 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15), which was active against both 3'-processing and strand transfer with IC(50) values of 11±4 and 5±2 μM, respectively. The compounds also inhibited HIV replication with potencies comparable with their integrase inhibitory potencies. Thus, 5-bromo-2-hydroxy-3-[3-(2,3,6-trichlorophenyl)acryloyl]benzoic acid (25) and 5-bromo-3-[3-(4-bromophenyl)acryloyl]-2-hydroxybenzoic acid (15) inhibited HIV-1 replication with EC(50) values of 7.3 and 8.7 μM, respectively. A PHASE pharmacophore hypothesis was developed and validated by 3D-QSAR, which gave a predictive r(2) of 0.57 for an external test set of ten compounds. Phamacophore derived molecular alignments were used for CoMFA and CoMSIA 3D-QSAR modeling. CoMSIA afforded the best model with q(2) and r(2) values of 0.54 and 0.94, respectively. This model predicted all the ten compounds of the test set within 0.56 log units of the actual pIC(50) values; and can be used to guide the rational design of more potent novel 3-keto salicylic acid integrase inhibitors.
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Affiliation(s)
- Horrick Sharma
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 847 Monroe Avenue, Suite 327, TN 38163, USA
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25
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Hu JZ, Bai L, Chen DG, Xu QT, Southerland WM. Computational investigation of the anti-HIV activity of Chinese medicinal formula Three-Huang Powder. Interdiscip Sci 2010; 2:151-6. [PMID: 20640783 DOI: 10.1007/s12539-010-0074-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
An essential step in the life cycle of human immunodeficiency virus type 1 (HIV-1) is integration of the double-stranded retroviral DNA into the genome of the host cell. HIV-1 integrase, the enzyme that inserts the vital DNA into the host chromosome, is an attractive and rational target for anti-AIDS drug design because it is essential for HIV replication and there are no known counterparts in the host cell. Inhibitors of this enzyme have the great potential to complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. Natural products have provided a source of new drug candidates for anti-AIDS therapy. Baicalein and baicalin, identified components of a Chinese herbal medicine Scutellaria baicalensis Georgi, have been shown to inhibit infectivity and replication of HIV. They are therefore promising lead compounds for developing new anti-AIDS drugs. To understand how the inhibitors work and therefore design more potent and specific inhibitors, we have used molecular modeling techniques to investigate the binding modes of these inhibitors. The three-dimensional structures of these inhibitors were first built. Then, computational binding studies of these inhibitors, based on the crystal structure of the HIV-1 integrase catalytic domain, were performed to study the complex structure. The preliminary results of our computational modeling study demonstrated that Baicalein binds to the active site region of the HIV-1 integrase. Our study will be of help to identify the pharmacophores of inhibitors binding to HIV-1 integrase and design new pharmaceuticals for the treatment of AIDS.
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Affiliation(s)
- Jack Z Hu
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, DC 20059, USA.
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26
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He H, Liu B, Zhang X, Chen W, Wang C. Development of a high-throughput assay for the HIV-1 integrase disintegration reaction. SCIENCE CHINA. LIFE SCIENCES 2010; 53:241-247. [PMID: 20596834 DOI: 10.1007/s11427-010-0006-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 07/02/2009] [Indexed: 05/29/2023]
Abstract
Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in vitro. In this study, IN and IN-CCD proteins were expressed and purified, and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration reaction. IN exhibited a marked preference for Mn(2+) over Mg(2+) as the divalent cation cofactor in disintegration. Baicalein, a known IN inhibitor, was found to be an IN-CCD inhibitor. The assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN, especially targeting IN-CCD.
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Affiliation(s)
- HongQiu He
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
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27
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Hu Z, Chen D, Dong L, Southerland WM. Prediction of the interaction of HIV-1 integrase and its dicaffeoylquinic acid inhibitor through molecular modeling approach. Ethn Dis 2010; 20:S1-49. [PMID: 20521384 PMCID: PMC3089943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
An essential step in the life cycle of human immunodeficiency virus type 1 (HIV-1) is integration of the double-stranded retroviral DNA into the genome of the host cell. HIV-1 integrase, the enzyme that inserts the vital DNA into the host chromosome, is an attractive and rational target for anti-AIDS drug design because it is essential for HIV replication and there are no known counterparts in the host cell. Inhibitors of this enzyme have a great potential to complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. Natural products have provided a source of new drug candidates for anti-AIDS therapy. Dicaffeoylquinic acids, isolated from traditional medicinal plants, are a novel class of integrase inhibitors. These compounds are potent inhibitors of HIV-1 replication in cultured cell lines and catalytic activities of integrase in vitro. They are therefore promising compounds for developing new anti-AIDS drugs. To understand how the inhibitors work and therefore design more potent and specific inhibitors, we have used molecular modeling techniques to investigate the binding modes of 3,4-dicaffeoylquinic acid. Our computational modeling study demonstrated that the inhibitor of this compound on HIV integrase is likely to proceed by two different but equivalent mechanisms with one bound to the active site region of the enzyme and another docked into the binding pocket located on the other side of the catalytic site. Our study will be of help to design new pharmaceuticals for the treatment of AIDS.
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Affiliation(s)
- Zengjian Hu
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, DC 20059, USA.
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29
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Ramajayam R, Mahera NB, Neamati N, Yadav MR, Giridhar R. Synthesis and anti-HIV-1 integrase activity of cyano pyrimidinones. Arch Pharm (Weinheim) 2009; 342:710-5. [PMID: 19899101 DOI: 10.1002/ardp.200900066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A series of 2-phenethyl/benzylthio-6-oxo-4-phenyl-1,6-dihydropyrimidine-5-carbonitrile were synthesized and tested against recombinant HIV-1 integrase in an enzyme assay. 2-(Phenethylthio)-4-(4-chlorophenyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile 4m and 2-(phenethylthio)-4-(3-chlorophenyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile 4o showed significant inhibition against integrase in the assay (strand transfer: IC(50) values of 16 and 17 microM, respectively).
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Affiliation(s)
- R Ramajayam
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara, India
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30
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Engelman A. Mechanistic and pharmacological analyses of HIV-1 integration. Methods 2009; 47:225-8. [PMID: 19389610 PMCID: PMC2709961 DOI: 10.1016/j.ymeth.2009.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 03/16/2009] [Indexed: 11/30/2022] Open
Abstract
Significant advances have transpired in the human immunodeficiency virus type 1 (HIV-1) integration field in recent years. Considering its essential nature, integrase has long been a target of interest for antiviral drug development. The most significant advance was the approval of the Merck compound raltegravir, the first licensed integrase inhibitor, in October 2007. Another milestone was the identification and characterization of specific nucleoprotein complexes that mediate integrase 3' processing and DNA strand transfer activities in vitro. Genome-wide distribution analyses have furthermore revealed that different retroviruses differentially target distinctive regions of chromatin during integration. For examples, lentiviruses favor actively transcribed genes whereas gammaretroviruses such as Moloney murine leukemia virus prefer transcriptional start sites. Though the underlying mechanisms are unknown for most retroviruses, the lentiviral preference is in large part guided through the interaction with the integrase binding protein lens epithelium-derived growth factor (LEDGF)/p75. Experimental methods that formed the foundations for each of these advances, as well as other techniques topical to the study of HIV-1 integration, are described in this issue of Methods.
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Affiliation(s)
- Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 44 Binney Street, CLSB-1010, Boston, MA 02115, USA, Email address: , Tel: +1 617 632 4361, Fax: +1 617 632 4338
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31
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Grobler JA, Stillmock KA, Hazuda DJ. Scintillation proximity assays for mechanistic and pharmacological analyses of HIV-1 integration. Methods 2009; 47:249-53. [PMID: 19285556 DOI: 10.1016/j.ymeth.2009.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/02/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022] Open
Abstract
The early events of HIV-1 replication are highlighted by reverse transcription and integration, and the reverse transcriptase and integrase enzymes are important therapeutic targets. Integration proceeds through a series of steps including assembly of integrase on the viral donor DNA ends, 3'-processing, and DNA strand transfer. First generation integrase assays typically included all biochemical reagents in solution where excess donor substrate could serve as the target for DNA strand transfer. These conditions, though valuable for understanding mechanistic aspects of HIV-1 integration, fell short of critical pharmacological designs as most early inhibitors were found to block assembly instead of enzyme function. Second generation designs, which decoupled assembly from DNA strand transfer, afforded the specificity required to identify clinically relevant compounds. Here, we describe versatile scintillation proximity-based assays whereby integrase is assembled onto donor DNA that is immobilized onto the surface of beads. Immobilization and subsequent washing of excess donor DNA eliminates its potential to serve as target DNA, allowing investigation of the DNA strand transfer reaction in isolation. Assembled complexes can be used in high-throughput DNA strand transfer assays if radio labeled target DNA is employed or in integrase binding assays using a suitable radioligand.
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Affiliation(s)
- Jay A Grobler
- Department of Antiviral Research, Merck Research Laboratories, WP26A-3000, 770 Sumneytown Pike, P.O. Box 4, West Point, PA 19486, USA.
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Design, synthesis and anti-HIV integrase evaluation of 4-oxo-4H-quinolizine-3-carboxylic acid derivatives. Molecules 2009; 14:868-83. [PMID: 19255545 PMCID: PMC6254011 DOI: 10.3390/molecules14020868] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 01/16/2009] [Accepted: 02/06/2009] [Indexed: 11/23/2022] Open
Abstract
4-Oxo-4H-quinolizine-3-carboxylic acid derivatives bearing sulfamido, carboxylamido, benzimidazole and benzothiazole substituents have been designed and synthesized. The structures of these new compounds were confirmed by 1H-NMR, 13C- NMR, IR and ESI (or HRMS) spectra. Compounds were screened for possible HIV integrase inhibitory activity.
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33
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He HQ, Ma XH, Liu B, Chen WZ, Wang CX, Cheng SH. A novel high-throughput format assay for HIV-1 integrase strand transfer reaction using magnetic beads. Acta Pharmacol Sin 2008; 29:397-404. [PMID: 18298906 DOI: 10.1111/j.1745-7254.2008.00748.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
AIM To develop a novel high-throughput format assay to monitor the integrase (IN) strand transfer (ST) reaction in vitro and apply it to a reaction character study and the identification of antiviral drugs. METHODS The donor DNA duplex, with a sequence identical to the U5 end of HIV-1 long terminal repeats, is labeled at its 5' end with biotin (BIO). The target DNA duplex is labeled at its 3' end with digoxin (DIG). IN mediates the integration of donor DNA into target DNA and results in a 5' BIO and 3' DIG-labeled duplex DNA product. Streptavidin-coated magnetic beads were used to capture the product, and the amount of DIG was measured as the ST reaction product. The assay was optimized in 96-well microplate format for high-throughput screening purpose. Moreover, the assay was applied in a ST reaction character study, and the efficiency of the assay in the identification of antiviral compounds was tested. RESULTS The end-point values, measured as absorbance at 405 nm was approximately 1.5 for the IN-mediated ST reaction as compared with no more than 0.05 of background readings. The ST reaction character and the half maximal inhibitory concentration (IC50) values of 2 known IN inhibitors obtained in our assay were similar to previously reported results using other assays. The evaluation parameter Z' factor for this assay ranged from 0.6 to 0.9. CONCLUSION The assay presented here has been proven to be rapid, sensitive, and specific for the detection of IN ST activity, the reaction character study, as well as for the identification of antiviral drugs targeting IN.
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Affiliation(s)
- Hong-qiu He
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
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Chiang CC, Mouscadet JF, Tsai HJ, Liu CT, Hsu LY. Synthesis and HIV-1 integrase inhibition of novel bis- or tetra-coumarin analogues. Chem Pharm Bull (Tokyo) 2008; 55:1740-3. [PMID: 18057750 DOI: 10.1248/cpb.55.1740] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Present studies were undertaken on the preparation of synthetic analogues of bis- or tetra-coumarins and their activity against HIV-1 integrase (HIV-1 IN). Among these coumarin analogues, compounds 14, 16 and 18 were found to be potent molecules against HIV-1 IN at IC50 values of 0.96, 0.58, and 0.49 microM, respectively. The results provided a tool for guiding the further design of more potent antiviral agents and for predicting the affinity of related compounds.
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Affiliation(s)
- Chih-Chia Chiang
- Department of Applied Chemistry and Materials Science, Institute of Technology, National Defense University, Ta-shi, Tao-yuan, Taiwan, ROC
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35
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Dubey S, Satyanarayana YD, Lavania H. Development of integrase inhibitors for treatment of AIDS: An overview. Eur J Med Chem 2007; 42:1159-68. [PMID: 17367896 DOI: 10.1016/j.ejmech.2007.01.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 01/18/2007] [Accepted: 01/19/2007] [Indexed: 11/22/2022]
Abstract
HIV-1 integrase (IN) is an essential enzyme for retroviral replication. It is involved in the integration of HIV DNA into host chromosomal DNA. The unique properties of IN makes it an ideal target for drug design. First, there appears to have no functional equivalent in human cells and the reactions catalyzed by IN are unique. Second, IN is absolutely required for viral replication and mutations in a number of key residues block the viral replication. Third, IN has been validated as a legitimate target and the results from the molecules like S-1,360, JKT-303 which are under phase II/III clinical trials suggest synergistic effect with reverse transcriptase (RT) and protease (PR) inhibitors. During the past 10 years a plethora of inhibitors have been identified and some were shown to be selective against IN and block viral replication. The classes under which inhibitors of integrase can be classified are catechol-containing hydroxylated aromatics, diketoacid-containing aromatics, quninolines and others (non-catechol containing). In the present article we review all the recent small molecules reported to inhibit recombinant HIV-1 IN under these heads. It seems likely that the efficient use of HIV IN as target for rational design can give potent anti-HIV agents, which can be used alone or in combination regimens with other classes of anti-HIV drugs.
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Affiliation(s)
- Sonal Dubey
- K.L.E.S. College of Pharmacy, Rajajinagar II Block, Bangalore 560010, Karnataka, India.
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36
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Bona R, Andreotti M, Buffa V, Leone P, Galluzzo CM, Amici R, Palmisano L, Mancini MG, Michelini Z, Di Santo R, Costi R, Roux A, Pommier Y, Marchand C, Vella S, Cara A. Development of a human immunodeficiency virus vector-based, single-cycle assay for evaluation of anti-integrase compounds. Antimicrob Agents Chemother 2006; 50:3407-17. [PMID: 17005823 PMCID: PMC1610086 DOI: 10.1128/aac.00517-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Therapeutic strategies aimed at inhibiting human immunodeficiency virus type 1 (HIV-1) replication employ a combination of drugs targeted to two viral enzymes (reverse transcriptase and protease) and to the viral entry/fusion step. However, the high propensity of HIV-1 to develop resistance makes the development of novel compounds targeting different steps of the HIV-1 life cycle essential. Among these, integrase (IN) inhibitors have successfully passed the early phases of clinical development. By preventing integration, IN inhibitors preclude viral replication while allowing production of extrachromosomal forms of viral DNA (E-DNA). Here, we describe an improved and standardized assay aimed at evaluating IN inhibitors by taking advantage of the transcriptional activity of E-DNA produced by HIV-derived vectors in the absence of replication-competent virus. In this context, the use of the firefly luciferase gene as a reporter gene provides a rapid and quantitative measure of viral-vector infectivity, thus making it a safe and cost-effective assay for evaluating novel IN inhibitors.
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Affiliation(s)
- Roberta Bona
- National AIDS Center, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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37
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Ren G, Gao K, Bushman FD, Yeager M. Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA. J Mol Biol 2006; 366:286-94. [PMID: 17157316 PMCID: PMC1855144 DOI: 10.1016/j.jmb.2006.11.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/07/2006] [Accepted: 11/07/2006] [Indexed: 01/26/2023]
Abstract
The HIV integrase enzyme (IN) catalyzes the initial DNA breaking and joining reactions that integrate viral DNA in the host chromosome. Structures for individual IN domains have been determined by X-ray crystallography and NMR spectroscopy, but the structure of the complete IN-DNA complex has remained elusive. Homogeneous complexes of IN tetramers were assembled on DNA three-way junction substrates designed to resemble integration intermediates. Electron microscopy and single-particle image analysis of these complexes yielded a three-dimensional reconstruction at approximately 27 A resolution. The map of the IN-DNA complex displays four lobes of density approximately 50 A in diameter. Three of the lobes form a roughly triangular base with a central channel approximately 20 A in diameter. The fourth lobe is centered between two lobes and extends approximately 40 A above the base. We propose that the central channel tethers the target DNA, and two of the lobes may bind the ends of the viral DNA. The asymmetry of the complex is a feature not incorporated in previous structural models and potentially provides the first view of an asymmetric reaction intermediate.
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Affiliation(s)
- Gang Ren
- The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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38
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Abstract
HIV-1 integrase, which catalyzes the joining of viral DNA to the host cell DNA, has attracted considerable attention as a target for the design and screening of novel anti-HIV drugs as it is essential for virus replication and the establishment of persistent infection. Progress in the identification of different classes of compounds that block integrase activity has been summarized recently in several excellent reviews. Here, we present a brief overview of integrase inhibition, highlighting some of the unusual properties of this protein and important considerations in searching for potential new inhibitors and their evaluation.
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Affiliation(s)
- Joseph Ramcharan
- Locus Pharmaceuticals Inc., 4 Valley Square, 512 East Township Line Road, Blue Bell, PA 19422, USA
| | - Anna Marie Skalka
- Fox Chase Cancer Center, Institute for Cancer Research, Philadelphia, PA 19111, USA
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39
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Tsurutani N, Yasuda J, Yamamoto N, Choi BI, Kadoki M, Iwakura Y. Nuclear import of the preintegration complex is blocked upon infection by human immunodeficiency virus type 1 in mouse cells. J Virol 2006; 81:677-88. [PMID: 17079325 PMCID: PMC1797461 DOI: 10.1128/jvi.00870-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mouse cells do not support human immunodeficiency virus type 1 (HIV-1) replication because of host range barriers at steps including virus entry, transcription, RNA splicing, polyprotein processing, assembly, and release. The exact mechanisms for the suppression, however, are not completely understood. To elucidate further the barriers against HIV-1 replication in mouse cells, we analyzed the replication of the virus in lymphocytes from human CD4/CXCR4 transgenic mice. Although primary splenocytes and thymocytes allowed the entry and reverse transcription of HIV-1, the integration efficiency of the viral DNA was greatly reduced in these cells relative to human peripheral blood mononuclear cells, suggesting an additional block(s) before or at the point of host chromosome integration of the viral DNA. Preintegration processes were further analyzed using HIV-1 pseudotyped viruses. The reverse transcription step of HIV-1 pseudotyped with the envelope of murine leukemia virus or vesicular stomatitis virus glycoprotein was efficiently supported in both human and mouse cells, but nuclear import of the preintegration complex (PIC) of HIV-1 was blocked in mouse cells. We found that green fluorescent protein (GFP)-labeled HIV-1 integrase, which is known to be important in the nuclear localization of the PIC, could not be imported into the nucleus of mouse cells, in contrast to human cells. On the other hand, GFP-Vpr localized exclusively to the nuclei of both mouse and human cells. These observations suggest that, due to the dysfunction of integrase, the nuclear localization of PIC is suppressed in mouse cells.
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Affiliation(s)
- Naomi Tsurutani
- Center for Experimental Medicine, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Tokyo 108-8639, Japan
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40
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Abstract
Currently, there are three distinct mechanistic classes of antiretrovirals: inhibitors of the HIV- 1 reverse transcriptase and protease enzymes and inhibitors of HIV entry, including receptor and coreceptor binding and cell fusion. A new drug class that inhibits the HIV-1 integrase enzyme (IN) is in development and may soon be available in the clinic. IN is an attractive drug target because it is essential for a stable and productive HIV-1 infection and there is no mammalian homologue of IN. Inhibitors of integrase enzyme (INI) block the integration of viral double-stranded DNA into the host cell's chromosomal DNA. HIV-1 integration has many potential steps that can be inhibited and several new compounds that target specific integration steps have been identified by drug developers. Recently, two INIs, GS-9137 and MK-0518, demonstrated promising early clinical trial results and have been advanced into later stage trials. In this review, we describe how IN facilitates HIV-1 integration, the needed enzyme cofactors, and the resultant byproducts created during integration. Furthermore, we review the different INIs under development, their mechanism of actions, site of IN inhibition, potency, resistance patterns, and discuss the early clinical trial results.
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Affiliation(s)
- Max Lataillade
- Division of Infectious Diseases, Yale University School of Medicine, LLCI 100D, 300 Cedar Street, Suite 169, New Haven, Connecticut 06520, USA.
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41
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Kondapi AK, Satyanarayana N, Saikrishna AD. A study of the Topoisomerase II activity in HIV-1 replication using the ferrocene derivatives as probes. Arch Biochem Biophys 2006; 450:123-32. [PMID: 16712776 DOI: 10.1016/j.abb.2006.04.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Revised: 04/01/2006] [Accepted: 04/04/2006] [Indexed: 11/17/2022]
Abstract
Human Topoisomerase II is present in two isoforms, 170KDa alpha and 180KDa beta. Both the isoforms play a crucial role in maintenance of topological changes during DNA replication and recombination. It has been shown that Topoisomerase II activity is required for HIV-1 replication and the enzyme is phosphorylated during early time points of HIV-1 replication. In the present study, we have studied the molecular action of Topoisomerase II inhibitors, azalactone ferrocene (AzaFecp), Thiomorpholide amido methyl ferrocene (ThioFecp), and Ruthenium benzene amino pyridine (Ru(ben)Apy) on cell proliferation and also on various events of HIV-1 replication cycle. The Topoisomerase II beta over-expressing neuroblastoma cell line shows a higher sensitivity to these compounds compared to the Sup-T1 cell line. All the three Topoisomerase II inhibitors show significant anti-HIV activity at nanomolar concentrations against an Indian isolate of HIV-1(93IN101) in Sup-T1 cell line. An analysis of action of these compounds on proviral DNA synthesis at 5h of post-infection shows that they inhibit proviral DNA synthesis as well as the formation of pre-integration complexes completely. Further analysis, using polymerase chain reaction and western blot, showed that both the Topoisomerase II alpha and beta isoforms are present in the pre-integration complexes, suggesting their significant role in HIV-1 replication.
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Affiliation(s)
- Anand K Kondapi
- Department of Biochemistry, University of Hyderabad, School of Life Sciences, Hyderabad 500 046, India.
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42
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Maurin C, Bailly F, Mbemba G, Mouscadet JF, Cotelle P. Design, synthesis, and anti-integrase activity of catechol–DKA hybrids. Bioorg Med Chem 2006; 14:2978-84. [PMID: 16412645 DOI: 10.1016/j.bmc.2005.12.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 11/24/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
Following the discovery of diketoacid-containing compounds as HIV-1 integrase (IN) inhibitors, a plethora of new molecules have been published leading to four drugs under clinical trial. In an attempt to rationally design new dimeric diketoacids (DKAs) targeting two divalent metal ions on the active site of IN, potent inhibitors against purified IN were found with varied selectivity for strand transfer. In this context, we designed and synthesized a new series of catechol-DKA hybrids. These compounds presented micromolar anti-integrase activities with moderate antiviral properties.
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Affiliation(s)
- Cédric Maurin
- Laboratoire de Chimie Organique et Macromoléculaire, UMR CNRS 8009, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq, France
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43
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Meadows DC, Mathews TB, North TW, Hadd MJ, Kuo CL, Neamati N, Gervay-Hague J. Synthesis and biological evaluation of geminal disulfones as HIV-1 integrase inhibitors. J Med Chem 2005; 48:4526-34. [PMID: 15999991 DOI: 10.1021/jm049171v] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Integration of HIV-1 viral DNA into the host genome is carried out by HIV-integrase (IN) and is a critical step in viral replication. Although several classes of compounds have been reported to inhibit IN in enzymatic assays, inhibition is not always correlated with antiviral activity. Moreover, potent antiviral IN inhibitors such as the chicoric acids do not act upon the intended enzymatic target but behave as entry inhibitors instead. The charged nature of the chicoric acids contributes to poor cellular uptake, and these compounds are further plagued by rapid ester hydrolysis in vivo. To address these critical deficiencies, we designed neutral, nonhydrolyzable analogues of the chicoric acids. Herein, we report the synthesis, enzyme inhibition studies, and cellular antiviral data for a series of geminal disulfones. Of the 10 compounds evaluated, 8 showed moderate to high inhibition of IN in purified enzyme assays. The purified enzyme data correlated with antiviral assays for all but two compounds, suggesting alternative modes of inhibition. Time-of-addition studies were performed on these analogues, and the results indicate that they inhibit an early stage in the replication process, perhaps entry. In contrast, the most potent member of the correlative group shows behavior consistent with IN being the cellular target.
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44
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Yuan H, Parrill A. Cluster analysis and three-dimensional QSAR studies of HIV-1 integrase inhibitors. J Mol Graph Model 2005; 23:317-28. [PMID: 15670952 DOI: 10.1016/j.jmgm.2004.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2003] [Revised: 10/14/2004] [Accepted: 10/14/2004] [Indexed: 11/15/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D QSAR) and cluster analysis were applied to a variety of HIV-1 integrase inhibitors. One structure was chosen from each of 11 classes of inhibitors to represent the whole class in descriptor-based cluster analysis. The 11 classes of inhibitors were classified into two groups. The molecular field analysis (MFA) models for these two clusters had r2 values of 0.90 and 0.95 and q2 values of 0.85 and 0.91 that were noticeably enhanced from those of conventional QSAR models. The five test compounds, which were proposed to have a common binding site near the metal in HIV-1 integrase based on docking studies by Sotriffer et al., were utilized to compare the predictive capability of MFA and conventional QSAR models. Among these five compounds, only L-chicoric acid belongs to cluster 1 and the other four belong to cluster 2. MFA models give better overall predictions and more importantly the activity of these test compounds is better predicted by the MFA model derived from the cluster each test compound belongs to. The necessity of dividing the inhibitors into two groups to obtain predictive QSAR models supports the likelihood of two separate binding sites.
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Affiliation(s)
- Hongbin Yuan
- Chemistry Department, The University of Memphis, Memphis, TN 38152, USA
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45
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Rochfort S, Ford J, Ovenden S, Wan SS, George S, Wildman H, Tait RM, Meurer-Grimes B, Cox S, Coates J, Rhodes D. A novel aspochalasin with HIV-1 integrase inhibitory activity from Aspergillus flavipes. J Antibiot (Tokyo) 2005; 58:279-83. [PMID: 15981416 DOI: 10.1038/ja.2005.34] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A novel aspochalasin, aspochalasin L (1), was isolated from the fermentation broth of a soil-derived fungal culture identified as Aspergillus flavipes (Deuteromycota). Structure elucidation of 1 was accomplished by detailed spectroscopic data analyses and by comparison with related cytochalasins. Aspochalasin L demonstrated activity against HIV integrase with an IC50 of 71.7microM.
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Affiliation(s)
- Simone Rochfort
- Cerylid Biosciences, 576 Swan Street, Richmond, Victoria 3121, Australia.
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46
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Ason B, Knauss DJ, Balke AM, Merkel G, Skalka AM, Reznikoff WS. Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors. Antimicrob Agents Chemother 2005; 49:2035-43. [PMID: 15855529 PMCID: PMC1087639 DOI: 10.1128/aac.49.5.2035-2043.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 10/12/2004] [Accepted: 12/29/2004] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) type 1 (HIV-1) integrase is an underutilized drug target for the treatment of HIV infection. One limiting factor is the lack of costructural data for use in the rational design or modification of integrase inhibitors. Tn5 transposase is a structurally well characterized, related protein that may serve as a useful surrogate. However, little data exist on inhibitor cross-reactivity. Here we screened 16,000 compounds using Tn5 transposase as the target and identified 20 compounds that appear to specifically inhibit complex assembly. Six were found to also inhibit HIV-1 integrase. These compounds likely interact with a highly conserved region presumably within the catalytic core. Most promising, several cinnamoyl derivatives were found to inhibit HIV transduction in cells. The identification of integrase inhibitors from a screen using Tn5 transposase as the target illustrates the utility of Tn5 as a surrogate for HIV-1 integration even though the relationship between the two systems is limited to the active site architecture and catalytic mechanism.
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Affiliation(s)
- Brandon Ason
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
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47
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Abstract
HIV integrase is a rational target for treating HIV infection and preventing AIDS. It took approximately 12 years to develop clinically usable inhibitors of integrase, and Phase I clinical trials of integrase inhibitors have just begun. This review focuses on the molecular basis and rationale for developing integrase inhibitors. The main classes of lead compounds are also described, as well as the concept of interfacial inhibitors of protein-nucleic-acid interactions that might apply to the clinically used strand-transfer inhibitors.
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Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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48
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Tramontano E, Onidi L, Esposito F, Badas R, La Colla P. The use of a new in vitro reaction substrate reproducing both U3 and U5 regions of the HIV-1 3'-ends increases the correlation between the in vitro and in vivo effects of the HIV-1 integrase inhibitors. Biochem Pharmacol 2004; 67:1751-61. [PMID: 15081874 DOI: 10.1016/j.bcp.2004.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2003] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) integrase (IN) is an attractive target for the development of new antiviral therapies. Recently, several HIV-1 recombinant IN (rIN) in vitro inhibitors have been described. However, the great majority of them failed to block the virus replication in cell-based assays, suggesting the inadequacy of the in vitro assay systems used for inhibitor screening. To improve these systems, we designed a 40(mer) duplex DNA reaction substrate consisting of recognition sequences from both U3 and U5 HIV-1 long terminal repeat (LTR) termini. The HIV-1 rIN was able to catalyze its enzyme activities recognizing both ends of the 40(mer) dsDNA. Using this substrate we assayed the effects on rIN catalysis of different classes of compounds which inhibit the HIV-1 rIN in vitro when the reaction substrate is the standard 21(mer) U5 dsDNA, and that are either active or inactive on the HIV-1 replication. We also compared the efficacy of these compounds when added to the reaction before or after the formation of the rIN-dsDNA complex. In this system, the enzyme preincubation with the two-ended 40(mer) dsDNA before the addition of the compounds allowed a strong correlation between the effects of hydroxylated aromatics derivatives on rIN activity in cell-free assays and their effects on viral replication in cell-culture assays. This increase in drug selectivity of the rIN in vitro assay was explored by investigating whether it was due to the length of the 40(mer), longer than the standard 21(mer), or to presence of both viral ends, versus only one viral end. To this purpose we designed four 40(mer) oligonucleotides containing either only one viral end or two-repetitive ends, finding that the architecture of the rIN-dsDNA complex and its compound susceptibility is significantly influenced by the sequence of the dsDNA substrate.
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Affiliation(s)
- Enzo Tramontano
- Department of Sciences and Biomedical Technologies, University of Cagliari, Cittadella Universitaria SS554, 09142 Monserrato, Cagliari, Italy.
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Svarovskaia ES, Barr R, Zhang X, Pais GCG, Marchand C, Pommier Y, Burke TR, Pathak VK. Azido-containing diketo acid derivatives inhibit human immunodeficiency virus type 1 integrase in vivo and influence the frequency of deletions at two-long-terminal-repeat-circle junctions. J Virol 2004; 78:3210-22. [PMID: 15016842 PMCID: PMC371038 DOI: 10.1128/jvi.78.7.3210-3222.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously found that azido-containing beta-diketo acid derivatives (DKAs) are potent inhibitors of human immunodeficiency virus type 1 (HIV-1) integrase (IN) (X. Zhang et al., Bioorg. Med. Chem. Lett., 13:1215-1219, 2003). To characterize the intracellular mechanisms of action of DKAs, we analyzed the antiviral activities of two potent azido-containing DKAs with either a monosubstitution or a disubstitution of azido groups, using single- and multiple-replication-cycle assays. Both azido-containing DKAs significantly inhibited HIV-1 infection in 293T, CEM-SS, and H9 cells (50% inhibitory concentration = 2 to 13 micro M) and exhibited low cytotoxicity (50% cytotoxic concentration = 60 to 600 micro M). Inhibition of HIV-1 IN in vivo was demonstrated by the observation that previously described L-708,906 resistance mutations in HIV-1 IN (T66I and T66I/S153Y) also conferred resistance to the azido-group-containing DKAs. In vitro assays and in vivo analysis indicated that the DKAs did not significantly inhibit the 3' processing and selectively inhibited the strand transfer reaction. In addition, quantitative PCR indicated that two-long-terminal-repeat (2-LTR) circles were elevated in the presence of the azido-containing DKAs, confirming that HIV-1 IN was the intracellular target of viral inhibition. To gain insight into the mechanism by which the DKAs increased 2-LTR-circle formation of 3'-processed viral DNAs, we performed extensive DNA sequencing analysis of 2-LTR-circle junctions. The results indicated that the frequency of deletions at the circle junctions was elevated from 19% for the untreated controls to 32 to 41% in the presence of monosubstituted (but not disubstituted) DKAs. These results indicate that the structure of the DKAs can influence the extent of degradation of viral DNA ends by host nucleases and the frequency of deletions at the 2-LTR-circle junctions. Thus, sequencing analysis of 2-LTR-circle junctions can elucidate the intracellular mechanisms of action of HIV-1 IN inhibitors.
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Affiliation(s)
- Evguenia S Svarovskaia
- HIV Drug Resistance Program. Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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Singh SB, Ondeyka JG, Schleif WA, Felock P, Hazuda DJ. Chemistry and structure-activity relationship of HIV-1 integrase inhibitor integracide B and related natural products. JOURNAL OF NATURAL PRODUCTS 2003; 66:1338-1344. [PMID: 14575434 DOI: 10.1021/np030211s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Integracides, 4,4-dimethylergostane triterpenoids, are inhibitors of HIV-1 integrase, a critical enzyme in replication of HIV-1. The chemistry and structure-activity relationship of integracide B and related natural products are described. A charged group, e.g., a sulfate, carboxyl, or amino, is required for the HIV-1 integrase activity. These compounds showed HIV-1 integrase activity with IC(50) values in the range 4.8-15 muM and exhibited antiviral activity in a viral spread assay, but with only a small or no therapeutic window.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, P.O. Box 2000, Rahway, New Jersey 07065, USA.
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