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Ilgova E, Galkin S, Khrenova M, Serebryakova M, Gottikh M, Anisenko A. Complex of HIV-1 Integrase with Cellular Ku Protein: Interaction Interface and Search for Inhibitors. Int J Mol Sci 2022; 23:ijms23062908. [PMID: 35328329 PMCID: PMC8951179 DOI: 10.3390/ijms23062908] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/27/2022] Open
Abstract
The interaction of HIV-1 integrase and the cellular Ku70 protein is necessary for HIV replication due to its positive effect on post-integration DNA repair. We have previously described in detail the Ku70 binding site within integrase. However, the integrase binding site in Ku70 remained poorly characterized. Here, using a peptide fishing assay and site-directed mutagenesis, we have identified residues I72, S73, and I76 of Ku70 as key for integrase binding. The molecular dynamics studies have revealed a possible way for IN to bind to Ku70, which is consistent with experimental data. According to this model, residues I72 and I76 of Ku70 form a "leucine zipper" with integrase residues, and, therefore, their concealment by low-molecular-weight compounds should impede the Ku70 interaction with integrase. We have identified such compounds by molecular docking and have confirmed their capacity to inhibit the formation of the integrase complex with Ku70. Our data demonstrate that the site of IN binding within Ku70 identified in the present work may be used for further search for inhibitors of the integrase binding to Ku70.
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Affiliation(s)
- Ekaterina Ilgova
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
| | - Simon Galkin
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Maria Khrenova
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marina Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Marina Gottikh
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Andrey Anisenko
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Correspondence:
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2
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Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
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Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
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3
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Galkin S, Rozina A, Zalevsky A, Gottikh M, Anisenko A. A Fluorescent Assay to Search for Inhibitors of HIV-1 Integrase Interactions with Human Ku70 Protein, and Its Application for Characterization of Oligonucleotide Inhibitors. Biomolecules 2020; 10:E1236. [PMID: 32854330 PMCID: PMC7563236 DOI: 10.3390/biom10091236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
The search for compounds that can inhibit the interaction of certain viral proteins with their cellular partners is a promising trend in the development of antiviral drugs. We have previously shown that binding of HIV-1 integrase with human Ku70 protein is essential for viral replication. Here, we present a novel, cheap, and fast assay to search for inhibitors of these proteins' binding based on the usage of genetically encoded fluorescent tags linked to both integrase and Ku70. Using this approach, we have elucidated structure-activity relationships for a set of oligonucleotide conjugates with eosin and shown that their inhibitory activity is primarily achieved through interactions between the conjugate nucleic bases and integrase. Molecular modeling of HIV-1 integrase in complex with the conjugates suggests that they can shield E212/L213 residues in integrase, which are crucial for its efficient binding to Ku70, in a length-dependent manner. Using the developed system, we have found the 11-mer phosphorothioate bearing 3'-end eosin-Y to be the most efficient inhibitor among the tested conjugates.
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Affiliation(s)
- Simon Galkin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
| | - Anna Rozina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
| | - Arthur Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Marina Gottikh
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Andrey Anisenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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4
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Huang YM, Alharbi NS, Sun B, Shantharam CS, Rakesh KP, Qin HL. Synthetic routes and structure-activity relationships (SAR) of anti-HIV agents: A key review. Eur J Med Chem 2019; 181:111566. [PMID: 31401538 DOI: 10.1016/j.ejmech.2019.111566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/05/2023]
Abstract
The worldwide increase of AIDS, an epidemic infection in constant development has an essential and still requires potent antiretroviral chemotherapeutic agents for reducing the integer of deaths caused by HIV. Thus, there is an urgent need for new anti-HIV drug candidates with increased strength, new targets, superior pharmacokinetic properties, and compact side effects. From this viewpoint, we first review present strategies of anti-HIV drug innovation and the synthesis of heterocyclic or natural compound as anti-HIV agents for facilitating the development of more influential and successful anti-HIV agents.
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Affiliation(s)
- Yu-Mei Huang
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China
| | - Njud S Alharbi
- Biotechnology Research Group, Deportment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bing Sun
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - C S Shantharam
- Department of Chemistry, Pooja Bhagavath Memorial Mahajana Education Centre, Mysuru, 570016, Karnataka, India
| | - K P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
| | - Hua-Li Qin
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR China.
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Scala A, Piperno A, Micale N, Christ F, Debyser Z. Synthesis and Anti-HIV Profile of a Novel Tetrahydroindazolylbenzamide Derivative Obtained by Oxazolone Chemistry. ACS Med Chem Lett 2019; 10:398-401. [PMID: 30996769 PMCID: PMC6466547 DOI: 10.1021/acsmedchemlett.8b00511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/15/2018] [Indexed: 01/11/2023] Open
Abstract
![]()
A new
tetrahydroindazolylbenzamide derivative has been synthesized, characterized,
and evaluated as HIV-inhibitor. The biological data revealed the ability
to inhibit HIV proliferation with low cytotoxicity allowing for significant
selectivity (EC50 2.77 μM; CC50 118.7
μM; SI = 68). The compound did not inhibit the viral integrase
as demonstrated by in vitro studies. QPCR experiments
showed that the block of viral replication occurred at early replication
steps, prior to integration, profiling it as a late reverse transcription
inhibitor. An efficient multistep strategy was adopted for the synthesis
of the scaffold, consisting of a sequential ring-opening reaction
of oxazol-5-(4H)-one with 1,3-diketone, followed
by cyclocondensation with hydrazine and hydrolysis of the nitrile
to the desired carboxamide.
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Affiliation(s)
- Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno D’Alcontres 31, Messina I-98166, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno D’Alcontres 31, Messina I-98166, Italy
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno D’Alcontres 31, Messina I-98166, Italy
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, UZ St. Rafael, Kapucijnenvoer 33, BE-3000 Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, UZ St. Rafael, Kapucijnenvoer 33, BE-3000 Leuven, Belgium
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How to win the HIV-1 drug resistance hurdle race: running faster or jumping higher? Biochem J 2017; 474:1559-1577. [PMID: 28446620 DOI: 10.1042/bcj20160772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/17/2022]
Abstract
Infections by the human immunodeficiency virus type 1 (HIV-1), the causative agent of the acquired immunodeficiency syndrome (AIDS), are still totaling an appalling 36.7 millions worldwide, with 1.1 million AIDS deaths/year and a similar number of yearly new infections. All this, in spite of the discovery of HIV-1 as the AIDS etiological agent more than 30 years ago and the introduction of an effective combinatorial antiretroviral therapy (cART), able to control disease progression, more than 20 years ago. Although very effective, current cART is plagued by the emergence of drug-resistant viral variants and most of the efforts in the development of novel direct-acting antiviral agents (DAAs) against HIV-1 have been devoted toward the fighting of resistance. In this review, rather than providing a detailed listing of all the drugs and the corresponding resistance mutations, we aim, through relevant examples, at presenting to the general reader the conceptual shift in the approaches that are being taken to overcome the viral resistance hurdle. From the classic 'running faster' strategy, based on the development of novel DAAs active against the mutant viruses selected by the previous drugs and/or presenting to the virus a high genetic barrier toward the development of resilience, to a 'jumping higher' approach, which looks at the cell, rather than the virus, as a source of valuable drug targets, in order to make the cellular environment non-permissive toward the replication of both wild-type and mutated viruses.
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Fazi R, Tintori C, Brai A, Botta L, Selvaraj M, Garbelli A, Maga G, Botta M. Homology Model-Based Virtual Screening for the Identification of Human Helicase DDX3 Inhibitors. J Chem Inf Model 2015; 55:2443-54. [PMID: 26544088 DOI: 10.1021/acs.jcim.5b00419] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Targeting cellular cofactors instead of viral enzymes represents a new strategy to combat infectious diseases, which should help to overcome the problem of viral resistance. Recently, it has been revealed that the cellular ATPase/RNA helicase X-linked DEAD-box polypeptide 3 (DDX3) is an essential host factor for the replication of several viruses such as HIV, HCV, JEV, Dengue, and West Nile. Accordingly, a drug targeting DDX3 could theoretically inhibit all viruses that are dependent on this host factor. Herein, for the first time, a model of hDDX3 in its closed conformation, which binds the viral RNA was developed by using the homology module of Prime through the Maestro interface of Schrodinger. Next, a structure-based virtual screening protocol was applied to identify DDX3 small molecule inhibitors targeting the RNA binding pocket. As a result, an impressive hit rate of 40% was obtained with the identification of 10 active compounds out of the 25 tested small molecules. The best poses of the active ligands highlighted the crucial residues to be targeted for the inhibition of the helicase activity of DDX3. The obtained results confirm the reliability of the constructed DDX3/RNA model and the proposed computational strategy for investigating novel DDX3 inhibitors.
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Affiliation(s)
- Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Cristina Tintori
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Lorenzo Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Manikandan Selvaraj
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR , Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via A. De Gasperi 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University , Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
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