1
|
Renzi G, Carta F, Supuran CT. The Integrase: An Overview of a Key Player Enzyme in the Antiviral Scenario. Int J Mol Sci 2023; 24:12187. [PMID: 37569561 PMCID: PMC10419282 DOI: 10.3390/ijms241512187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Integration of a desossiribonucleic acid (DNA) copy of the viral ribonucleic acid (RNA) into host genomes is a fundamental step in the replication cycle of all retroviruses. The highly conserved virus-encoded Integrase enzyme (IN; EC 2.7.7.49) catalyzes such a process by means of two consecutive reactions named 3'-processing (3-P) and strand transfer (ST). The Authors report and discuss the major discoveries and advances which mainly contributed to the development of Human Immunodeficiency Virus (HIV) -IN targeted inhibitors for therapeutic applications. All the knowledge accumulated over the years continues to serve as a valuable resource for the design and development of effective antiretroviral drugs.
Collapse
Affiliation(s)
| | - Fabrizio Carta
- Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (G.R.); (C.T.S.)
| | | |
Collapse
|
2
|
Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
Collapse
|
3
|
Carcelli M, Rogolino D, Sechi M, Rispoli G, Fisicaro E, Compari C, Grandi N, Corona A, Tramontano E, Pannecouque C, Naesens L. Antiretroviral activity of metal-chelating HIV-1 integrase inhibitors. Eur J Med Chem 2014; 83:594-600. [PMID: 24996145 DOI: 10.1016/j.ejmech.2014.06.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/09/2014] [Accepted: 06/22/2014] [Indexed: 02/07/2023]
Abstract
Data regarding the activity of metal complexes against HIV virus in cell are surprisingly scarce. In this study, we present the antiviral activity against HIV-infected cells of different types of chelating ligands and of their metal complexes. In particular, the carboxamide chelating scaffold and the corresponding coordination compounds demonstrated an interesting antiviral profile in the nanomolar range. These molecules inhibit not only HIV integrase catalytic activity, but they also interfere with the function of the RNase H component of the HIV reverse transcriptase. Here we also discuss the thermodynamic characterization in solution of the metal complexes of the most active ligands, affording to the best of our knowledge for the first time this type of data for complexes with anti-HIV activity.
Collapse
Affiliation(s)
- Mauro Carcelli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, I-43124 Parma, Italy.
| | - Dominga Rogolino
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, I-43124 Parma, Italy
| | - Mario Sechi
- Dipartimento di Chimica e Farmacia, Università di Sassari, Via Vienna 2, I-07100 Sassari, Italy
| | - Gabriele Rispoli
- Dipartimento di Chimica, Università di Parma, Parco Area delle Scienze 17/A, I-43124 Parma, Italy
| | - Emilia Fisicaro
- Dipartimento di Farmacia, Università di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Carlotta Compari
- Dipartimento di Farmacia, Università di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Nicole Grandi
- Dipartimento di Scienze della Vita e dell'Ambiente-Sezione Biomedica-Università di Cagliari Cittadella Universitaria SS554, I-09042 Monserrato, CA, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente-Sezione Biomedica-Università di Cagliari Cittadella Universitaria SS554, I-09042 Monserrato, CA, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente-Sezione Biomedica-Università di Cagliari Cittadella Universitaria SS554, I-09042 Monserrato, CA, Italy
| | | | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| |
Collapse
|
4
|
Arora R, de Beauchene IC, Polanski J, Laine E, Tchertanov L. Raltegravir flexibility and its impact on recognition by the HIV-1 IN targets. J Mol Recognit 2013; 26:383-401. [PMID: 23836466 DOI: 10.1002/jmr.2277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 04/04/2013] [Accepted: 04/07/2013] [Indexed: 01/10/2023]
Abstract
HIV-1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN-specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV-1 targets - the unbound IN, the vDNA, and the IN•vDNA complex - mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well-defined cavity formed by the active site, the vDNA, and the shortened loop in the IN•vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg(2+) cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H-bonds similar to those observed in DNA base pair G-C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity.
Collapse
Affiliation(s)
- Rohit Arora
- Bioinformatics, Molecular Dynamics & Modeling (BiMoDyM), Laboratoire de Biologie et Pharmacologie Appliquée (LBPA-CNRS), Ecole Normale Supérieure de Cachan, 61 avenue du Président Wilson, 94235, Cachan, France
| | | | | | | | | |
Collapse
|
5
|
Rusconi S, Vitiello P, Adorni F, Bruzzone B, De Luca A, Micheli V, Meraviglia P, Maserati R, Di Pietro M, Colao G, Penco G, Di Biagio A, Punzi G, Monno L, Zazzi M. Factors associated with virological success with raltegravir-containing regimens and prevalence of raltegravir-resistance-associated mutations at failure in the ARCA database. Clin Microbiol Infect 2013; 19:936-42. [PMID: 23289841 DOI: 10.1111/1469-0691.12100] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/27/2012] [Accepted: 11/04/2012] [Indexed: 02/03/2023]
Abstract
Raltegravir (RAL) is the only licensed human immunodeficiency virus (HIV) integrase inhibitor. The factors associated with the virological response to RAL-containing regimens and the prevalence of integrase mutations associated with RAL failure deserve further investigation. From the Antiretroviral Resistance Cohort Analysis database, we selected triple-class-experienced subjects failing their current treatment with complete treatment history available. Selection criteria included HIV-RNA, CD4 count and HIV genotype within 3 months of RAL initiation. Factors associated with 24-week response were analysed; genotypic sensitivity scores (GSS) and weighted-GSS were evaluated. Virological response was achieved in 74.3% of 105 subjects. Mutations associated with RAL failure were detected in 12/24 subjects with an integrase genotype, with the prevalence of Q148H + G140S. Each extra unit of GSS (p 0.05, OR 2.62; 95% CI 1.00-6.87). was found to be a associated with response. Weighted-GSS had borderline statistical significance (p 0.063, OR 2.04; 95% CI 0.96-4.33) When stratifying for different cut-offs (<1 as reference, 1-1.49, ≥1.5), a borderline significant increase in the probability of response appeared for GSS ≥1.5 (p 0.053, OR 4.00; 95% CI 0.98-16.25). GSS ≥1 showed the highest sensitivity, 82.6%. Receiver operating characteristic curves depicted the widest area under the curve (0.663, p 0.054) of GSS ≥1. Unresponsiveness to RAL-containing regimens among triple-class-experienced subjects was low. The activity of the background regimen was strongly associated with response. Although few integrase genotypes were available at failure, half of these were without integrase resistance mutations. The substantial rate of RAL failure in the absence of known RAL-resistance mutations may be associated with adherence issues and this issue warrants further analysis in longer observations.
Collapse
Affiliation(s)
- S Rusconi
- Divisione Clinicizzata di Malattie Infettive, Dipartimento di Scienze Biomediche e Cliniche "Luigi Sacco", Universita' degli Studi di Milano, Milano, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Integrase (IN) is a clinically validated target for the treatment of human immunodeficiency virus infections and raltegravir exhibits remarkable clinical activity. The next most advanced IN inhibitor is elvitegravir. However, mutant viruses lead to treatment failure and mutations within the IN coding sequence appear to confer cross-resistance. The characterization of those mutations is critical for the development of second generation IN inhibitors to overcome resistance. This review focuses on IN resistance based on structural and biochemical data, and on the role of the IN flexible loop i.e., between residues G140-G149 in drug action and resistance.
Collapse
Affiliation(s)
| | | | | | - Yves Pommier
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-496-5944; Fax: +1-301-402-0752
| |
Collapse
|
7
|
da Silva FA, Li M, Rato S, Maia S, Malhó R, Warren K, Harrich D, Craigie R, Barbas C, Goncalves J. Recombinant rabbit single-chain antibodies bind to the catalytic and C-terminal domains of HIV-1 integrase protein and strongly inhibit HIV-1 replication. Biotechnol Appl Biochem 2012; 59:353-66. [PMID: 23586912 PMCID: PMC3917493 DOI: 10.1002/bab.1034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/26/2012] [Indexed: 11/11/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) integrase (IN) protein plays an important role during the early stages of the retroviral life cycle and therefore is an attractive target for therapeutic intervention. We immunized rabbits with HIV-1 IN protein and developed a combinatorial single-chain variable fragment (scFv) library against IN. Five different scFv antibodies with high binding activity and specificity for IN were identified. These scFvs recognize the catalytic and C-terminal domains of IN and block the strand-transfer process. Cells expressing anti-IN-scFvs were highly resistant to HIV-1 replication due to an inhibition of the integration process itself. These results provide proof-of-concept that rabbit anti-IN-scFv intrabodies can be designed to block the early stages of HIV-1 replication without causing cellular toxicity. Therefore, these anti-IN-scFvs may be useful agents for "intracellular immunization"-based gene therapy strategies. Furthermore, because of their epitope binding characteristics, these scFvs can be used also as new tools to study the structure and function of HIV-1 IN protein.
Collapse
Affiliation(s)
- Frederico Aires da Silva
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sylvie Rato
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Sara Maia
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| | - Rui Malhó
- Faculdade de Ciências de Lisboa, Universidade de Lisboa, BioFIG, Lisbon, Portugal
| | - Kylie Warren
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
| | - David Harrich
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Barbas
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joao Goncalves
- URIA—Centro de Patogénese Molecular, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
- IMM—Instituto de Medicina Molecular, Lisbon, Portugal
| |
Collapse
|
8
|
Xue B, Mizianty MJ, Kurgan L, Uversky VN. Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. Cell Mol Life Sci 2012; 69:1211-59. [PMID: 22033837 PMCID: PMC11114566 DOI: 10.1007/s00018-011-0859-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Many proteins and protein regions are disordered in their native, biologically active states. These proteins/regions are abundant in different organisms and carry out important biological functions that complement the functional repertoire of ordered proteins. Viruses, with their highly compact genomes, small proteomes, and high adaptability for fast change in their biological and physical environment utilize many of the advantages of intrinsic disorder. In fact, viral proteins are generally rich in intrinsic disorder, and intrinsically disordered regions are commonly used by viruses to invade the host organisms, to hijack various host systems, and to help viruses in accommodation to their hostile habitats and to manage their economic usage of genetic material. In this review, we focus on the structural peculiarities of HIV-1 proteins, on the abundance of intrinsic disorder in viral proteins, and on the role of intrinsic disorder in their functions.
Collapse
Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
| | - Marcin J. Mizianty
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region Russia
| |
Collapse
|
9
|
Structure-analysis of the HIV-1 integrase Y143C/R raltegravir resistance mutation in association with the secondary mutation T97A. Antimicrob Agents Chemother 2011; 55:3187-94. [PMID: 21576445 DOI: 10.1128/aac.00071-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The HIV-1 integrase (IN) mutations Y143C/R are known as raltegravir (RAL) primary resistance mutations. In a previous study (S. Reigadas et al., PLoS One 5:e10311, 2010), we investigated the genetic pathway and the dynamics of emergence of the Y143C/R mutations in three patients failing RAL-containing regimens. In these patients, the Y143C/R mutation was associated with the T97A mutation. The aim of the present biochemical and molecular studies in vitro was to evaluate whether the secondary mutation, T97A, associated with the Y143C/R mutation could increase the level of resistance to RAL and impact IN activities. Site-directed mutagenesis experiments were performed with expression vectors harboring the region of the pol gene coding for IN. With a 3'-end processing assay, the 50% inhibitory concentrations (IC(50)) were 1.2 μM, 1.2 μM, 2.4 μM (fold change [FC], 2), and 20 μM (FC, 16.7) for IN wild type (WT), the IN T97A mutation, the IN Y143C/T97A mutation, and the IN Y143R/T97A mutation, respectively. FCs of 18 and 100 were observed with the strand transfer assay for IN Y143C/T97A and Y143R/T97A mutations, with IC(50) of 0.625 μM and 2.5 μM, respectively. In the strand transfer assay, the IN Y143C or R mutation combined with the secondary mutation T97A severely impaired susceptibility to RAL compared to results with the IN Y143C or R mutation alone. Assays without RAL suggested that the T97A mutation could rescue the catalytic activity which was impaired by the presence of the Y143C/R mutation. The combination of the T97A mutation with the primary RAL resistance mutations Y143C/R strongly reduces the susceptibility to RAL and rescues the catalytic defect due to the Y143C/R mutation. This result indicates that the emergence of the Y143C/R/T97A double-mutation pattern in patients is a signature of a high resistance level.
Collapse
|
10
|
Rafiee MA, Partoee T. Investigation of the Binding Affinity between Styrylquinoline Inhibitors and HIV Integrase Using Calculated Nuclear Quadrupole Coupling Constant (NQCC) Parameters (A Theoretical ab initio Study). B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.1.208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
|
12
|
Ceccherini-Silberstein F, Malet I, Fabeni L, Dimonte S, Svicher V, D'Arrigo R, Artese A, Costa G, Bono S, Alcaro S, d'Arminio Monforte A, Katlama C, Calvez V, Antinori A, Marcelin AG, Perno CF. Specific HIV-1 integrase polymorphisms change their prevalence in untreated versus antiretroviral-treated HIV-1-infected patients, all naive to integrase inhibitors. J Antimicrob Chemother 2010; 65:2305-18. [DOI: 10.1093/jac/dkq326] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
13
|
Ceccherini-Silberstein F, Van Baelen K, Armenia D, Trignetti M, Rondelez E, Fabeni L, Scopelliti F, Pollicita M, Van Wesenbeeck L, Van Eygen V, Dori L, Sarmati L, Aquaro S, Palamara G, Andreoni M, Stuyver LJ, Perno CF. Secondary integrase resistance mutations found in HIV-1 minority quasispecies in integrase therapy-naive patients have little or no effect on susceptibility to integrase inhibitors. Antimicrob Agents Chemother 2010; 54:3938-48. [PMID: 20479206 PMCID: PMC2935022 DOI: 10.1128/aac.01720-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/05/2010] [Accepted: 05/05/2010] [Indexed: 11/20/2022] Open
Abstract
The goal of this study was to explore the presence of integrase strand transfer inhibitor (InSTI) resistance mutations in HIV-1 quasispecies present in InSTI-naïve patients and to evaluate their in vitro effects on phenotypic susceptibility to InSTIs and their replication capacities. The RT-RNase H-IN region was PCR amplified from plasma viral RNA obtained from 49 HIV-1 subtype B-infected patients (21 drug naïve and 28 failing highly active antiretroviral therapy [HAART] not containing InSTIs) and recombined with an HXB2-based backbone with RT and IN deleted. Recombinant viruses were tested against raltegravir and elvitegravir and for replication capacity. Three-hundred forty-four recombinant viruses from 49 patients were successfully analyzed both phenotypically and genotypically. The majority of clones were not phenotypically resistant to InSTIs: 0/344 clones showed raltegravir resistance, and only 3 (0.87%) showed low-level elvitegravir resistance. No primary resistance mutations for raltegravir and elvitegravir were found as major or minor species. The majority of secondary mutations were also absent or rarely present. Secondary mutations, such as T97A and G140S, found rarely and only as minority quasispecies, were present in the elvitegravir-resistant clones. A novel mutation, E92G, although rarely found in minority quasispecies, showed elvitegravir resistance. Preexisting genotypic and phenotypic raltegravir resistance was extremely rare in InSTI-naïve patients and confined to only a restricted minority of secondary variants. Overall, these results, together with others based on population and ultradeep sequencing, suggest that at this point IN genotyping in all patients before raltegravir treatment may not be cost-effective and should not be recommended until evidence of transmitted drug resistance to InSTIs or the clinical relevance of IN minor variants/polymorphisms is determined.
Collapse
|
14
|
Hadi V, Koh YH, Sanchez TW, Barrios D, Neamati N, Jung KW. Development of the next generation of HIV-1 integrase inhibitors: pyrazolone as a novel inhibitor scaffold. Bioorg Med Chem Lett 2010; 20:6854-7. [PMID: 20864343 DOI: 10.1016/j.bmcl.2010.08.057] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 08/11/2010] [Indexed: 10/19/2022]
Abstract
HIV-1 integrase (IN), one of the essential enzymes in HIV infection, has been validated as a target for HIV treatment. While more than 20 drugs have been approved by the FDA to treat HIV/AIDS, only one drug, Raltegravir (1), was approved as an IN inhibitor. The rapid mutation of the virus, which leads to multidrug resistant HIV strains, presents an urgent need to find potent compounds that can serve as second-generation IN inhibitors. The pyrazolone scaffold, predicted by a computational modeling study using GS-9137(2) as a pharmacophoric model, has shown to inhibit the IN catalytic activities in low micromolar range. We have synthesized various analogs based on the pyrazolone scaffold and performed SAR studies. This paper will showcase the up-to-date result of this scaffold as a promising HIV-1 IN inhibitor.
Collapse
Affiliation(s)
- Victor Hadi
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States
| | | | | | | | | | | |
Collapse
|
15
|
Abstract
Integration of the HIV-1 viral DNA generated by reverse transcription of the RNA genome into the host cell chromosomes is a key step of viral replication, catalyzed by the viral integrase. In October 2007, the first integrase inhibitor, raltegravir, was approved for clinical use under the name of Isentress™. The results of the various clinical trials that have evaluated raltegravir have been very encouraging with regard to the immunological and virological efficacy and tolerance. However, as observed for other anti-retrovirals, specific resistance mutations have been identified in patients failing to respond to treatment with raltegravir. Although knowledge of the integrase structural biology remains fragmentary, the structures and modeling data available might provide relevant clues on the origin of the emergence of these resistance mutations. In this review, we describe the mechanism of action of this drug and the main data relating to its use in vivo, together with recent structural data important to our understanding of the origin of viral resistance.
Collapse
Affiliation(s)
- Jean-Francois Mouscadet
- LBPA, CNRS UMR8113, Ecole Normale Superieure de Cachan, 61 avenue du President Wilson, 94235 Cachan Cedex, France.
| | | |
Collapse
|
16
|
Fitzkee NC, Masse JE, Shen Y, Davies DR, Bax A. Solution conformation and dynamics of the HIV-1 integrase core domain. J Biol Chem 2010; 285:18072-84. [PMID: 20363759 DOI: 10.1074/jbc.m110.113407] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) integrase (IN) is a critical enzyme involved in infection. It catalyzes two reactions to integrate the viral cDNA into the host genome, 3' processing and strand transfer, but the dynamic behavior of the active site during catalysis of these two processes remains poorly characterized. NMR spectroscopy can reveal important structural details about enzyme mechanisms, but to date the IN catalytic core domain has proven resistant to such an analysis. Here, we present the first NMR studies of a soluble variant of the catalytic core domain. The NMR chemical shifts are found to corroborate structures observed in crystals, and confirm prior studies suggesting that the alpha4 helix extends toward the active site. We also observe a dramatic improvement in NMR spectra with increasing MgCl(2) concentration. This improvement suggests a structural transition not only near the active site residues but also throughout the entire molecule as IN binds Mg(2+). In particular, the stability of the core domain is linked to the conformation of its C-terminal helix, which has implications for relative domain orientation in the full-length enzyme. (15)N relaxation experiments further show that, although conformationally flexible, the catalytic loop of IN is not fully disordered in the absence of DNA. Indeed, automated chemical shift-based modeling of the active site loop reveals several stable clusters that show striking similarity to a recent crystal structure of prototype foamy virus IN bound to DNA.
Collapse
Affiliation(s)
- Nicholas C Fitzkee
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | |
Collapse
|
17
|
Carayon K, Leh H, Henry E, Simon F, Mouscadet JF, Deprez E. A cooperative and specific DNA-binding mode of HIV-1 integrase depends on the nature of the metallic cofactor and involves the zinc-containing N-terminal domain. Nucleic Acids Res 2010; 38:3692-708. [PMID: 20164093 PMCID: PMC2887959 DOI: 10.1093/nar/gkq087] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 integrase catalyzes the insertion of the viral genome into chromosomal DNA. We characterized the structural determinants of the 3′-processing reaction specificity—the first reaction of the integration process—at the DNA-binding level. We found that the integrase N-terminal domain, containing a pseudo zinc-finger motif, plays a key role, at least indirectly, in the formation of specific integrase–DNA contacts. This motif mediates a cooperative DNA binding of integrase that occurs only with the cognate/viral DNA sequence and the physiologically relevant Mg2+ cofactor. The DNA-binding was essentially non-cooperative with Mn2+ or using non-specific/random sequences, regardless of the metallic cofactor. 2,2′-Dithiobisbenzamide-1 induced zinc ejection from integrase by covalently targeting the zinc-finger motif, and significantly decreased the Hill coefficient of the Mg2+-mediated integrase–DNA interaction, without affecting the overall affinity. Concomitantly, 2,2′-dithiobisbenzamide-1 severely impaired 3′-processing (IC50 = 11–15 nM), suggesting that zinc ejection primarily perturbs the nature of the active integrase oligomer. A less specific and weaker catalytic effect of 2,2′-dithiobisbenzamide-1 is mediated by Cys 56 in the catalytic core and, notably, accounts for the weaker inhibition of the non-cooperative Mn2+-dependent 3′-processing. Our data show that the cooperative DNA-binding mode is strongly related to the sequence-specific DNA-binding, and depends on the simultaneous presence of the Mg2+ cofactor and the zinc effector.
Collapse
Affiliation(s)
- Kevin Carayon
- LBPA, CNRS, Ecole Normale Supérieure de Cachan, 61 av. du Président Wilson, 94235 Cachan, France
| | | | | | | | | | | |
Collapse
|
18
|
Hobaika Z, Zargarian L, Boulard Y, Maroun RG, Mauffret O, Fermandjian S. Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix. Nucleic Acids Res 2010; 37:7691-700. [PMID: 19808934 PMCID: PMC2794180 DOI: 10.1093/nar/gkp824] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
HIV-1 integrase integrates retroviral DNA through 3′-processing and strand transfer reactions in the presence of a divalent cation (Mg2+ or Mn2+). The α4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of the α4 helix, oligonucleotides mimicking processed and unprocessed U5 LTR end and 5 mM Mg2+. Circular dichroism, fluorescence and NMR experiments confirmed the implication of the α4 helix polar/charged face in specific and non-specific bindings to LTR ends. The specific binding requires unprocessed LTR ends—i.e. an unaltered 3′-processing site CA↓GT3′—and is reinforced by Mg2+ (Kd decreases from 2 to 0.8 nM). The latter likely interacts with the ApG and GpT3′ steps of the 3′-processing site. With deletion of GT3′, only persists non-specific binding (Kd of 100 μM). Proton chemical shift deviations showed that specific binding need conserved amino acids in the α4 helix and conserved nucleotide bases and backbone groups at LTR ends. We suggest a conserved recognition mechanism based on both direct and indirect readout and which is subject to evolutionary pressure.
Collapse
Affiliation(s)
- Zeina Hobaika
- Laboratoire de Biotechnologies et Pharmacologie génétique Appliquée (LBPA), UMR 8113 CNRS, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan Cedex, France
| | | | | | | | | | | |
Collapse
|
19
|
|
20
|
Mirambeau G. [How proviral DNA is integrated into the host cell DNA and how this process can be inhibited]. Enferm Infecc Microbiol Clin 2009; 26 Suppl 12:11-6. [PMID: 19572420 DOI: 10.1016/s0213-005x(08)76567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HIV replication cycle passes through a stage of integrating proviral DNA into the cell's DNA. In this process, the viral enzyme, integrase, catalyses two reactions. The first reaction, which seems to occur in the cytoplasm, involves 3'-end processing, in which two nucleotides are removed from the 3' ends of the viral DNA by integrase. The second reaction, which occurs in the nucleus, involves the strand transfer reaction, catalyzed by integrase, in which the recessed 3' ends of the viral DNA are joined to the protruding 5' ends in the target DNA. Although this activity has not yet been completely defined and the structure of the active form of integrase, probably a tetramer, has not been resolved, drugs of the diketoacid (DKA) family have been found. These drugs are highly potent inhibitors of the second phase, the strand transfer reaction. Through a series of optimizations, a highly effective molecule for clinical use, raltegravir, has been achieved. The present article provides a summary of basic knowledge on integrase, as well as the activity and the modes of inhibition of this enzyme. Also discussed is the reduced, but nevertheless real, development of resistance to raltegravir, requiring second-generation integrase inhibitors to be designed.
Collapse
Affiliation(s)
- Gilles Mirambeau
- Unitat de Recerca de la Sida, Fundació Clinic-IDIBAPS, Pare Cientific de Barcelona, Universidad de Barcelona, Barcelona, España.
| |
Collapse
|
21
|
Small molecule targets Env for endoplasmic reticulum-associated protein degradation and inhibits human immunodeficiency virus type 1 propagation. J Virol 2009; 83:10075-84. [PMID: 19640982 DOI: 10.1128/jvi.01700-08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is dependent on its envelope glycoprotein (Env) to bind, fuse, and subsequently infect a cell. We show here that treatment of HIV-1-infected cells with glycyl-prolyl-glycine amide (GPG-NH(2)), dramatically reduced the infectivity of the released viral particles by decreasing their Env incorporation. The mechanism of GPG-NH(2) was uncovered by examining Env expression and maturation in treated cells. GPG-NH(2) treatment was found to affect Env by significantly decreasing its steady-state levels, its processing into gp120/gp41, and its mass by inducing glycan removal in a manner dependent on its native signal sequence and the proteasome. Therefore, GPG-NH(2) negatively impacts Env maturation, facilitating its targeting for endoplasmic reticulum-associated protein degradation, where Env is deglycosylated en route to its degradation. These findings illustrate that nontoxic drugs such as GPG-NH(2), which can selectively target glycoproteins to existing cellular degradation pathways, may be useful for pathogen therapy.
Collapse
|
22
|
Menéndez-Arias L. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res 2009; 85:210-31. [PMID: 19616029 DOI: 10.1016/j.antiviral.2009.07.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/26/2009] [Accepted: 07/03/2009] [Indexed: 11/25/2022]
Abstract
Antiretroviral therapy has led to a significant decrease in human immunodeficiency virus (HIV)-related mortality. Approved antiretroviral drugs target different steps of the viral life cycle including viral entry (coreceptor antagonists and fusion inhibitors), reverse transcription (nucleoside and non-nucleoside inhibitors of the viral reverse transcriptase), integration (integrase inhibitors) and viral maturation (protease inhibitors). Despite the success of combination therapies, the emergence of drug resistance is still a major factor contributing to therapy failure. Viral resistance is caused by mutations in the HIV genome coding for structural changes in the target proteins that can affect the binding or activity of the antiretroviral drugs. This review provides an overview of the molecular mechanisms involved in the acquisition of resistance to currently used and promising investigational drugs, emphasizing the structural role of drug resistance mutations. The optimization of current antiretroviral drug regimens and the development of new drugs are still challenging issues in HIV chemotherapy. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
Collapse
Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| |
Collapse
|
23
|
Chirch LM, Morrison S, Steigbigel RT. Treatment of HIV infection with raltegravir. Expert Opin Pharmacother 2009; 10:1203-11. [DOI: 10.1517/14656560902911488] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
24
|
Design, synthesis, molecular modeling, and anti-HIV-1 integrase activity of a series of photoactivatable diketo acid-containing inhibitors as affinity probes. Antiviral Res 2009; 81:267-76. [PMID: 19135482 DOI: 10.1016/j.antiviral.2008.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Revised: 12/06/2008] [Accepted: 12/11/2008] [Indexed: 11/23/2022]
Abstract
The diketo acid (DKA) class of HIV-1 integrase (IN) inhibitors is thought to function by chelating divalent metal ions on the enzyme catalytic site. However, differences in mutations conferring resistance to various DKA inhibitors suggest that multiple binding orientations may exist. In order to facilitate identification of DKA binding sites, a series of photoactivable analogues of two potent DKAs was prepared as novel photoaffinity probes. In cross-linking assays designed to measure disruption of substrate DNA binding, the photoprobes behaved similarly to a reference DKA inhibitor. Molecular modeling studies suggest that such photoprobes interact within the IN active site in a manner similar to that of the parent DKAs. Analogues Ia-c are novel photoaffinity ligands useful in clarifying the HIV-1 binding interactions of DKA inhibitors.
Collapse
|
25
|
Integrase and integration: biochemical activities of HIV-1 integrase. Retrovirology 2008; 5:114. [PMID: 19091057 PMCID: PMC2615046 DOI: 10.1186/1742-4690-5-114] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/17/2008] [Indexed: 01/12/2023] Open
Abstract
Integration of retroviral DNA is an obligatory step of retrovirus replication because proviral DNA is the template for productive infection. Integrase, a retroviral enzyme, catalyses integration. The process of integration can be divided into two sequential reactions. The first one, named 3'-processing, corresponds to a specific endonucleolytic reaction which prepares the viral DNA extremities to be competent for the subsequent covalent insertion, named strand transfer, into the host cell genome by a trans-esterification reaction. Recently, a novel specific activity of the full length integrase was reported, in vitro, by our group for two retroviral integrases (HIV-1 and PFV-1). This activity of internal cleavage occurs at a specific palindromic sequence mimicking the LTR-LTR junction described into the 2-LTR circles which are peculiar viral DNA forms found during viral infection. Moreover, recent studies demonstrated the existence of a weak palindromic consensus found at the integration sites. Taken together, these data underline the propensity of retroviral integrases for binding symmetrical sequences and give perspectives for targeting specific sequences used for gene therapy.
Collapse
|
26
|
Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system. J Clin Microbiol 2008; 46:4087-90. [PMID: 18945845 DOI: 10.1128/jcm.01246-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sequencing assay for detection of mutations conferring resistance to human immunodeficiency virus type 1 (HIV-1) integrase inhibitors raltegravir and elvitegravir was developed using the automated TruGene sequencing system. The assay returned clear sequencing results for samples with >or=500 RNA copies/ml for mutation detection and HIV-1 subtyping across a spectrum of HIV-1 subtypes.
Collapse
|
27
|
Sechi M, Azzena U, Delussu MP, Dallocchio R, Dessì A, Cosseddu A, Pala N, Neamati N. Design and synthesis of bis-amide and hydrazide-containing derivatives of malonic acid as potential HIV-1 integrase inhibitors. Molecules 2008; 13:2442-61. [PMID: 18830166 PMCID: PMC6245433 DOI: 10.3390/molecules13102442] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 09/19/2008] [Accepted: 09/19/2008] [Indexed: 12/03/2022] Open
Abstract
HIV-1 integrase (IN) is an attractive and validated target for the development of novel therapeutics against AIDS. In the search for new IN inhibitors, we designed and synthesized three series of bis-amide and hydrazide-containing derivatives of malonic acid. We performed a docking study to investigate the potential interactions of the title compounds with essential amino acids on the IN active site.
Collapse
Affiliation(s)
- Mario Sechi
- Dipartimento Farmaco Chimico Tossicologico, Università di Sassari, Via Muroni 23/A, 07100 Sassari, Italy; E-mails: (M-P. D.); (N. P.)
- Authors to whom correspondence should be addressed; E-mail: (M. S.); (N. N.); Tel.: +39 079228 753 (M. S.); Tel.: +1 323-442-2341 (N. N.); Fax: +39 079 228 720 (M. S.); Fax: +1 323-442-1390 (N. N.)
| | - Ugo Azzena
- Dipartimento di Chimica, Università di Sassari, Via Vienna 2, 07100 Sassari, Italy; E-mail:
| | - Maria Paola Delussu
- Dipartimento Farmaco Chimico Tossicologico, Università di Sassari, Via Muroni 23/A, 07100 Sassari, Italy; E-mails: (M-P. D.); (N. P.)
| | - Roberto Dallocchio
- CNR-Istituto di Chimica Biomolecolare, Sassari, 07040 Li Punti, Italy; E-mails: (R. D.); (A. D.)
| | - Alessandro Dessì
- CNR-Istituto di Chimica Biomolecolare, Sassari, 07040 Li Punti, Italy; E-mails: (R. D.); (A. D.)
| | - Alessia Cosseddu
- Dipartimento Farmaco Chimico Tecnologico, Università di Siena, Via A. Moro, 53100 Siena, Italy; E-mail:
| | - Nicolino Pala
- Dipartimento Farmaco Chimico Tossicologico, Università di Sassari, Via Muroni 23/A, 07100 Sassari, Italy; E-mails: (M-P. D.); (N. P.)
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, PSC 304, Los Angeles, California, 90089, USA
- Authors to whom correspondence should be addressed; E-mail: (M. S.); (N. N.); Tel.: +39 079228 753 (M. S.); Tel.: +1 323-442-2341 (N. N.); Fax: +39 079 228 720 (M. S.); Fax: +1 323-442-1390 (N. N.)
| |
Collapse
|
28
|
Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, Shafer RW. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology 2008; 5:74. [PMID: 18687142 PMCID: PMC2546438 DOI: 10.1186/1742-4690-5-74] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2008] [Accepted: 08/07/2008] [Indexed: 11/10/2022] Open
Abstract
HIV-1 integrase is the third enzymatic target of antiretroviral (ARV) therapy. However, few data have been published on the distribution of naturally occurring amino acid variation in this enzyme. We therefore characterized the distribution of integrase variants among more than 1,800 published group M HIV-1 isolates from more than 1,500 integrase inhibitor (INI)-naïve individuals. Polymorphism rates equal or above 0.5% were found for 34% of the central core domain positions, 42% of the C-terminal domain positions, and 50% of the N-terminal domain positions. Among 727 ARV-naïve individuals in whom the complete pol gene was sequenced, integrase displayed significantly decreased inter- and intra-subtype diversity and a lower Shannon's entropy than protease or RT. All primary INI-resistance mutations with the exception of E157Q--which was present in 1.1% of sequences--were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%.
Collapse
Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Tommy F Liu
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Mark Kiuchi
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rafael Zioni
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robert J Gifford
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|