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Palazzotti D, Felicetti T, Sabatini S, Moro S, Barreca ML, Sturlese M, Astolfi A. Fighting Antimicrobial Resistance: Insights on How the Staphylococcus aureus NorA Efflux Pump Recognizes 2-Phenylquinoline Inhibitors by Supervised Molecular Dynamics (SuMD) and Molecular Docking Simulations. J Chem Inf Model 2023; 63:4875-4887. [PMID: 37515548 PMCID: PMC10428217 DOI: 10.1021/acs.jcim.3c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 07/31/2023]
Abstract
The superbug Staphylococcus aureus (S. aureus) exhibits several resistance mechanisms, including efflux pumps, that strongly contribute to antimicrobial resistance. In particular, the NorA efflux pump activity is associated with S. aureus resistance to fluoroquinolone antibiotics (e.g., ciprofloxacin) by promoting their active extrusion from cells. Thus, since efflux pump inhibitors (EPIs) are able to increase antibiotic concentrations in bacteria as well as restore their susceptibility to these agents, they represent a promising strategy to counteract bacterial resistance. Additionally, the very recent release of two NorA efflux pump cryo-electron microscopy (cryo-EM) structures in complex with synthetic antigen-binding fragments (Fabs) represents a real breakthrough in the study of S. aureus antibiotic resistance. In this scenario, supervised molecular dynamics (SuMD) and molecular docking experiments were combined to investigate for the first time the molecular mechanisms driving the interaction between NorA and efflux pump inhibitors (EPIs), with the ultimate goal of elucidating how the NorA efflux pump recognizes its inhibitors. The findings provide insights into the dynamic NorA-EPI intermolecular interactions and lay the groundwork for future drug discovery efforts aimed at the identification of novel molecules to fight antimicrobial resistance.
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Affiliation(s)
- Deborah Palazzotti
- Department
of Pharmaceutical Sciences, Department of Excellence 2018−2022, University of Perugia, Via del Liceo, 1, 06123 Perugia, Italy
| | - Tommaso Felicetti
- Department
of Pharmaceutical Sciences, Department of Excellence 2018−2022, University of Perugia, Via del Liceo, 1, 06123 Perugia, Italy
| | - Stefano Sabatini
- Department
of Pharmaceutical Sciences, Department of Excellence 2018−2022, University of Perugia, Via del Liceo, 1, 06123 Perugia, Italy
| | - Stefano Moro
- Molecular
Modeling Section (MMS), Department of Pharmaceutical and Pharmacological
Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Maria Letizia Barreca
- Department
of Pharmaceutical Sciences, Department of Excellence 2018−2022, University of Perugia, Via del Liceo, 1, 06123 Perugia, Italy
| | - Mattia Sturlese
- Molecular
Modeling Section (MMS), Department of Pharmaceutical and Pharmacological
Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Andrea Astolfi
- Department
of Pharmaceutical Sciences, Department of Excellence 2018−2022, University of Perugia, Via del Liceo, 1, 06123 Perugia, Italy
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2
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Cancian M, Loreto ELS. A Mos1 transposase in vivo assay to screen new HIV-1 integrase inhibitors. Genetica 2018; 146:243-247. [PMID: 29352755 DOI: 10.1007/s10709-018-0007-1] [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: 02/10/2017] [Accepted: 01/11/2018] [Indexed: 11/27/2022]
Abstract
The integrase and transposase enzymes of retrovirus and transposons, respectively, share the catalytic DDE domain. In vitro assays showed that inhibitors of HIV-1 integrase generally inhibit the mariner Mos1 transposase. Using a Drosophila strain in which the mobilisation of the mariner element can be quantified by mosaic eyes, we showed that flies maintained in medium containing 210 µM to 4 mM of raltegravir, or 1 or 2 mM of dolutegravir, which are HIV-1 integrase inhibitor used in AIDS treatment, have 23-33% less somatic mobilisation in mosaic eyes when treated with raltegravir and 28-32% when treated with dolutegravir. The gene expression of the mariner transposase gene, estimated by qPCR, is similar among treated and control flies. The results suggest that in vivo assays using Drosophila can be used as a primary screening of inhibitory drugs for transposase and retroviral integrase. The advantages of this assay are that it is easy, quick, cheap and is an in vivo test, meaning that the tested substance has to have been taken in by cells and has arrived at the target site, which is not the case when in vitro assays are applied.
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Affiliation(s)
- Mariana Cancian
- Curso Ciências Biológicas, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Elgion L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Federal University of Santa Maria (UFSM), Av. Roraima 1000, Camobi, Santa Maria, RS, 97105-900, Brazil.
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Dalton N, Gordon CP, Boyle TP, Vandegraaf N, Deadman J, Rhodes DI, Coates JA, Pyne SG, Keller PA, Bremner JB. The discovery of allyltyrosine based tripeptides as selective inhibitors of the HIV-1 integrase strand-transfer reaction. Org Biomol Chem 2016; 14:6010-23. [PMID: 27225230 DOI: 10.1039/c6ob00950f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From library screening of synthetic antimicrobial peptides, an O-allyltyrosine-based tripeptide was identified to possess inhibitory activity against HIV-1 integrase (IN) exhibiting an IC50 value of 17.5 μM in a combination 3'-processing and strand transfer microtitre plate assay. The tripeptide was subjected to structure-activity relationship (SAR) studies with 28 peptides, incorporating an array of natural and non-natural amino acids. Resulting SAR analysis revealed the allyltyrosine residue was a key feature for IN inhibitory activity whilst incorporation of a lysine residue and extended hydrophilic chains bearing a terminal methyl ester was advantageous. Addition of hydrophobic aromatic moieties to the N-terminal of the scaffold afforded compounds with improved inhibitory activity. Consolidation of these functionalities lead to the development of the tripeptide 96 which specifically inhibited the IN strand-transfer reaction with an IC50 value of 2.5 μM.
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Affiliation(s)
- Neal Dalton
- School of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia.
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Balaraju T, Kumar A, Bal C, Chattopadhyay D, Jena N, Bal NC, Sharon A. Aromatic interaction profile to understand the molecular basis of raltegravir resistance. Struct Chem 2012. [DOI: 10.1007/s11224-012-0181-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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dos Santos MS, Bernardino AMR, Pinheiro LCS, Canto-Cavalheiro MM, Leon LL. An Efficient Synthesis of New 5-(1-Aryl-1H-pyrazole-4-yl)-1H-tetrazoles from 1-Aryl-1H-pyrazole-4-carbonitrilesvia[3 + 2] Cycloaddition Reaction. J Heterocycl Chem 2012. [DOI: 10.1002/jhet.928] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maurício S. dos Santos
- Universidade Federal de Itajubá; Instituto de Ciências Exatas, Departamento de Física e Química; 37500-903; Itajubá; MG; Brazil
| | - Alice M. R. Bernardino
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica; Programa de Pós-Graduação em Química; Campus do Valonguinho; 24210-150; Niterói; RJ; Brazil
| | - Luiz C. S. Pinheiro
- Universidade Federal Fluminense, Instituto de Química, Departamento de Química Orgânica; Programa de Pós-Graduação em Química; Campus do Valonguinho; 24210-150; Niterói; RJ; Brazil
| | | | - Leonor L. Leon
- Fundação Oswaldo Cruz; Laboratório de Bioquímica de Tripanosomatídeos; 21040-900; Rio de Janeiro; RJ; Brazil
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Gupta M, Madan AK. Diverse Models for the Prediction of HIV Integrase Inhibitory Activity of Substituted Quinolone Carboxylic Acids. Arch Pharm (Weinheim) 2012; 345:989-1000. [DOI: 10.1002/ardp.201100316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 07/04/2012] [Accepted: 07/11/2012] [Indexed: 11/07/2022]
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7
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Hu JP, He HQ, Tang DY, Sun GF, Zhang YQ, Fan J, Chang S. Study on the interactions between diketo-acid inhibitors and prototype foamy virus integrase-DNA complex via molecular docking and comparative molecular dynamics simulation methods. J Biomol Struct Dyn 2012; 31:734-47. [PMID: 22913375 DOI: 10.1080/07391102.2012.709458] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an important drug target for anti-acquired immune deficiency disease (AIDS) treatment and diketo-acid (DKA) inhibitors are potent and selective inhibitors of HIV-1 IN. Due to lack of three-dimensional structures including detail interactions between HIV-1 IN and its substrate viral DNA, the drug design and screening platform remains incompleteness and deficient. In addition, the action mechanism of DKA inhibitors with HIV-1 IN is not well understood. In view of the high homology between the structure of prototype foamy virus (PFV) IN and that of HIV-1 IN, we used PFV IN as a surrogate model for HIV-1 IN to investigate the inhibitory mechanism of raltegravir (RLV) and the binding modes with a series of DKA inhibitors. Firstly, molecular dynamics simulations of PFV IN, IN-RLV, IN-DNA, and IN-DNA-RLV systems were performed for 10 ns each. The interactions and inhibitory mechanism of RLV to PFV IN were explored through overall dynamics behaviors, catalytic loop conformation distribution, and hydrogen bond network analysis. The results show that the coordinated interactions of RLV with IN and viral DNA slightly reduce the flexibility of catalytic loop region of IN, and remarkably restrict the mobility of the CA end of viral DNA, which may lead to the partial loss of the inhibitory activity of IN. Then, we docked a series of DKA inhibitors into PFV IN-DNA receptor and obtained the IN-DNA-inhibitor complexes. The docking results between PFV IN-DNA and DKA inhibitors agree well with the corresponding complex of HIV-1 IN, which proves the dependability of PFV IN-DNA used for the anti-AIDS drug screening. Our study may help to make clear some theoretical questions and to design anti-AIDS drug based on the structure of IN.
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Affiliation(s)
- Jian-Ping Hu
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China.
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8
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Gupta P, Garg P, Roy N. Identification of Novel HIV-1 Integrase Inhibitors Using Shape-Based Screening, QSAR, and Docking Approach. Chem Biol Drug Des 2012; 79:835-49. [DOI: 10.1111/j.1747-0285.2012.01326.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Liao C, Nicklaus MC. Tautomerism and magnesium chelation of HIV-1 integrase inhibitors: a theoretical study. ChemMedChem 2010; 5:1053-66. [PMID: 20533499 DOI: 10.1002/cmdc.201000039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The tautomerism and corresponding transition states of four authentic HIV-1 integrase (IN) inhibitor prototype structures, alpha,gamma-diketo acid, alpha,gamma-diketotriazole, dihydroxypyrimidine carboxamide and 4-quinolone-3-carboxylic acid, were investigated at the B3LYP/6-311++G(d,p) level in vacuum and in aqueous solvent models. To study the possible chelating modes of these tautomers with two magnesium ions--a process important for inhibition--we modeled an assembly of three formic acids, four water molecules and two Mg(2+) ions as a template mimicking the binding site of IN. The DFT calculation results show that deprotonated enolized or phenolic hydroxy groups of specific tautomers in water lead to the most stable complexes, with the two magnesium ions separated by a distance of approximately 3.70 to 3.74 A, and with each magnesium ion at the center of an octahedron. The drug candidate GS-9137 (Gilead), based on the 4-quinolone-3-carboxylic acid scaffold, and its analogues form similar but different chelating modes. When one water molecule in the complex is replaced by a methanol molecule, which mimics the terminal 3'-OH of viral DNA, a good chelating complex is retained. This supports the hypothesis that, in the binding site of IN after 3'-processing, the terminal 3'-OH of viral DNA interacts with one Mg(2+) by chelation.
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Affiliation(s)
- Chenzhong Liao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, NCI-Frederick, 376 Boyles St, Frederick, MD 21702, USA
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11
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Ferro S, Luca LD, Barreca ML, Grazia SD, Christ F, Debyser Z, Chimirri A. New chloro,fluorobenzylindole derivatives as integrase strand-transfer inhibitors (INSTIs) and their mode of action. Bioorg Med Chem 2010; 18:5510-8. [DOI: 10.1016/j.bmc.2010.06.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 06/11/2010] [Accepted: 06/16/2010] [Indexed: 11/30/2022]
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12
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Barreca ML, Iraci N, De Luca L, Chimirri A. Induced-fit docking approach provides insight into the binding mode and mechanism of action of HIV-1 integrase inhibitors. ChemMedChem 2009; 4:1446-56. [PMID: 19544345 DOI: 10.1002/cmdc.200900166] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A three-dimensional model of a complex between HIV-1 integrase (IN), viral DNA, and metal ions that we recently built was used as a target for a docking method (induced-fit docking, IFD) that accurately predicts ligand binding modes and concomitant structural changes in the receptor. Six different well-known integrase strand transfer inhibitors (INSTIs): L-708,906, L-731,988, S-1360, L-870,810, raltegravir, and elvitegravir were thus used as ligands for our docking simulations. The obtained IFD results are consistent with the mechanism of action proposed for this class of IN inhibitors, that is, metal chelating/binding agents. This study affords new insight into the possible mechanism of inhibition and binding conformations for INSTIs. The impact on our hypothesis of specific mutations associated with IN inhibitor resistance was also evaluated. All these findings might have implications for integrase-directed HIV-1 drug discovery efforts.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento di Chimica e Tecnologia del Farmaco, Facoltà di Farmacia, Università di Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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13
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In search of second-generation HIV integrase inhibitors: targeting integration beyond strand transfer. Future Med Chem 2009; 1:1259-74. [DOI: 10.4155/fmc.09.86] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Highly active antiretroviral therapy combines antiviral drugs targeting different steps in the HIV replication cycle in order to reduce viral loads in patients to undetectable levels. Since HIV readily develops resistance and can therefore escape the action of existing drugs, novel drugs with novel mechanisms of action must be developed. The integration of the viral genome into the human genome is an essential and critical replication step that is catalyzed by the viral integrase with the help of cellular cofactors. Although HIV-1 integrase has been studied for more than two decades, the first integrase inhibitor, raltegravir, was only recently approved for clinical use. A second compound, elvitegravir, is currently in advanced clinical trials. Both drugs interfere with the strand-transfer reaction of integrase. Due to the complexity and multistep nature of the integration reaction, several other functions of integrase can be exploited for drug discovery. In this review, we will describe these alternative strategies to inhibit integration. They have recently attracted considerable interest for the development of second-generation integrase inhibitors.
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14
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Zhao XZ, Maddali K, Marchand C, Pommier Y, Burke TR. Diketoacid-genre HIV-1 integrase inhibitors containing enantiomeric arylamide functionality. Bioorg Med Chem 2009; 17:5318-24. [PMID: 19527935 DOI: 10.1016/j.bmc.2009.05.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 04/29/2009] [Accepted: 05/01/2009] [Indexed: 11/30/2022]
Abstract
Using our recently disclosed 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one and 4,5-dihydroxy-1H-isoindole-1,3(2H)-dione integrase inhibitors, we report differential effects on inhibitory potency induced by introduction of an alpha-chiral center into a key aryl substituent. We show that introduction of the chiral center is uniformly deleterious to binding, with the (R)-enantiomer being more deleterious than the (S)-enantiomer. A greater enantiomeric difference in potency is shown by inhibitors that have restricted rotation of the aryl ring, with the larger difference being due to poorer potency of the (R)-enantiomer rather than higher potency of the (S)-enantiomer. The potency difference for enantiomers based on the isoindoline-1,3-dione ring system is less than for those derived from the isoindol-1-one ring system. Our findings provide useful information that should aid in understanding molecular binding interactions of DKA-derived IN inhibitors.
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Affiliation(s)
- Xue Zhi Zhao
- Laboratory of Medicinal, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, United States
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15
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Langley DR, Samanta HK, Lin Z, Walker MA, Krystal MR, Dicker IB. The terminal (catalytic) adenosine of the HIV LTR controls the kinetics of binding and dissociation of HIV integrase strand transfer inhibitors. Biochemistry 2009; 47:13481-8. [PMID: 18991395 DOI: 10.1021/bi801372d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Specific HIV integrase strand transfer inhibitors are thought to bind to the integrase active site, positioned to coordinate with two catalytic magnesium atoms in a pocket flanked by the end of the viral LTR. A structural role for the 3' terminus of the viral LTR in the inhibitor-bound state has not previously been examined. This study describes the kinetics of binding of a specific strand transfer inhibitor to integrase variants assembled with systematic changes to the terminal 3' adenosine. Kinetic experiments are consistent with a two-step binding model in which there are different functions for the terminal adenine base and the terminal deoxyribose sugar. Adenine seems to act as a "shield" which retards the rate of inhibitor association with the integrase active site, possibly by acting as an internal competitive inhibitor. The terminal deoxyribose is responsible for retarding the rate of inhibitor dissociation, either by sterically blocking inhibitor egress or by a direct interaction with the bound inhibitor. These findings further our understanding of the details of the inhibitor binding site of specific strand transfer inhibitors.
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Affiliation(s)
- David R Langley
- Department of Computer Assisted Drug Design, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, USA
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16
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Ferro S, De Luca L, Barreca ML, Iraci N, De Grazia S, Christ F, Witvrouw M, Debyser Z, Chimirri A. Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions. J Med Chem 2008; 52:569-73. [DOI: 10.1021/jm8009266] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefania Ferro
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Laura De Luca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Nunzio Iraci
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Sara De Grazia
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Myriam Witvrouw
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Alba Chimirri
- Dipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168 Messina, Italy, Dipartimento di Chimica e Tecnologia del Farmaco, Via del Liceo 1, 06123 Perugia, Italy, Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium, and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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17
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Pasquini S, Mugnaini C, Tintori C, Botta M, Trejos A, Arvela RK, Larhed M, Witvrouw M, Michiels M, Christ F, Debyser Z, Corelli F. Investigations on the 4-Quinolone-3-carboxylic Acid Motif. 1. Synthesis and Structure−Activity Relationship of a Class of Human Immunodeficiency Virus type 1 Integrase Inhibitors. J Med Chem 2008; 51:5125-9. [DOI: 10.1021/jm8003784] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Serena Pasquini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Claudia Mugnaini
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Cristina Tintori
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Alejandro Trejos
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Riina K. Arvela
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Mats Larhed
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Myriam Witvrouw
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Martine Michiels
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Frauke Christ
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
| | - Federico Corelli
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via A. Moro, 53100 Siena, Italy, Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden, Molecular Medicine, Katholieke Universiteit Leuven and IRC KULAK, Kapucijnenvoer 33, B-3000 Leuven, Flanders, Belgium
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18
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A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid. Biophys J 2007; 94:2443-51. [PMID: 17981909 DOI: 10.1529/biophysj.107.107623] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy for wild-type and N155S mutant HIV-1 IN, both complexed with a DKA. This hybrid methodology has the advantage of the inclusion of quantum effects such as ligand polarization upon binding, which can be very important when highly polarizable groups are embedded in anisotropic environments, for example in metal-containing active sites. Furthermore, an energy terms decomposition analysis was performed to determine contributions of individual residues to the enzyme-inhibitor interactions. The results reveal that there is a strong interaction between the Lys-159, Lys-156, and Asn-155 residues and Mg(2+) cation and the DKA inhibitor. Our calculations show that the binding energy is higher in wild-type than in the N155S mutant, in accordance with the experimental results. The role of the mutated residue has thus been checked as maintaining the structure of the ternary complex formed by the protein, the Mg(2+) cation, and the inhibitor. These results might be useful to design compounds with more interesting anti-HIV-1 IN activity on the basis of its three-dimensional structure.
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Barreca ML, Ortuso F, Iraci N, De Luca L, Alcaro S, Chimirri A. Tn5 transposase as a useful platform to simulate HIV-1 integrase inhibitor binding mode. Biochem Biophys Res Commun 2007; 363:554-60. [PMID: 17889829 DOI: 10.1016/j.bbrc.2007.08.199] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 08/30/2007] [Indexed: 11/22/2022]
Abstract
The targeting of HIV-1 integrase (IN) for the design of novel antiviral compounds has until now proceeded slowly, mainly due to the lack of three-dimensional structures reporting detail interactions between IN and its DNA substrates as well as the complete enzyme with its three domains. Recently, we have proposed that Tn5 transposase (Tnp) can be used as a useful surrogate model for IN in attempt to address the potential binding modes of Integrase Strand Transfer Inhibitors. In order to strengthen our hypothesis, molecular dynamics simulations of IN inhibitors bound to Tn5 Tnp active site are now reported. A comparison of the obtained results with well documented specific mutations associated with resistance to HIV-1 IN inhibitors confirmed that Tn5 Tnp can provide a valuable platform for the structure-based discovery of new ligands.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento Farmaco-Chimico, Università di Messina,Viale Annunziata, I-98168 Messina, Italy.
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20
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Savarino A, Pistello M, D'Ostilio D, Zabogli E, Taglia F, Mancini F, Ferro S, Matteucci D, De Luca L, Barreca ML, Ciervo A, Chimirri A, Ciccozzi M, Bendinelli M. Human immunodeficiency virus integrase inhibitors efficiently suppress feline immunodeficiency virus replication in vitro and provide a rationale to redesign antiretroviral treatment for feline AIDS. Retrovirology 2007; 4:79. [PMID: 17971219 PMCID: PMC2244644 DOI: 10.1186/1742-4690-4-79] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 10/30/2007] [Indexed: 01/14/2023] Open
Abstract
Background Treatment of feline immunodeficiency virus (FIV) infection has been hampered by the absence of a specific combination antiretroviral treatment (ART). Integrase strand transfer inhibitors (INSTIs) are emerging as a promising new drug class for HIV-1 treatment, and we evaluated the possibility of inhibiting FIV replication using INSTIs. Methods Phylogenetic analysis of lentiviral integrase (IN) sequences was carried out using the PAUP* software. A theoretical three-dimensional structure of the FIV IN catalytic core domain (CCD) was obtained by homology modeling based on a crystal structure of HIV-1 IN CCD. The interaction of the transferred strand of viral DNA with the catalytic cavity of FIV IN was deduced from a crystal structure of a structurally similar transposase complexed with transposable DNA. Molecular docking simulations were conducted using a genetic algorithm (GOLD). Antiviral activity was tested in feline lymphoblastoid MBM cells acutely infected with the FIV Petaluma strain. Circular and total proviral DNA was quantified by real-time PCR. Results The calculated INSTI-binding sites were found to be nearly identical in FIV and HIV-1 IN CCDs. The close similarity of primate and feline lentivirus IN CCDs was also supported by phylogenetic analysis. In line with these bioinformatic analyses, FIV replication was efficiently inhibited in acutely infected cell cultures by three investigational INSTIs, designed for HIV-1 and belonging to different classes. Of note, the naphthyridine carboxamide INSTI, L-870,810 displayed an EC50 in the low nanomolar range. Inhibition of FIV integration in situ was shown by real-time PCR experiments that revealed accumulation of circular forms of FIV DNA within cells treated with L-870,810. Conclusion We report a drug class (other than nucleosidic reverse transcriptase inhibitors) that is capable of inhibiting FIV replication in vitro. The present study helped establish L-870,810, a compound successfully tested in human clinical trials, as one of the most potent anti-FIV agents ever tested in vitro. This finding may provide new avenues for treating FIV infection and contribute to the development of a small animal model mimicking the effects of ART in humans.
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Affiliation(s)
- Andrea Savarino
- Dept. of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.
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21
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Alves CN, Martí S, Castillo R, Andrés J, Moliner V, Tuñón I, Silla E. A Quantum Mechanics/Molecular Mechanics Study of the Protein–Ligand Interaction for Inhibitors of HIV-1 Integrase. Chemistry 2007; 13:7715-24. [PMID: 17570717 DOI: 10.1002/chem.200700040] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-containing active sites. Furthermore, an energy decomposition analysis was performed to determine the contributions of individual residues to the enzyme-inhibitor interactions on averaged structures obtained from rather extensive conformational sampling. Analysis of the results reveals first that there is a correlation between protein-ligand interaction energy and experimental strand transfer into human chromosomes and secondly that the Asn-155, Lys-156 and Lys-159 residues and the Mg(2+) ion are crucial to anti-HIV IN activity. These results may explain the available experimental data.
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Affiliation(s)
- Cláudio N Alves
- Departamento de Química, Centro de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110 Belém, PA, Brazil.
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22
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Cox AG, Nair V. Novel HIV integrase inhibitors with anti-HIV activity: insights into integrase inhibition from docking studies. Antivir Chem Chemother 2007; 17:343-53. [PMID: 17249248 DOI: 10.1177/095632020601700604] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mechanism of integrase is generally accepted to be dependant on the presence of two divalent metal ions in the active site. However, the only available crystal structures of HIV-1 integrase contain either one or no metal ions, hampering structure-based design studies of integrase inhibitors. For this reason, a two-metal ion model of integrase was constructed. This model was used for computational docking studies with novel diketoacid integrase inhibitors containing pyrimidine nucleobase scaffolds. The docking protocol allowed for some steric contact between the ligand and protein during docking simulations, which implicitly accounted for potential conformational changes in the protein as a result of binding viral DNA or the ligand. The results suggest that the aromatic rings in these diketo acids bind to regions close to the viral DNA and may interfere with mobility of a vital catalytic loop. The docking data also suggest that the ligand can be prevented from adopting a favourable conformation by changes in the relative orientation of its diketo side-chain and aromatic rings. The docked pose of each of the active compounds coordinated both of the metal ions present in the active site of integrase through the diketo acid functionality of these compounds. This result is more consistent with theoretical data on inhibitor mechanism, and thus recommends this docking approach over rigid use of one-metal ion models derived from current crystal structures of integrase.
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Affiliation(s)
- Arthur G Cox
- The Center for Drug Discovery and Department of Pharmaceutical and Biomedical Sciences, The University of Georgia, Athens, GA, USA
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23
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Savarino A. In-Silico docking of HIV-1 integrase inhibitors reveals a novel drug type acting on an enzyme/DNA reaction intermediate. Retrovirology 2007; 4:21. [PMID: 17374162 PMCID: PMC1847836 DOI: 10.1186/1742-4690-4-21] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 03/20/2007] [Indexed: 02/06/2023] Open
Abstract
Background HIV-1 integrase (IN) is an emerging drug target, as IN strand transfer inhibitors (INSTIs) are proving potent antiretroviral agents in clinical trials. One credible theory sees INSTIs as docking at the cellular (acceptor) DNA-binding site after IN forms a transitional complex with viral (donor) DNA. However, mapping of the DNA and INSTI binding sites within the IN catalytic core domain (CCD) has been uncertain. Methods Structural superimpositions were conducted using the SWISS PDB and Cn3D free software. Docking simulations of INSTIs were run by a widely validated genetic algorithm (GOLD). Results Structural superimpositions suggested that a two-metal model for HIV-1 IN CCD in complex with small molecule, 1-(5-chloroindol-3-yl)-3-(tetrazoyl)-1,3-propandione-ene (5CITEP) could be used as a surrogate for an IN/viral DNA complex, because it allowed replication of contacts documented biochemically in viral DNA/IN complexes or displayed by a crystal structure of the IN-related enzyme Tn5 transposase in complex with transposable DNA. Docking simulations showed that the fitness of different compounds for the catalytic cavity of the IN/5CITEP complex significantly (P < 0.01) correlated with their 50% inhibitory concentrations (IC50s) in strand transfer assays in vitro. The amino acids involved in inhibitor binding matched those involved in drug resistance. Both metal binding and occupation of the putative viral DNA binding site by 5CITEP appeared to be important for optimal drug/ligand interactions. The docking site of INSTIs appeared to overlap with a putative acceptor DNA binding region adjacent to but distinct from the putative donor DNA binding site, and homologous to the nucleic acid binding site of RNAse H. Of note, some INSTIs such as 4,5-dihydroxypyrimidine carboxamides/N-Alkyl-5-hydroxypyrimidinone carboxamides, a highly promising drug class including raltegravir/MK-0518 (now in clinical trials), displayed interactions with IN reminiscent of those displayed by fungal molecules from Fusarium sp., shown in the 1990s to inhibit HIV-1 integration. Conclusion The 3D model presented here supports the idea that INSTIs dock at the putative acceptor DNA-binding site in a IN/viral DNA complex. This mechanism of enzyme inhibition, likely to be exploited by some natural products, might disclose future strategies for inhibition of nucleic acid-manipulating enzymes.
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Affiliation(s)
- Andrea Savarino
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
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Savarino A. A historical sketch of the discovery and development of HIV-1 integrase inhibitors. Expert Opin Investig Drugs 2006; 15:1507-22. [PMID: 17107277 DOI: 10.1517/13543784.15.12.1507] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The long process of HIV-1 integrase inhibitor discovery and development can be attributed to both the complexity of HIV-1 integration and poor 'integration' of these researches into mainstream investigations on antiretroviral therapy in the mid-1990s. Of note, some fungal extracts investigated during this period contain the beta-hydroxyketo group, later recognised to be a key structural requirement for keto-enol acids (also referred to as diketo acids) and other integrase inhibitors. This review reconstructs (in the general context of the history of AIDS research) the principal steps that led to the integrase inhibitors currently in clinical trials, and discusses possible future directions.
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Affiliation(s)
- Andrea Savarino
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità Viale Regina Elena, 299. 00161- Rome, Italy.
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25
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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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