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Gersch M, Kolb R, Alte F, Groll M, Sieber SA. Disruption of oligomerization and dehydroalanine formation as mechanisms for ClpP protease inhibition. J Am Chem Soc 2013; 136:1360-6. [PMID: 24106749 DOI: 10.1021/ja4082793] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over 100 protease inhibitors are currently used in the clinics, and most of them use blockage of the active site for their mode of inhibition. Among the protease drug targets are several enzymes for which the correct multimeric assembly is crucial to their activity, such as the proteasome and the HIV protease. Here, we present a novel mechanism of protease inhibition that relies on active-site-directed small molecules that disassemble the protease complex. We show the applicability of this mechanism within the ClpP protease family, whose members are tetradecameric serine proteases and serve as regulators of several cellular processes, including homeostasis and virulence. Compound binding to ClpP in a substoichiometric fashion triggers the formation of completely inactive heptamers. Moreover, we report the selective β-sultam-induced dehydroalanine formation of the active site serine. This reaction proceeds through sulfonylation and subsequent elimination, thereby obliterating the catalytic charge relay system. The identity of the dehydroalanine was confirmed by mass spectrometry and crystallography. Activity-based protein profiling experiments suggest the formation of a dehydroalanine moiety in living S. aureus cells upon β-sultam treatment. Collectively, these findings extend our view on multicomponent protease inhibition that until now has mainly relied on blockage of the active site or occupation of a regulatory allosteric site.
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Affiliation(s)
- Malte Gersch
- Center for Integrated Protein Science at the Department of Chemistry, Institute of Advanced Studies IAS and ‡Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München , Lichtenbergstrasse 4, Garching D-85747, Germany
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52
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Jaffe EK. Impact of quaternary structure dynamics on allosteric drug discovery. Curr Top Med Chem 2013; 13:55-63. [PMID: 23409765 DOI: 10.2174/1568026611313010006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 11/22/2022]
Abstract
The morpheein model of allosteric regulation draws attention to proteins that can exist as an equilibrium of functionally distinct assemblies where: one subunit conformation assembles into one multimer; a different subunit conformation assembles into a different multimer; and the various multimers are in a dynamic equilibrium whose position can be modulated by ligands that bind to a multimer-specific ligand binding site. The case study of porphobilinogen synthase (PBGS) illustrates how such an equilibrium holds lessons for disease mechanisms, drug discovery, understanding drug side effects, and identifying proteins wherein drug discovery efforts might focus on quaternary structure dynamics. The morpheein model of allostery has been proposed as applicable for a wide assortment of disease-associated proteins (Selwood, T., Jaffe, E., (2012) Arch. Bioch. Biophys, 519:131-143). Herein we discuss quaternary structure dynamics aspects to drug discovery for the disease-associated putative morpheeins phenylalanine hydroxylase, HIV integrase, pyruvate kinase, and tumor necrosis factor α. Also highlighted is the quaternary structure equilibrium of transthyretin and successful drug discovery efforts focused on controlling its quaternary structure dynamics.
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Affiliation(s)
- Eileen K Jaffe
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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53
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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.
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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
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54
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Mahalka AK, Kinnunen PKJ. Class specific peptide inhibitors for secretory phospholipases A2. Biochem Biophys Res Commun 2013; 436:349-53. [PMID: 23747420 DOI: 10.1016/j.bbrc.2013.05.110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 05/26/2013] [Indexed: 01/03/2023]
Abstract
Phospholipases A2 (PLA2) catalyze the hydrolytic cleavage of free fatty acids from the sn-2 OH-moiety of glycerophospholipids. These enzymes have a number of functions, from digestion to signaling and toxicity of several venoms. They have also been implicated in inflammation and are connected to diverse diseases, such as cancer, ischemia, atherosclerosis, and schizophrenia. Accordingly, there is a keen interest to develop selective inhibitors for therapeutic use. We recently proposed a novel mechanism for the control of PLA2 activity with highly active protofibrils of PLA2 existing transiently before conversion to inactive amyloid fibrils [19]. In keeping with the above mechanism several algorithms identified (85)KMYFNLI(91) and (17)AALSYGFYG(25) in bee venom (bv) and human lacrimal fluid (Lf) PLA2, respectively, as a regions potentially forming amyloid type aggregates. Interestingly, in keeping with the proposed role of these sequences in the control of the activity of these enzymes, preincubation of 2nM bvPLA2 with (85)KMYFNLI(91) caused complete inhibition of PLA2 activity while the scrambled control peptide YNFLIMK had no effect. Approximately 36% attenuation of the hydrolytic activity of LfPLA2 present in human lacrimal fluid was observed in the presence of 80nM (17)AALSYGFYG(25).
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Affiliation(s)
- Ajay K Mahalka
- Helsinki Biophysics and Biomembrane Group, Department of Biomedical Engineering and Computational Science, Aalto University, Espoo, Finland
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55
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Desimmie BA, Schrijvers R, Demeulemeester J, Borrenberghs D, Weydert C, Thys W, Vets S, Van Remoortel B, Hofkens J, De Rijck J, Hendrix J, Bannert N, Gijsbers R, Christ F, Debyser Z. LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions. Retrovirology 2013; 10:57. [PMID: 23721378 PMCID: PMC3671127 DOI: 10.1186/1742-4690-10-57] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/07/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND LEDGINs are novel allosteric HIV integrase (IN) inhibitors that target the lens epithelium-derived growth factor (LEDGF)/p75 binding pocket of IN. They block HIV-1 integration by abrogating the interaction between LEDGF/p75 and IN as well as by allosterically inhibiting the catalytic activity of IN. RESULTS Here we demonstrate that LEDGINs reduce the replication capacity of HIV particles produced in their presence. We systematically studied the molecular basis of this late effect of LEDGINs and demonstrate that HIV virions produced in their presence display a severe replication defect. Both the late effect and the previously described, early effect on integration contribute to LEDGIN antiviral activity as shown by time-of-addition, qPCR and infectivity assays. The late effect phenotype requires binding of LEDGINs to integrase without influencing proteolytic cleavage or production of viral particles. LEDGINs augment IN multimerization during virion assembly or in the released viral particles and severely hamper the infectivity of progeny virions. About 70% of the particles produced in LEDGIN-treated cells do not form a core or display aberrant empty cores with a mislocalized electron-dense ribonucleoprotein. The LEDGIN-treated virus displays defective reverse transcription and nuclear import steps in the target cells. The LEDGIN effect is possibly exerted at the level of the Pol precursor polyprotein. CONCLUSION Our results suggest that LEDGINs modulate IN multimerization in progeny virions and impair the formation of regular cores during the maturation step, resulting in a decreased infectivity of the viral particles in the target cells. LEDGINs thus profile as unique antivirals with combined early (integration) and late (IN assembly) effects on the HIV replication cycle.
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Affiliation(s)
- Belete Ayele Desimmie
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Rik Schrijvers
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Jonas Demeulemeester
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, KU Leuven, Celestijnenlaan 200F, Heverlee, Flanders, 3001, Belgium
| | - Caroline Weydert
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Wannes Thys
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Sofie Vets
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Barbara Van Remoortel
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, KU Leuven, Celestijnenlaan 200F, Heverlee, Flanders, 3001, Belgium
| | - Jan De Rijck
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, KU Leuven, Celestijnenlaan 200F, Heverlee, Flanders, 3001, Belgium
| | - Norbert Bannert
- Robert Koch Institute, Centre for HIV and Retrovirology, Nordufer 20, Berlin, 13353, Germany
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Frauke Christ
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
| | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, KU Leuven, Kapucijnenvoer 33, Leuven, Flanders, 3000, Belgium
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56
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Zych C, Domling A, Ayyavoo V. Development of a robust cell-based high-throughput screening assay to identify targets of HIV-1 viral protein R dimerization. Drug Des Devel Ther 2013; 7:403-12. [PMID: 23737660 PMCID: PMC3668091 DOI: 10.2147/dddt.s44139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Targeting protein-protein interactions (PPI) is an emerging field in drug discovery. Dimerization and PPI are essential properties of human immunodeficiency virus (HIV)-1 proteins, their mediated functions, and virus biology. Additionally, dimerization is required for the functional interaction of HIV-1 proteins with many host cellular components. In this study, a bimolecular fluorescence complementation (BiFC)-based screening assay was developed that can quantify changes in dimerization, using HIV-1 viral protein R (Vpr) dimerization as a "proof of concept." Results demonstrated that Venus Vpr (generated by BiFC Vpr constructs) could be competed off in a dose-dependent manner using untagged, full-length Vpr as a competitor molecule. The change in signal intensity was measured quantitatively through flow cytometry and fluorescence microscopy in a high content screening assay. High content imaging was used to screen a library of small molecules for an effect on Vpr dimerization. Among the tested molecules, a few of the small molecules demonstrate an effect on Vpr dimerization in a dose-dependent manner.
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Affiliation(s)
- Courtney Zych
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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57
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Engelman A, Kessl JJ, Kvaratskhelia M. Allosteric inhibition of HIV-1 integrase activity. Curr Opin Chem Biol 2013; 17:339-45. [PMID: 23647983 DOI: 10.1016/j.cbpa.2013.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/03/2013] [Accepted: 04/09/2013] [Indexed: 01/28/2023]
Abstract
HIV-1 integrase is an important therapeutic target in the fight against HIV/AIDS. Integrase strand transfer inhibitors (INSTIs), which target the enzyme active site, have witnessed clinical success over the past 5 years, but the generation of drug resistance poses challenges to INSTI-based therapies moving forward. Integrase is a dynamic protein, and its ordered multimerization is critical to enzyme activity. The integrase tetramer, bound to viral DNA, interacts with host LEDGF/p75 protein to tether integration to active genes. Allosteric integrase inhibitors (ALLINIs) that compete with LEDGF/p75 for binding to integrase disrupt integrase assembly with viral DNA and allosterically inhibit enzyme function. ALLINIs display steep dose response curves and synergize with INSTIs ex vivo, highlighting this novel inhibitor class for clinical development.
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Affiliation(s)
- Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA 02215, USA.
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58
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Reddy KK, Singh SK, Tripathi SK, Selvaraj C. Identification of potential HIV-1 integrase strand transfer inhibitors: in silico virtual screening and QM/MM docking studies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:581-595. [PMID: 23521430 DOI: 10.1080/1062936x.2013.772919] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
HIV-1 integrase (IN) is a retroviral enzyme that catalyses integration of the reverse-transcribed viral DNA into the host genome, which is necessary for efficient viral replication. In this study, we have performed an in silico virtual screening for the identification of potential HIV-1 IN strand transfer (ST) inhibitors. Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to 3-Hydroxypyrimidine-2,4-diones. Based on the ligand-based pharmacophore model, we obtained a five-point pharmacophore with two hydrogen bond acceptors (A), one hydrogen bond donor (D), one hydrophobic group (H) and one aromatic ring (R) as pharmacophoric features. The pharmacophore hypothesis AADHR was used as a 3D query in a sequential virtual screening study to filter small molecule databases Maybridge, ChemBridge and Asinex. Hits matching with pharmacophore hypothesis AADHR were retrieved and passed progressively through Lipinski's rule of five filtering, molecular docking and hierarchical clustering. The five compounds with best hits with novel and diverse chemotypes were subjected to QM/MM docking, which showed improved docking accuracy. We further performed molecular dynamics simulation and found three compounds that form stable interactions with key residues. These compounds could be used as a leads for further drug development and rational design of HIV-1 IN inhibitors.
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Affiliation(s)
- K K Reddy
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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59
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Guy S, Rotem D, Hayouka Z, Gabizon R, Levin A, Zemel L, Loyter A, Porath D, Friedler A. Monitoring the HIV-1 integrase enzymatic activity using atomic force microscopy in a 2LTR system. Chem Commun (Camb) 2013; 49:3113-5. [PMID: 23463374 DOI: 10.1039/c3cc40748a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Integration of the HIV cDNA into the host chromosome is a key event in the viral replication cycle. It is mediated by the viral integrase (IN) enzyme, which is an attractive anti-HIV drug target. Here we present the first AFM imaging of IN-mediated DNA integration products in a two-LTR system.
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Affiliation(s)
- Shlomit Guy
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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60
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Rotem-Bamberger S, Katz C, Friedler A. Regulation of ASPP2 interaction with p53 core domain by an intramolecular autoinhibitory mechanism. PLoS One 2013; 8:e58470. [PMID: 23472201 PMCID: PMC3589414 DOI: 10.1371/journal.pone.0058470] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022] Open
Abstract
ASPP2 is a key protein in regulating apoptosis both in p53-dependent and-independent pathways. The C-terminal part of ASPP2 contains four ankyrin repeats and an SH3 domain (Ank-SH3) that mediate the interactions of ASPP2 with apoptosis related proteins such as p53, Bcl-2 and the p65 subunit of NFκB. p53 core domain (p53CD) binds the n-src loop and the RT loop of ASPP2 SH3. ASPP2 contains a disordered proline rich domain (ASPP2 Pro) that forms an intramolecular autoinhibitory interaction with the Ank-SH3 domains. Here we show how this intramolecular interaction affects the intermolecular interactions of ASPP2 with p53, Bcl-2 and NFkB. We used biophysical methods to obtain better understanding of the relationship between ASPP2 and its partners for getting a comprehensive view on ASPP2 pathways. Fluorescence anisotropy competition experiments revealed that both ASPP2 Pro and p53CD competed for binding the n-src loop of the ASPP2 SH3, indicating regulation of p53CD binding to this loop by ASPP2 Pro. Peptides derived from the ASPP2-binding interface of Bcl-2 did not compete with p53CD or NFkB peptides for binding the ASPP2 n-src loop. However, p53CD displaced the NFκB peptide (residues 303–332) from its complex with ASPP2 Ank-SH3, indicating that NFκB 303–332 and p53CD bind a partly overlapping site in ASPP2 SH3, mostly in the RT loop. These results are in agreement with previous docking studies, which showed that ASPP2 Ank-SH3 binds Bcl-2 and NFκB mostly via distinct sites from p53. However they show some overlap between the binding sites of p53CD and NFkB in ASPP2 Ank-SH3. Our results provide experimental evidence that the intramolecular interaction in ASPP2 regulates its binding to p53CD and that ASPP2 Ank-SH3 binds Bcl-2 and NFκB via distinct sites.
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Affiliation(s)
- Shahar Rotem-Bamberger
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Chen Katz
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
- * E-mail:
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61
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Rosenberg MM, Ronen D, Lahav N, Nazirov E, Ravid S, Friedler A. High resolution characterization of myosin IIC protein tailpiece and its effect on filament assembly. J Biol Chem 2013; 288:9779-9789. [PMID: 23426373 DOI: 10.1074/jbc.m112.430173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The motor protein nonmuscle myosin II (NMII) must undergo dynamic oligomerization into filaments to perform its cellular functions. A small nonhelical region at the tail of the long coiled-coil region (tailpiece) is a common feature of all dynamically assembling myosin II proteins. This tailpiece is a key regulatory domain affecting NMII filament assembly properties and is subject to phosphorylation in vivo. We previously demonstrated that the positively charged region of the tailpiece binds to assembly-incompetent NMII-C fragments, inducing filament assembly. In the current study, we investigated the molecular mechanisms by which the tailpiece regulates NMII-C self-assembly. Using alanine scan, we found that specific positive and aromatic residues within the positively charged region of the tailpiece are important for inducing NMII-C filament assembly and for filament elongation. Combining peptide arrays with deletion studies allowed us to identify the tailpiece binding sites in the coiled-coil rod. Elucidation of the mechanism by which the tailpiece induces filament assembly permitted us further investigation into the role of tailpiece phosphorylation. Sedimentation and CD spectroscopy identified that phosphorylation of Thr(1957) or Thr(1960) inhibited the ability of the tailpiece to bind the coiled-coil rod and to induce NMII-C filament formation. This study provides molecular insight into the role of specific residues within the NMII-C tailpiece that are responsible for shifting the oligomeric equilibrium of NMII-C toward filament assembly and determining its morphology.
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Affiliation(s)
- Masha M Rosenberg
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904
| | - Daniel Ronen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Noa Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904
| | - Elvira Nazirov
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shoshana Ravid
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904.
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62
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Christ F, Debyser Z. The LEDGF/p75 integrase interaction, a novel target for anti-HIV therapy. Virology 2013; 435:102-9. [PMID: 23217620 DOI: 10.1016/j.virol.2012.09.033] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 01/12/2023]
Abstract
To accomplish their viral life cycle, lentiviruses such as HIV highjack host proteins, the so-called cellular co-factors of replication. Lens Epithelium-derived Growth factor (LEDGF/p75), a transcriptional co-activator, is a co-factor of HIV-integrase (IN) and is required for the tethering and correct integration of the viral genome into the host chromatin. Due to its important role in HIV-replication the LEDGF/p75-IN interaction is an attractive antiviral novel target for the treatment of HIV/AIDS. Intensive drug discovery efforts over the past years have validated the LEDGF/p75-IN interaction as a drugable target for antiviral therapy and have resulted in the design and synthesis of LEDGINs, small molecule inhibitors binding to the dimer interface of HIV-integrase and inhibiting viral replication with a dual mechanism of action: potent inhibition of the LEDGF/p75-IN protein-protein interaction and allosteric inhibition of the catalytic function. Furthermore they inhibit both early and late steps of the replication cycle which increases their potential for further clinical development. In this review we will highlight the research validating the LEDGF/p75-IN interaction as a target for anti-HIV drug discovery and the recent advances in the design and development of LEDGINs.
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Affiliation(s)
- Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, KU Leuven, Kapucijnenvoer 33, 3000 Leuven, Belgium.
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63
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Bojja RS, Andrake MD, Merkel G, Weigand S, Dunbrack RL, Skalka AM. Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. J Biol Chem 2013; 288:7373-86. [PMID: 23322775 DOI: 10.1074/jbc.m112.434431] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have applied small angle x-ray scattering and protein cross-linking coupled with mass spectrometry to determine the architectures of full-length HIV integrase (IN) dimers in solution. By blocking interactions that stabilize either a core-core domain interface or N-terminal domain intermolecular contacts, we show that full-length HIV IN can form two dimer types. One is an expected dimer, characterized by interactions between two catalytic core domains. The other dimer is stabilized by interactions of the N-terminal domain of one monomer with the C-terminal domain and catalytic core domain of the second monomer as well as direct interactions between the two C-terminal domains. This organization is similar to the "reaching dimer" previously described for wild type ASV apoIN and resembles the inner, substrate binding dimer in the crystal structure of the PFV intasome. Results from our small angle x-ray scattering and modeling studies indicate that in the absence of its DNA substrate, the HIV IN tetramer assembles as two stacked reaching dimers that are stabilized by core-core interactions. These models of full-length HIV IN provide new insight into multimer assembly and suggest additional approaches for enzyme inhibition.
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Affiliation(s)
- Ravi Shankar Bojja
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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64
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Gabizon R, Faust O, Benyamini H, Nir S, Loyter A, Friedler A. Structure–activity relationship studies using peptide arrays: the example of HIV-1 Rev–integrase interaction. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20225e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used peptide arrays to perform structure–activity relationship studies on anti-HIV peptides derived from HIV-1 integrase.
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Affiliation(s)
- Ronen Gabizon
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Ofrah Faust
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Hadar Benyamini
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Sivan Nir
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
| | - Abraham Loyter
- Department of Biological Chemistry
- The Alexander Silberman Institute of Life Sciences
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
| | - Assaf Friedler
- Institute of Chemistry
- The Hebrew University of Jerusalem
- Safra Campus
- Jerusalem
- Israel
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65
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Métifiot M, Marchand C, Pommier Y. HIV integrase inhibitors: 20-year landmark and challenges. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 67:75-105. [PMID: 23885999 DOI: 10.1016/b978-0-12-405880-4.00003-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the discovery of HIV as the cause for AIDS 30 years ago, major progress has been made, including the discovery of drugs that now control the disease. Here, we review the integrase (IN) inhibitors from the discovery of the first compounds 20 years ago to the approval of two highly effective IN strand transfer inhibitors (INSTIs), raltegravir (Isentress) and elvitegravir (Stribild), and the promising clinical activity of dolutegravir. After summarizing the molecular mechanism of action of the INSTIs as interfacial inhibitors, we discuss the remaining challenges. Those include: overcoming resistance to clinical INSTIs, long-term safety of INSTIs, cost of therapy, place of the INSTIs in prophylactic treatments, and the development of new classes of inhibitors (the LEDGINs) targeting IN outside its catalytic site. We also discuss the role of chromatin and host DNA repair factor for the completion of integration.
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Affiliation(s)
- Mathieu Métifiot
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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66
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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67
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Ellis KE, Frato KE, Elliott SJ. Impact of quaternary structure upon bacterial cytochrome c peroxidases: does homodimerization matter? Biochemistry 2012. [PMID: 23189923 DOI: 10.1021/bi301150n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All known active forms of diheme bacterial cytochrome c peroxidase (bCcP) enzymes are described by a homodimeric state. Further, the majority of bCcPs reported display activity only when the high-potential electron transfer heme of the protein (Fe(H)) is reduced to the ferrous oxidation state. Reduction of Fe(H) results in a set of conformational changes allowing for the low-potential peroxidatic heme (Fe(L)) to adopt a high-spin, five-coordinate state that is capable of binding substrate. Here we examine the impact of dimerization upon the activity of the Shewanella oneidensis (So) bCcP by the preparation of single charge-reversal mutants at the dimer interface and use the resulting constructs to illustrate why dimerization is likely a requirement for activity in bCcPs. The E258K mutant is found to form a monomeric state in solution as characterized by size exclusion chromatography and analytical ultracentrifugation analyses. The resulting E258K monomer has an unfolding stability comparable to that of wild-type So bCcP and an activity that is only slightly diminished (k(cat)/K(m) = 23 × 10(6) M(-1) s(-1)). Spectroscopic and potentiometric analyses reveal that while the thermodynamic stability of the activated form of the enzyme is unchanged (characterized by the E(m) value of the Fe(H)(II)/Fe(H)(III) couple), the kinetic stability of the activated form of the enzyme has been greatly diminished upon generation of the monomer. Together, these data suggest a model in which dimerization of bCcP enzymes is required to stabilize the lifetime of the activated form of the enzyme against reoxidation of Fe(H) and deactivation of Fe(L).
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Affiliation(s)
- Katie E Ellis
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
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68
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Lo YS, Lin SY, Wang SM, Wang CT, Chiu YL, Huang TH, Hou MH. Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein. FEBS Lett 2012. [PMID: 23178926 PMCID: PMC7089611 DOI: 10.1016/j.febslet.2012.11.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
N and N bind by cross‐linking study (View Interaction: 1, 2, 3, 4) ► The role of the C‐terminal tail of the HCoV‐229E N protein in oligomerization. ► A correlation between oligomerization and thermostability. ► The C‐terminal tail peptide interferes with the oligomerization. ► The development of drugs to disrupt the oligomerization of the viral N protein.
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Affiliation(s)
- Yu-Sheng Lo
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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69
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Gupta K, Curtis JE, Krueger S, Hwang Y, Cherepanov P, Bushman FD, Van Duyne GD. Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA. Structure 2012; 20:1918-28. [PMID: 23000384 DOI: 10.1016/j.str.2012.08.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/20/2012] [Accepted: 08/20/2012] [Indexed: 12/30/2022]
Abstract
Using small-angle X-ray and neutron scattering (SAXS/SANS), in combination with analytical centrifugation and light scattering, we have determined the solution properties of PFV IN alone and its synaptic complex with processed U5 viral DNA and related these properties to models derived from available crystal structures. PFV IN is a monomer in solution, and SAXS analysis indicates an ensemble of conformations that differ from that observed in the crystallographic DNA-bound state. Scattering data indicate that the PFV intasome adopts a shape in solution that is consistent with the tetrameric assembly inferred from crystallographic symmetry, and these properties are largely preserved in the presence of divalent ions and clinical strand transfer inhibitors. Using contrast variation methods, we have reconstructed the solution structure of the PFV intasome complex and have located the distal domains of IN that were unresolved by crystallography. These results provide important insights into the architecture of the retroviral intasome.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine and Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
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70
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Serrao E, Thys W, Demeulemeester J, Al-Mawsawi LQ, Christ F, Debyser Z, Neamati N. A symmetric region of the HIV-1 integrase dimerization interface is essential for viral replication. PLoS One 2012; 7:e45177. [PMID: 23028829 PMCID: PMC3445459 DOI: 10.1371/journal.pone.0045177] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/17/2012] [Indexed: 01/06/2023] Open
Abstract
HIV-1 integrase (IN) is an important target for contemporary antiretroviral drug design research. Historically, efforts at inactivating the enzyme have focused upon blocking its active site. However, it has become apparent that new classes of allosteric inhibitors will be necessary to advance the antiretroviral field in light of the emergence of viral strains resistant to contemporary clinically used IN drugs. In this study we have characterized the importance of a close network of IN residues, distant from the active site, as important for the obligatory multimerization of the enzyme and viral replication as a whole. Specifically, we have determined that the configuration of six residues within a highly symmetrical region at the IN dimerization interface, composed of a four-tiered aromatic interaction flanked by two salt bridges, significantly contributes to proper HIV-1 replication. Additionally, we have utilized a quantitative luminescence assay to examine IN oligomerization and have determined that there is a very low tolerance for amino acid substitutions along this region. Even conservative residue substitutions negatively impacted IN multimerization, resulting in an inactive viral enzyme and a non-replicative virus. We have shown that there is a very low tolerance for amino acid variation at the symmetrical dimeric interface region characterized in this study, and therefore drugs designed to target the amino acid network detailed here could be expected to yield a significantly reduced number of drug-resistant escape mutations compared to contemporary clinically-evaluated antiretrovirals.
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Affiliation(s)
- Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Wannes Thys
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Jonas Demeulemeester
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Laith Q. Al-Mawsawi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Division of Molecular Medicine, Katholieke Universiteit Leuven, Flanders, Belgium
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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Christ F, Shaw S, Demeulemeester J, Desimmie BA, Marchand A, Butler S, Smets W, Chaltin P, Westby M, Debyser Z, Pickford C. Small-molecule inhibitors of the LEDGF/p75 binding site of integrase block HIV replication and modulate integrase multimerization. Antimicrob Agents Chemother 2012; 56:4365-74. [PMID: 22664975 PMCID: PMC3421592 DOI: 10.1128/aac.00717-12] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/30/2012] [Indexed: 02/02/2023] Open
Abstract
Targeting the HIV integrase (HIV IN) is a clinically validated approach for designing novel anti-HIV therapies. We have previously described the discovery of a novel class of integration inhibitors, 2-(quinolin-3-yl)acetic acid derivatives, blocking HIV replication at a low micromolar concentration through binding in the LEDGF/p75 binding pocket of HIV integrase, hence referred to as LEDGINs. Here we report the detailed characterization of their mode of action. The design of novel and more potent analogues with nanomolar activity enabled full virological evaluation and a profound mechanistic study. As allosteric inhibitors, LEDGINs bind to the LEDGF/p75 binding pocket in integrase, thereby blocking the interaction with LEDGF/p75 and interfering indirectly with the catalytic activity of integrase. Detailed mechanism-of-action studies reveal that the allosteric mode of inhibition is likely caused by an effect on HIV-1 integrase oligomerization. The multimodal inhibition by LEDGINs results in a block in HIV integration and in a replication deficiency of progeny virus. The allosteric nature of LEDGINs leads to synergy in combination with the clinically approved active site HIV IN strand transfer inhibitor (INSTI) raltegravir, and cross-resistance profiling proves the distinct mode of action of LEDGINs and INSTIs. The allosteric nature of inhibition and compatibility with INSTIs underline an interest in further (clinical) development of LEDGINs.
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Affiliation(s)
- Frauke Christ
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | | | - Jonas Demeulemeester
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | - Belete A. Desimmie
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
| | | | | | - Wim Smets
- CISTIM, CISTIM Leuven Vzw, Leuven, Belgium
| | - Patrick Chaltin
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
- CISTIM, CISTIM Leuven Vzw, Leuven, Belgium
| | | | - Zeger Debyser
- Katholieke Universiteit Leuven, Molecular Virology and Gene Therapy (VCTB+5), Leuven, Belgium
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72
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Maes M, Loyter A, Friedler A. Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions. FEBS J 2012; 279:2795-809. [PMID: 22742518 DOI: 10.1111/j.1742-4658.2012.08680.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 integrase (IN) is one of the key enzymes in the viral replication cycle. It mediates the integration of viral cDNA into the host cell genome. IN activity requires interactions with several viral and cellular proteins, as well as IN oligomerization. Inhibition of IN is an important target for the development of anti-HIV therapies, but there is currently only one anti-HIV drug used in the clinic that targets IN. Several other small-molecule anti-IN drug leads are either undergoing clinical trials or in earlier stages of development. These molecules specifically inhibit one of the IN-mediated reactions necessary for successful integration. However, small-molecule inhibitors of protein-protein interactions are difficult to develop. In this review, we focus on peptides that inhibit IN. Peptides have advantages over small-molecule inhibitors of protein-protein interactions: they can mimic the structures of the binding domains within proteins, and are large enough to competitively inhibit protein-protein interactions. The development of peptides that bind IN and inhibit its protein-protein interactions will increase our understanding of the IN mode of action, and lead to the development of new drug leads, such as small molecules derived from these peptides, for better anti-HIV therapy.
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Affiliation(s)
- Michal Maes
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
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73
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Levin A, Hayouka Z, Friedler A, Loyter A. Transportin 3 and importin α are required for effective nuclear import of HIV-1 integrase in virus-infected cells. Nucleus 2012; 1:422-31. [PMID: 21326825 DOI: 10.4161/nucl.1.5.12903] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 07/02/2010] [Accepted: 07/07/2010] [Indexed: 01/25/2023] Open
Abstract
Unlike other retroviruses, human immunodeficiency virus type-1 (HIV-1) can infect terminally differentiated cells, due to the ability of its pre-integration complex (PIC) to translocate via the host nuclear pore complex (NPC). The PIC Nuclear import has been suggested to be mediated by the viral integrase protein (IN), via either the importin α or transportin 3 (TNPO3/transportin-SR2) pathways.We show that in virus-infected cells, IN interacts with both importin α and TNPO3, simultaneously or separately, suggesting a multiple use of nuclear import pathways. Disruption of either the IN-importin α or IN-TNPO3 complexes in virus-infected cells by specific cell-permeable-peptides resulted in inhibition of IN and viral cDNA nuclear import. Here we show that peptides which disrupt either one of these complexes block virus infection, indicating involvement of both pathways in efficient viral replication. Formation of IN-importin α and IN-TNPO3 complexes has also been observed in IN-transfected cultured cells. Using specific peptides, we demonstrate that in transfected cells but not in virus infected cells the importin α pathway overrides that of TNPO3. The IN-importin α and IN-TNPO3 complexes were not observed in virus-infected Rev-expressing cells, indicating the Rev protein's ability to disrupt both complexes.Our work suggests that IN nuclear import requires the involvement of both importin α and TNPO3. The ability to inhibit nuclear import of the IN-DNA complex and consequently, virus infection by peptides that interrupt IN's interaction with either importin α or TNPO3 indicates that for efficient infection, nuclear import of IN should be mediated by both nuclear-import receptors.
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Affiliation(s)
- Aviad Levin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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74
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Gabizon R, Brandt T, Sukenik S, Lahav N, Lebendiker M, Shalev DE, Veprintsev D, Friedler A. Specific recognition of p53 tetramers by peptides derived from p53 interacting proteins. PLoS One 2012; 7:e38060. [PMID: 22693587 PMCID: PMC3365014 DOI: 10.1371/journal.pone.0038060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 05/02/2012] [Indexed: 11/25/2022] Open
Abstract
Oligomerization plays a major role in regulating the activity of many proteins, and in modulating their interactions. p53 is a homotetrameric transcription factor that has a pivotal role in tumor suppression. Its tetramerization domain is contained within its C-terminal domain, which is a site for numerous protein-protein interactions. Those can either depend on or regulate p53 oligomerization. Here we screened an array of peptides derived from proteins known to bind the tetrameric p53 C-terminal domain (p53CTD) and identified ten binding peptides. We quantitatively characterized their binding to p53CTD using fluorescence anisotropy. The peptides bound tetrameric p53CTD with micromolar affinities. Despite the high charge of the binding peptides, electrostatics contributed only mildly to the interactions. NMR studies indicated that the peptides bound p53CTD at defined sites. The most significant chemical shift deviations were observed for the peptides WS100B(81-92), which bound directly to the p53 tetramerization domain, and PKCα(281-295), which stabilized p53CTD in circular dichroism thermal denaturation studies. Using analytical ultracentrifugation, we found that several of the peptides bound preferentially to p53 tetramers. Our results indicate that the protein-protein interactions of p53 are dependent on the oligomerization state of p53. We conclude that peptides may be used to regulate the oligomerization of p53.
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Affiliation(s)
- Ronen Gabizon
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tobias Brandt
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Shahar Sukenik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noa Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E. Shalev
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dmitry Veprintsev
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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75
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Kiburu IN, LaRonde-LeBlanc N. Interaction of Rio1 kinase with toyocamycin reveals a conformational switch that controls oligomeric state and catalytic activity. PLoS One 2012; 7:e37371. [PMID: 22629386 PMCID: PMC3358306 DOI: 10.1371/journal.pone.0037371] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/19/2012] [Indexed: 01/07/2023] Open
Abstract
Rio1 kinase is an essential ribosome-processing factor required for proper maturation of 40 S ribosomal subunit. Although its structure is known, several questions regarding its functional remain to be addressed. We report that both Archaeoglobus fulgidus and human Rio1 bind more tightly to an adenosine analog, toyocamycin, than to ATP. Toyocamycin has antibiotic, antiviral and cytotoxic properties, and is known to inhibit ribosome biogenesis, specifically the maturation of 40 S. We determined the X-ray crystal structure of toyocamycin bound to Rio1 at 2.0 Å and demonstrated that toyocamycin binds in the ATP binding pocket of the protein. Despite this, measured steady state kinetics were inconsistent with strict competitive inhibition by toyocamycin. In analyzing this interaction, we discovered that Rio1 is capable of accessing multiple distinct oligomeric states and that toyocamycin may inhibit Rio1 by stabilizing a less catalytically active oligomer. We also present evidence of substrate inhibition by high concentrations of ATP for both archaeal and human Rio1. Oligomeric state studies show both proteins access a higher order oligomeric state in the presence of ATP. The study revealed that autophosphorylation by Rio1 reduces oligomer formation and promotes monomerization, resulting in the most active species. Taken together, these results suggest the activity of Rio1 may be modulated by regulating its oligomerization properties in a conserved mechanism, identifies the first ribosome processing target of toyocamycin and presents the first small molecule inhibitor of Rio1 kinase activity.
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Affiliation(s)
- Irene N. Kiburu
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, and the University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland, College Park, Maryland, United States of America
| | - Nicole LaRonde-LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, and the University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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76
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Swapna LS, Srikeerthana K, Srinivasan N. Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PLoS One 2012; 7:e36688. [PMID: 22629324 PMCID: PMC3358323 DOI: 10.1371/journal.pone.0036688] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 04/11/2012] [Indexed: 11/21/2022] Open
Abstract
Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2∶1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.
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77
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Hayouka Z, Levin A, Hurevich M, Shalev DE, Loyter A, Gilon C, Friedler A. A comparative study of backbone versus side chain peptide cyclization: application for HIV-1 integrase inhibitors. Bioorg Med Chem 2012; 20:3317-22. [PMID: 22507205 DOI: 10.1016/j.bmc.2012.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 03/18/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
Abstract
Peptide cyclization is an important tool for overcoming the limitations of linear peptides as drugs. Backbone cyclization (BC) has advantages over side chain (SC) cyclization because it combines N-alkylation for extra peptide stability. However, the appropriate building blocks for BC are not yet commercially available. This problem can be overcome by preparing SC cyclic peptide analogs of the most active BC peptide using commercially available building blocks. We have recently developed BC peptides that inhibit the HIV-1 integrase enzyme (IN) activity and HIV-1 replication in infected cells. Here we used this system as a model for systematically comparing the BC and SC cyclization modes using biophysical, biochemical and structural methods. The most potent SC cyclic peptide was active almost as the BC peptide and inhibited IN activity in vitro and blocked IN activity in cells even after 6 days. We conclude that both cyclization types have their respective advantages: The BC peptide is more active and stable, probably due to the N-alkylation, while SC cyclic peptides are easier to synthesize. Due to the high costs and efforts involved in preparing BC peptides, SC may be a more approachable method in many cases. We suggest that both methods are interchangeable.
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Affiliation(s)
- Zvi Hayouka
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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78
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Kessl JJ, Jena N, Koh Y, Taskent-Sezgin H, Slaughter A, Feng L, de Silva S, Wu L, Le Grice SFJ, Engelman A, Fuchs JR, Kvaratskhelia M. Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors. J Biol Chem 2012; 287:16801-11. [PMID: 22437836 DOI: 10.1074/jbc.m112.354373] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The multifunctional HIV-1 enzyme integrase interacts with viral DNA and its key cellular cofactor LEDGF to effectively integrate the reverse transcript into a host cell chromosome. These interactions are crucial for HIV-1 replication and present attractive targets for antiviral therapy. Recently, 2-(quinolin-3-yl) acetic acid derivatives were reported to selectively inhibit the integrase-LEDGF interaction in vitro and impair HIV-1 replication in infected cells. Here, we show that this class of compounds impairs both integrase-LEDGF binding and LEDGF-independent integrase catalytic activities with similar IC(50) values, defining them as bona fide allosteric inhibitors of integrase function. Furthermore, we show that 2-(quinolin-3-yl) acetic acid derivatives block the formation of the stable synaptic complex between integrase and viral DNA by allosterically stabilizing an inactive multimeric form of integrase. In addition, these compounds inhibit LEDGF binding to the stable synaptic complex. This multimode mechanism of action concordantly results in cooperative inhibition of the concerted integration of viral DNA ends in vitro and HIV-1 replication in cell culture. Our findings, coupled with the fact that high cooperativity of antiviral inhibitors correlates with their increased instantaneous inhibitory potential, an important clinical parameter, argue strongly that improved 2-(quinolin-3-yl) acetic acid derivatives could exhibit desirable clinical properties.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
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79
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Selwood T, Jaffe EK. Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 2012; 519:131-43. [PMID: 22182754 PMCID: PMC3298769 DOI: 10.1016/j.abb.2011.11.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 11/20/2022]
Abstract
Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.
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Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
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80
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Katz C, Zaltsman-Amir Y, Mostizky Y, Kollet N, Gross A, Friedler A. Molecular basis of the interaction between proapoptotic truncated BID (tBID) protein and mitochondrial carrier homologue 2 (MTCH2) protein: key players in mitochondrial death pathway. J Biol Chem 2012; 287:15016-23. [PMID: 22416135 DOI: 10.1074/jbc.m111.328377] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The molecular basis of the interaction between mitochondrial carrier homologue 2 (MTCH2) and truncated BID (tBID) was characterized. These proteins participate in the apoptotic pathway, and the interaction between them may serve as a target for anticancer lead compounds. In response to apoptotic signals, MTCH2 recruits tBID to the mitochondria, where it activates apoptosis. A combination of peptide arrays screening with biochemical and biophysical techniques was used to characterize the mechanism of the interaction between tBID and MTCH2 at the structural and molecular levels. The regions that mediate the interaction between the proteins were identified. The two specific binding sites between the proteins were determined to be tBID residues 59-73 that bind MTCH2 residues 140-161, and tBID residues 111-125 that bind MTCH2 residues 240-290. Peptides derived from tBID residues 111-125 and 59-73 induced cell death in osteosarcoma cells. These peptides may serve as lead compounds for anticancer drugs that act by targeting the tBID-MTCH2 interaction.
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Affiliation(s)
- Chen Katz
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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81
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Demeulemeester J, Tintori C, Botta M, Debyser Z, Christ F. Development of an AlphaScreen-based HIV-1 integrase dimerization assay for discovery of novel allosteric inhibitors. ACTA ACUST UNITED AC 2012; 17:618-28. [PMID: 22337657 DOI: 10.1177/1087057111436343] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, HIV-1 integrase (IN) has become an established target in the field of antiretroviral drug discovery. However, its sole clinically approved inhibitor, the integrase strand transfer inhibitor (INSTI) raltegravir, has a surprisingly low genetic barrier for resistance. Furthermore, the only two other integrase inhibitors currently in advanced clinical trials, elvitegravir and dolutegravir, share its mechanism of action and certain resistance pathways. To maintain a range of treatment options, drug discovery efforts are now turning toward allosteric IN inhibitors, which should be devoid of cross-resistance with INSTIs. As IN requires a precise and dynamic equilibrium between several oligomeric species for its activities, the modulation of this equilibrium presents an interesting allosteric target. We report on the development, characterization, and validation of an AlphaScreen-based assay for high-throughput screening for modulators of HIV-1 IN dimerization. Compounds identified as hits in this assay proved to act as allosteric IN inhibitors. Additionally, the assay offers a flexible platform to study IN dimerization.
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82
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Demeulemeester J, Christ F, De Maeyer M, Debyser Z. Fueling HIV-1 integrase drug design with structural insights. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e175-e226. [PMID: 24064310 DOI: 10.1016/j.ddtec.2012.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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83
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Reingewertz TH, Shalev DE, Sukenik S, Blatt O, Rotem-Bamberger S, Lebendiker M, Larisch S, Friedler A. Mechanism of the interaction between the intrinsically disordered C-terminus of the pro-apoptotic ARTS protein and the Bir3 domain of XIAP. PLoS One 2011; 6:e24655. [PMID: 21949740 PMCID: PMC3176765 DOI: 10.1371/journal.pone.0024655] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 08/15/2011] [Indexed: 11/18/2022] Open
Abstract
ARTS (Sept4_i2) is a mitochondrial pro-apoptotic protein that functions as a tumor suppressor. Its expression is significantly reduced in leukemia and lymphoma patients. ARTS binds and inhibits XIAP (X-linked Inhibitor of Apoptosis protein) by interacting with its Bir3 domain. ARTS promotes degradation of XIAP through the proteasome pathway. By doing so, ARTS removes XIAP inhibition of caspases and enables apoptosis to proceed. ARTS contains 27 unique residues in its C-terminal domain (CTD, residues 248–274) which are important for XIAP binding. Here we characterized the molecular details of this interaction. Biophysical and computational methods were used to show that the ARTS CTD is intrinsically disordered under physiological conditions. Direct binding of ARTS CTD to Bir3 was demonstrated using NMR and fluorescence spectroscopy. The Bir3 interacting region in ARTS CTD was mapped to ARTS residues 266–274, which are the nine C-terminal residues in the protein. Alanine scan of ARTS 266–274 showed the importance of several residues for Bir3 binding, with His268 and Cys273 contributing the most. Adding a reducing agent prevented binding to Bir3. A dimer of ARTS 266–274 formed by oxidation of the Cys residues into a disulfide bond bound with similar affinity and was probably required for the interaction with Bir3. The detailed analysis of the ARTS – Bir3 interaction provides the basis for setting it as a target for anti cancer drug design: It will enable the development of compounds that mimic ARTS CTD, remove IAPs inhibition of caspases, and thereby induce apoptosis.
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Affiliation(s)
- Tali H. Reingewertz
- Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Deborah E. Shalev
- The Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Shahar Sukenik
- Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Ofrah Blatt
- Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
| | - Sarit Larisch
- Cell Death Research Laboratory, Department of Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Assaf Friedler
- Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel
- * E-mail:
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84
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Abstract
Protein-protein interactions (PPIs) govern all aspects of cell function and, as such, are a major target for research and therapeutic intervention. A major rate-limiting step in PPI research is the expression and purification of full-length proteins. The use of peptides to study PPIs significantly facilitates the structural and biophysical characterization of PPIs as well as the effort to develop drugs to control PPIs. Here we describe examples for the use of peptides to study PPI and some of the important experimental methods that are used in the field. Peptides have proved to be excellent tools to study PPIs and have been contributing both for understanding mechanisms of PPIs as well as for drug design for PPI modulation.
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85
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Abstract
Integration is a key step in the HIV-1 life cycle in which the ends of linear viral DNA are covalently joined with host chromosomal DNA. Integrase is the highly conserved and essential viral protein that performs two catalytically related reactions that ultimately lead to the insertion of the viral genome into that of the host cell. The only chemotherapeutic agents against integrase currently available for HIV-1 infected individuals are those that interrupt strand transfer, the second step of catalysis. Accordingly, this article outlines possible future strategies targeting the first catalytic step, 3' processing, as well as other nonenzymatic, yet indispensible, functions thought to be co-ordinated by integrase. Importantly, the interruption of irremediable recombination between viral and host DNAs represents the last step after viral entry at which an otherwise irreversible infection can be prevented.
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86
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Belitzky A, Melamed-Book N, Weiss A, Raviv U. The dynamic nature of amyloid beta (1-40) aggregation. Phys Chem Chem Phys 2011; 13:13809-14. [PMID: 21725546 DOI: 10.1039/c1cp20832b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this paper, we characterize the dynamic nature of the full amyloid beta (1-40) (Aβ (1-40)) aggregates. We labeled the peptide with either 5-carboxytetramethylrhodamine (TAMRA) or with fluorescein-isothiocyanate (FITC). The labeled peptides were mixed after separate fibrillization, and the dynamic changes in the structure of the fibrils were imaged using confocal microscopy. Fluorescence resonance energy transfer (FRET) measurements showed that the Aβ (1-40) peptides detach from and reattach to the fibrils in a biologically relevant timescale (days). With time, the two peptides mix at the molecular level. This process is concentration dependent and occurs primarily in the external parts of the aggregates with a half time between 4 and 7 days. This study shows that the combination of confocal microscopy and FRET analysis is a facile method for studying dynamic processes in supra-molecular aggregates.
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Affiliation(s)
- Alik Belitzky
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram Campus, 91904 Jerusalem, Israel
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87
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Bojja RS, Andrake MD, Weigand S, Merkel G, Yarychkivska O, Henderson A, Kummerling M, Skalka AM. Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking. J Biol Chem 2011; 286:17047-59. [PMID: 21454648 PMCID: PMC3089549 DOI: 10.1074/jbc.m110.212571] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/28/2011] [Indexed: 01/25/2023] Open
Abstract
We determined the size and shape of full-length avian sarcoma virus (ASV) integrase (IN) monomers and dimers in solution using small angle x-ray scattering. The low resolution data obtained establish constraints for the relative arrangements of the three component domains in both forms. Domain organization within the small angle x-ray envelopes was determined by combining available atomic resolution data for individual domains with results from cross-linking coupled with mass spectrometry. The full-length dimer architecture so revealed is unequivocally different from that proposed from x-ray crystallographic analyses of two-domain fragments, in which interactions between the catalytic core domains play a prominent role. Core-core interactions are detected only in cross-linked IN tetramers and are required for concerted integration. The solution dimer is stabilized by C-terminal domain (CTD-CTD) interactions and by interactions of the N-terminal domain in one subunit with the core and CTD in the second subunit. These results suggest a pathway for formation of functional IN-DNA complexes that has not previously been considered and possible strategies for preventing such assembly.
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Affiliation(s)
- Ravi S. Bojja
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Mark D. Andrake
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Steven Weigand
- the Dupont Northwestern Dow Collaborative Access Team Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439
| | - George Merkel
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Olya Yarychkivska
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Adam Henderson
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Marissa Kummerling
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
| | - Anna Marie Skalka
- From the Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111 and
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88
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De Luca L, Ferro S, Morreale F, De Grazia S, Chimirri A. Inhibitors of the interactions between HIV-1 IN and the cofactor LEDGF/p75. ChemMedChem 2011; 6:1184-91. [PMID: 21506277 DOI: 10.1002/cmdc.201100071] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/09/2011] [Indexed: 01/09/2023]
Abstract
The replication cycle of human immunodeficiency virus type 1 (HIV-1) is a complex multistep process that depends on both viral and host cell factors. The nuclear protein lens epithelium-derived growth factor (LEDGF/p75) is a multidomain protein, present in host cells, which plays an important role in the integration process. LEDGF/p75 not only binds HIV-1 integrase (IN) at its IN binding domain (IBD) but also contains several motifs that function in DNA and chromatin binding. The demonstrated importance of the association between IN and LEDGF/p75 in HIV-1 integration suggests the possibility that this protein-protein interaction (PPI) could be exploited as an antiviral target. We describe herein the progress to date in developing inhibitors of this promising target.
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Affiliation(s)
- Laura De Luca
- Dipartimento Farmaco-Chimico, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
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89
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Tsiang M, Jones GS, Hung M, Samuel D, Novikov N, Mukund S, Brendza KM, Niedziela-Majka A, Jin D, Liu X, Mitchell M, Sakowicz R, Geleziunas R. Dithiothreitol causes HIV-1 integrase dimer dissociation while agents interacting with the integrase dimer interface promote dimer formation. Biochemistry 2011; 50:1567-81. [PMID: 21222490 DOI: 10.1021/bi101504w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We have developed a homogeneous time-resolved fluorescence resonance energy transfer (FRET)-based assay that detects the formation of HIV-1 integrase (IN) dimers. The assay utilizes IN monomers that express two different epitope tags that are recognized by their respective antibodies, coupled to distinct fluorophores. Surprisingly, we found that dithiothreitol (DTT), a reducing agent essential for in vitro enzymatic activity of IN, weakened the interaction between IN monomers. This effect of DTT on IN is dependent on its thiol groups, since the related chemical threitol, which contains hydroxyls in place of thiols, had no effect on IN dimer formation. By studying mutants of IN, we determined that cysteines in IN appear to be dispensable for the dimer dissociation effect of DTT. Peptides derived from the IN binding domain (IBD) of lens epithelium derived growth factor/transcriptional coactivator p75 (LEDGF), a cellular cofactor that interacts with the IN dimer interface, were tested in this IN dimerization assay. These peptides, which compete with LEDGF for binding to IN, displayed an intriguing equilibrium binding dose-response curve characterized by a plateau rising to a peak, then descending to a second plateau. Mathematical modeling of this binding system revealed that these LEDGF-derived peptides promote IN dimerization and block subunit exchange between IN dimers. This dose-response behavior was also observed with a small molecule that interacts with the IN dimer interface and inhibits LEDGF binding to IN. In conclusion, this novel IN dimerization assay revealed that peptide and small molecule inhibitors of the IN-LEDGF interaction also stabilize IN dimers and promote their formation.
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Affiliation(s)
- Manuel Tsiang
- Gilead Sciences, 333 Lakeside Drive, Foster City, California 94404, United States.
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90
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Vanhee P, van der Sloot AM, Verschueren E, Serrano L, Rousseau F, Schymkowitz J. Computational design of peptide ligands. Trends Biotechnol 2011; 29:231-9. [PMID: 21316780 DOI: 10.1016/j.tibtech.2011.01.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 12/19/2022]
Abstract
Peptides possess several attractive features when compared to small molecule and protein therapeutics, such as high structural compatibility with target proteins, the ability to disrupt protein-protein interfaces, and small size. Efficient design of high-affinity peptide ligands via rational methods has been a major obstacle to the development of this potential drug class. However, structural insights into the architecture of protein-peptide interfaces have recently culminated in several computational approaches for the rational design of peptides that target proteins. These methods provide a valuable alternative to experimental high-resolution structures of target protein-peptide complexes, bringing closer the dream of in silico designed peptides for therapeutic applications.
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Affiliation(s)
- Peter Vanhee
- VIB SWITCH Laboratory, Flanders Institute of Biotechnology (VIB), Pleinlaan 2, 1050 Brussels, Belgium
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91
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LEDGF dominant interference proteins demonstrate prenuclear exposure of HIV-1 integrase and synergize with LEDGF depletion to destroy viral infectivity. J Virol 2011; 85:3570-83. [PMID: 21270171 DOI: 10.1128/jvi.01295-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Target cell overexpression of the integrase binding domain (IBD) of LEDGF/p75 (LEDGF) inhibits HIV-1 replication. The mechanism and protein structure requirements for this dominant interference are unclear. More generally, how and when HIV-1 uncoating occurs postentry is poorly defined, and it is unknown whether integrase within the evolving viral core becomes accessible to cellular proteins prior to nuclear entry. We used LEDGF dominant interference to address the latter question while characterizing determinants of IBD antiviral activity. Fusions of green fluorescent protein (GFP) with multiple C-terminal segments of LEDGF inhibited HIV-1 replication substantially, but minimal chimeras of either polarity (GFP-IBD or IBD-GFP) were most effective. Combining GFP-IBD expression with LEDGF depletion was profoundly antiviral. CD4(+) T cell lines were rendered virtually uninfectable, with single-cycle HIV-1 infectivity reduced 4 logs and high-input (multiplicity of infection = 5.0) replication completely blocked. We restricted GFP-IBD to specific intracellular locations and found that antiviral activity was preserved when the protein was confined to the cytoplasm or directed to the nuclear envelope. The life cycle block triggered by the cytoplasm-restricted protein manifested after nuclear entry, at the level of integration. We conclude that integrase within the viral core becomes accessible to host cell protein interaction in the cytoplasm. LEDGF dominant interference and depletion impair HIV-1 integration at distinct postentry stages. GFP-IBD may trigger premature or improper integrase oligomerization.
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92
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Levin A, Benyamini H, Hayouka Z, Friedler A, Loyter A. Peptides that bind the HIV-1 integrase and modulate its enzymatic activity - kinetic studies and mode of action. FEBS J 2010; 278:316-30. [DOI: 10.1111/j.1742-4658.2010.07952.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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93
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Hayouka Z, Hurevich M, Levin A, Benyamini H, Iosub A, Maes M, Shalev DE, Loyter A, Gilon C, Friedler A. Cyclic peptide inhibitors of HIV-1 integrase derived from the LEDGF/p75 protein. Bioorg Med Chem 2010; 18:8388-95. [DOI: 10.1016/j.bmc.2010.09.046] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/17/2010] [Accepted: 09/18/2010] [Indexed: 01/29/2023]
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94
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Friedler A. From peptides to proteins: lessons from my years at the Centre for Protein Engineering. Protein Eng Des Sel 2010; 24:241-5. [PMID: 21062759 DOI: 10.1093/protein/gzq080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The MRC Centre for Protein Engineering (CPE) hosted and trained many scientists over the years. It is a unique research environment that shaped the career of many scientists in all aspects. These include research directions and methodologies, but even more important--issues such as how to approach scientific problems and how to manage a research team. Alan Fersht was the director of the CPE when I joined it as a postdoc in the year 2000. In the current article for the PEDS special CPE issue, I will review how my scientific research and my approach to science developed from the days I arrived to the CPE as a young peptide chemist and throughout the years I spent at the CPE, and how it shaped my current research interests and attitude. I will focus on two major fields: (i) Using peptides to study and modulate the structure and interactions of proteins; (ii) Using quantitative biophysical methods to study proteins and their interactions at the molecular level.
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Affiliation(s)
- Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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95
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Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 2010; 78:2029-40. [PMID: 20455260 DOI: 10.1002/prot.22716] [Citation(s) in RCA: 313] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide-protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide-protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide-protein complexes will have significant impact on structure-based functional characterization, controlled manipulation of peptide interactions, and on peptide-based drug design.
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Affiliation(s)
- Barak Raveh
- Department of Microbiology and Molecular Genetics, Insitute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, Jerusalem, 91120 Israel
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96
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Tintori C, Veljkovic N, Veljkovic V, Botta M. Computational studies of the interaction between the HIV-1 integrase tetramer and the cofactor LEDGF/p75: Insights from molecular dynamics simulations and the Informational spectrum method. Proteins 2010; 78:3396-408. [DOI: 10.1002/prot.22847] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/22/2010] [Accepted: 08/03/2010] [Indexed: 01/05/2023]
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97
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Suzuki S, Urano E, Hashimoto C, Tsutsumi H, Nakahara T, Tanaka T, Nakanishi Y, Maddali K, Han Y, Hamatake M, Miyauchi K, Pommier Y, Beutler JA, Sugiura W, Fuji H, Hoshino T, Itotani K, Nomura W, Narumi T, Yamamoto N, Komano JA, Tamamura H. Peptide HIV-1 integrase inhibitors from HIV-1 gene products. J Med Chem 2010; 53:5356-60. [PMID: 20586421 DOI: 10.1021/jm1003528] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anti-HIV peptides with inhibitory activity against HIV-1 integrase (IN) have been found in overlapping peptide libraries derived from HIV-1 gene products. In a strand transfer assay using IN, inhibitory active peptides with certain sequential motifs related to Vpr- and Env-derived peptides were found. The addition of an octa-arginyl group to the inhibitory peptides caused a remarkable inhibition of the strand transfer and 3'-end-processing reactions catalyzed by IN and significant inhibition against HIV replication.
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Affiliation(s)
- Shintaro Suzuki
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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98
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Strategies to inhibit viral protein nuclear import: HIV-1 as a target. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1646-53. [PMID: 20719241 DOI: 10.1016/j.bbamcr.2010.07.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 07/16/2010] [Accepted: 07/29/2010] [Indexed: 12/22/2022]
Abstract
Nuclear import is a critical step in the life cycle of HIV-1. During the early (preintegration) stages of infection, HIV-1 has to transport its preintegration complex into the nucleus for integration into the host cell chromatin, while at the later (postintegration) stages viral regulatory proteins Tat and Rev need to get into the nucleus to stimulate transcription and regulate splicing and nuclear export of subgenomic and genomic RNAs. Given such important role of nuclear import in HIV-1 life cycle, this step presents an attractive target for antiviral therapeutic intervention. In this review, we describe the current state of our understanding of the interactions regulating nuclear import of the HIV-1 preintegration complex and describe current approaches to inhibit it. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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99
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Micozzi D, Pucciarelli S, Carpi FM, Costanzi S, De Sanctis G, Polzonetti V, Natalini P, Santarelli IF, Vita A, Vincenzetti S. Role of tyrosine 33 residue for the stabilization of the tetrameric structure of human cytidine deaminase. Int J Biol Macromol 2010; 47:471-82. [PMID: 20637228 DOI: 10.1016/j.ijbiomac.2010.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 06/30/2010] [Accepted: 07/01/2010] [Indexed: 10/19/2022]
Abstract
In the present work the effect of a mutation on tyrosine 33 residue (Y33G) of human cytidine deaminase (CDA) was investigated with regard to protein solubility and specific activity. Osmolytes and CDA ligands were used to increase the yield and the specific activity of the protein. The mutant enzyme was purified and subjected to a kinetic characterization and to stability studies. These investigations reinforced the hypothesis that in human CDA the side chain of Y33 is involved in intersubunit interactions with four glutamate residues (E108) forming a double latch that connects each of the two pairs of monomers of the tetrameric CDA.
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Affiliation(s)
- Daniela Micozzi
- School of Biosciences and Biotechnologies, via Gentile III da Varano, 62032 Camerino (MC), Italy.
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Garty S, Kimelman-Bleich N, Hayouka Z, Cohn D, Friedler A, Pelled G, Gazit D. Peptide-Modified “Smart” Hydrogels and Genetically Engineered Stem Cells for Skeletal Tissue Engineering. Biomacromolecules 2010; 11:1516-26. [DOI: 10.1021/bm100157s] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shai Garty
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Nadav Kimelman-Bleich
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Zvi Hayouka
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Daniel Cohn
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Assaf Friedler
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Gadi Pelled
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
| | - Dan Gazit
- Casali Institute of Applied Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, Skeletal Biotech Lab, Faculty of Dental Medicine, Hadassah Medical Campus, Ein Kerem, The Hebrew University of Jerusalem, Jerusalem, Israel, 91120, Department of Organic Chemistry, Institute of Chemistry, Edmond J. Safra, The Hebrew University of Jerusalem, Givaat Ram Campus, Jerusalem, Israel, 91904, and Department of Surgery and Cedars-Sinai
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