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Abstract
In the design and development of therapeutic agents, macromolecules with restricted structures have stronger competitive edges than linear biological entities since cyclization can overcome the limitations of linear structures. The common issues of linear peptides include susceptibility to degradation of the peptidase enzyme, off-target effects, and necessity of routine dosing, leading to instability and ineffectiveness. The unique conformational constraint of cyclic peptides provides a larger surface area to interact with the target at the same time, improving the membrane permeability and in vivo stability compared to their linear counterparts. Currently, cyclic peptides have been reported to possess various activities, such as antifungal, antiviral and antimicrobial activities. To date, there is emerging interest in cyclic peptide therapeutics, and increasing numbers of clinically approved cyclic peptide drugs are available on the market. In this review, the medical significance of cyclic peptides in the defence against viral infections will be highlighted. Except for chikungunya virus, which lacks specific antiviral treatment, all the viral diseases targeted in this review are those with effective treatments yet with certain limitations to date. Thus, strategies and approaches to optimise the antiviral effect of cyclic peptides will be discussed along with their respective outcomes. Apart from isolated naturally occurring cyclic peptides, chemically synthesized or modified cyclic peptides with antiviral activities targeting coronavirus, herpes simplex viruses, human immunodeficiency virus, Ebola virus, influenza virus, dengue virus, five main hepatitis viruses, termed as type A, B, C, D and E and chikungunya virus will be reviewed herein. Graphical Abstract
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Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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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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Vercruysse T, Pawar S, De Borggraeve W, Pardon E, Pavlakis GN, Pannecouque C, Steyaert J, Balzarini J, Daelemans D. Measuring cooperative Rev protein-protein interactions on Rev responsive RNA by fluorescence resonance energy transfer. RNA Biol 2011; 8:316-24. [PMID: 21358282 DOI: 10.4161/rna.8.2.13782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The export of viral RNA from the nucleus to the cytoplasm of the cellular host is a crucial step in the life cycle of HIV-1 that is mediated by the viral Rev protein. One aspect of the Rev function, its multimerization, is still unexplored as a target for antiviral therapy. This is partly due to the lack of a fast and solid system to measure Rev multimerization. We have developed a high throughput in vitro Rev multimerization assay based on fluorescence resonance energy transfer (FRET) in which real-time Rev-Rev interactions can be measured both in the absence and the presence of Rev specific RRE RNA. Well-characterized Rev multimerization deficient mutants showed reduced FRET as well as unlabeled Rev molecules were able to inhibit the FRET signal demonstrating the specificity of the assay. Upon multimerization along RRE RNA the FRET signal significantly increased but dropped again at equimolar Rev/RRE ratios suggesting that in this condition most Rev molecules are bound as monomers to the RRE. Furthermore, using this assay, we demonstrate that a previously selected llama heavy-chain only antibody was shown to not only prevent the development of Rev multimers but also disassemble the already formed complexes confirming the dynamic nature of the Rev-Rev interactions. The in vitro FRET based multimerization assay facilitates the further study of the basic mechanism of cooperative Rev multimerization along the RRE and is also widely applicable to study the assembly of other functional complexes involving protein homo-multimerization or cooperative protein-protein interactions on RNA or DNA.
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Affiliation(s)
- Thomas Vercruysse
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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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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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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Zoda MS, Zacharias M, Reissmann S. Syntheses and activities of backbone-side chain cyclic octapeptide ligands with N
-functionalized phosphotyrosine for the N
-terminal SH2-domain of the protein tyrosine phosphatase SHP-1. J Pept Sci 2010; 16:403-13. [DOI: 10.1002/psc.1256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Juliano RL, Alam R, Dixit V, Kang HM. Cell-targeting and cell-penetrating peptides for delivery of therapeutic and imaging agents. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 1:324-35. [PMID: 20049800 DOI: 10.1002/wnan.4] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review will discuss the basic concepts concerning the use of cell-targeting peptides (CTPs) and cell-penetrating peptides (CPPs) in the context of nanocarrier technology. It deals with the discovery and subsequent evolution of CTPs and CPPs, issues concerning their interactions with cells and their biodistribution in vivo, and their potential advantages and disadvantages as delivery agents. The article also briefly discusses several specific examples of the use of CTPs or CPPs to assist in the delivery of nanoparticles, liposomes, and other nanocarriers.
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Affiliation(s)
- Rudolph L Juliano
- Department of Pharmacology, University of North Carolina, Chapel Hill, USA.
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Su W, Weng Y, Zheng C, Zhang Y, Shi F, Hong B, Chen Z, Li J, Li Z. Recent Developments in the Use ofbis-(Trichloromethyl) Carbonate in Synthesis. ORG PREP PROCED INT 2009. [DOI: 10.1080/00304940902885839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Levin A, Hayouka Z, Helfer M, Brack-Werner R, Friedler A, Loyter A. Peptides derived from HIV-1 integrase that bind Rev stimulate viral genome integration. PLoS One 2009; 4:e4155. [PMID: 19127291 PMCID: PMC2607543 DOI: 10.1371/journal.pone.0004155] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/02/2008] [Indexed: 01/05/2023] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) integrase protein (IN), catalyzes the integration of viral DNA into the host cell genome. IN catalyzes the first step of the integration process, namely the 3′-end processing in which IN removes a pGT dinucleotide from the 3′ end of each viral long terminal repeat (LTR). Following nuclear import of the viral preintegration complex, the host chromosomal DNA becomes accessible to the viral cDNA and the second step of the integration process, namely the strand-transfer step takes place. This ordered sequence of events, centered on integration, is mandatory for HIV replication. Methodology/Principal Findings Using an integrase peptide library, we selected two peptides, designated INr-1 and INr-2, which interact with the Rev protein and probably mediate the Rev-integrase interaction. Using an in-vitro assay system, we show that INr-1 and INr-2 are able to abrogate the inhibitory effects exerted by Rev and Rev-derived peptides on integrase activity. Both INr-1 and INr-2 were found to be cell-permeable and nontoxic, allowing a study of their effect in HIV-1-infected cultured cells. Interestingly, both INr peptides stimulated virus infectivity as estimated by production of the viral P24 protein, as well as by determination of the appearance of newly formed virus particles. Furthermore, kinetics studies revealed that the cell-permeable INr peptides enhance the integration process, as was indeed confirmed by direct determination of viral DNA integration by real-time PCR. Conclusions/Significance The results of the present study raise the possibility that in HIV-infected cells, the Rev protein may be involved in the integration of proviral DNA by controlling/regulating the activity of the integrase. Release from such inhibition leads to stimulation of IN activity and multiple viral DNA integration events.
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Affiliation(s)
- Aviad Levin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Hayouka
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Markus Helfer
- Institute of Virology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
- Clinical Cooperation Group ‘Immune-Monitoring’, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Abraham Loyter
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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Chaloin L, Smagulova F, Hariton-Gazal E, Briant L, Loyter A, Devaux C. Potent inhibition of HIV-1 replication by backbone cyclic peptides bearing the Rev arginine rich motif. J Biomed Sci 2007; 14:565-84. [PMID: 17520355 DOI: 10.1007/s11373-007-9180-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 04/24/2007] [Indexed: 10/23/2022] Open
Abstract
Due to its essential role in the virus life cycle, the viral regulatory protein Rev constitutes an attractive target for the development of new antiviral molecules. In this work, a series of Backbone Cyclic Peptide (BCP) analogs that bear a conformationally constrained arginine rich motif (ARM) of Rev were tested for in vitro inhibition of HIV-1 replication. We observed a potent suppression of HIV-1 replication in chronically infected T lymphocytic cells treated with Rev-BCPs. We further investigated possible mechanisms of HIV-1 inhibition and showed that Rev-BCPs interfere slightly with the nuclear import process and are very efficient in blocking a mechanism that controls Pr55(gag) and gp160(env) synthesis. Interestingly, these protein precursors are known to be encoded by mRNAs that require Rev-binding for nuclear export. In situ hybridization using a Cy-3 conjugated HIV-1 gag oligonucleotide probe indicated that Rev-BCPs prevent the intracellular accumulation of unspliced viral RNA. As a model, the most promising analog, Rev-BCP 14, was studied by molecular modeling and dynamics in order to identify its binding site on the Rev Response Element (RRE). The annealing simulation suggests that upon binding on the RRE, Rev-BCP 14 widens the distorted major groove of the viral RNA. Numerous contacts between peptide and RNA were found within the complex and some were identified as key components for the interactions. Altogether, our data indicate that the use of conformationally constrained Rev-BCPs represents a promising strategy for the development of new peptide-based therapeutic agents against HIV-1.
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Affiliation(s)
- Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), Institut de Biologie, CNRS UMR5236-UM1-UM2, 4 Boulevard Henri IV, CS69033, 34965, Montpellier cedex 2, France.
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