1
|
Aptamers Regulating the Hemostasis System. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238593. [PMID: 36500686 PMCID: PMC9739204 DOI: 10.3390/molecules27238593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The hemostasis system is a complex structure that includes the fibrinolysis system, and Yes this is correct coagulation and anticoagulation parts. Due to the multicomponent nature, it becomes relevant to study the key changes in the functioning of signaling pathways, and develop new diagnostic methods and modern drugs with high selectivity. One of the ways to solve this problem is the development of molecular recognition elements capable of blocking one of the hemostasis systems and/or activating another. Aptamers can serve as ligands for targeting specific clinical needs, promising anticoagulants with minor side effects and significant biological activity. Aptamers with several clotting factors and platelet proteins are used for the treatment of thrombosis. This review is focused on the aptamers used for the correction of the hemostasis system, and their structural and functional features. G-rich nucleic acid aptamers, mostly versatile G-quadruplexes, recognize different components of the hemostasis system and are capable of correcting the functioning.
Collapse
|
2
|
Overview of the Therapeutic Potential of Aptamers Targeting Coagulation Factors. Int J Mol Sci 2021; 22:ijms22083897. [PMID: 33918821 PMCID: PMC8069679 DOI: 10.3390/ijms22083897] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences that bind target molecules with high specificity and affinity. Aptamers exhibit several notable advantages over protein-based therapeutics. Aptamers are non-immunogenic, easier to synthesize and modify, and can bind targets with greater affinity. Due to these benefits, aptamers are considered a promising therapeutic candidate to treat various conditions, including hematological disorders and cancer. An active area of research involves developing aptamers to target blood coagulation factors. These aptamers have the potential to treat cardiovascular diseases, blood disorders, and cancers. Although no aptamers targeting blood coagulation factors have been approved for clinical use, several aptamers have been evaluated in clinical trials and many more have demonstrated encouraging preclinical results. This review summarized our knowledge of the aptamers targeting proteins involved in coagulation, anticoagulation, fibrinolysis, their extensive applications as therapeutics and diagnostics tools, and the challenges they face for advancing to clinical use.
Collapse
|
3
|
Komarova N, Barkova D, Kuznetsov A. Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology. Int J Mol Sci 2020; 21:E8774. [PMID: 33233573 PMCID: PMC7699794 DOI: 10.3390/ijms21228774] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
Collapse
Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1–7 Shokin Square, Zelenograd, 124498 Moscow, Russia; (D.B.); (A.K.)
| | | | | |
Collapse
|
4
|
Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:605-619. [PMID: 30472639 PMCID: PMC6251793 DOI: 10.1016/j.omtn.2018.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/18/2022]
Abstract
Aptamer selections often yield distinct subpopulations, each with unique phenotypes that can be leveraged for specialized applications. Although most selections aim to attain ever higher specificity, we sought to identify aptamers that recognize increasingly divergent primate lentiviral reverse transcriptases (RTs). We hypothesized that aptamer subpopulations in libraries pre-enriched against a single RT may exhibit broad-spectrum binding and inhibition, and we devised a multiplexed poly-target selection to elicit those phenotypes against a panel of primate lentiviral RTs. High-throughput sequencing and coenrichment/codepletion analysis of parallel and duplicate selection trajectories rapidly narrowed the list of candidate aptamers by orders of magnitude and identified dozens of priority candidates for further screening. Biochemical characterization validated a novel aptamer motif and several rare and unobserved variants of previously known motifs that inhibited recombinant RTs to varying degrees. These broad-spectrum aptamers also suppressed replication of viral constructs carrying phylogenetically diverse RTs. The poly-target selection and coenrichment/codepletion approach described herein is a generalizable strategy for identifying cross-reactivity among related targets from combinatorial libraries.
Collapse
|
5
|
Shin S, Kim MK, Jung W, Chong Y. (-)-Epigallocatechin gallate derivatives reduce the expression of both urokinase plasminogen activator and plasminogen activator inhibitor-1 to inhibit migration, adhesion, and invasion of MDA-MB-231 cells. Phytother Res 2018; 32:2086-2096. [PMID: 30009577 DOI: 10.1002/ptr.6154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 01/02/2023]
Abstract
Urokinase plasminogen activator (uPA) and its inhibitor plasminogen activator inhibitor-1 (PAI-1) are established independent biomarkers for high metastasis risk in breast cancer. In this study, we investigated the regulatory activity of (-)-epigallocatechin-3-gallate (EGCG) and its derivatives on uPA and PAI-1 expression and thereby their anti-metastatic potential. EGCG showed only marginal effects on the uPA system and on the metastatic behavior of breast cancer cells (MDA-MB-231). However, the EGCG derivative 3e with a methyl-substituted carbonate substituent at the 4″-position showed potent inhibition of PAI-1 (62%) and uPA (50%) expression. The Ras-extracellular-signal-regulated kinase (ERK), p38 mitogen-activated protein kinase (MAPK), and phosphatidylinositol-3-kinase (PI3K)/Akt/NF-κB pathways, which regulate uPA and PAI-1 expression, were also affected by 3e (25%, 45%, and 25% reduction, respectively). In line with these findings, substantial reduction in metastatic behavior of MDA-MB-231 cells, such as adhesion (40%), invasion (56%), and migration (40%), was observed in the presence of 3e. It is also noteworthy that, in MDA-MB-231 cells, 3e did not exert any beneficial effect on the expression of matric metalloprotein (MMP) 2 and 9, which indicates that the anti-metastatic activity of 3e in MDA-MB-231 cells is not related to its regulation of the expression of MMPs. Taken together, we have shown that the EGCG derivative 3e could suppress the metastatic behavior of MDA-MB-231 cells through regulation of uPA and PAI-1.
Collapse
Affiliation(s)
- Sunhye Shin
- Department of Integrative Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Mi Kyoung Kim
- Department of Integrative Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| | - Woong Jung
- Department of Emergency Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Korea
| | - Youhoon Chong
- Department of Integrative Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
| |
Collapse
|
6
|
Bucci JC, McClintock CS, Chu Y, Ware GL, McConnell KD, Emerson JP, Peterson CB. Resolving distinct molecular origins for copper effects on PAI-1. J Biol Inorg Chem 2017; 22:1123-1135. [PMID: 28913669 PMCID: PMC5613068 DOI: 10.1007/s00775-017-1489-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022]
Abstract
Components of the fibrinolytic system are subjected to stringent control to maintain proper hemostasis. Central to this regulation is the serpin plasminogen activator inhibitor-1 (PAI-1), which is responsible for specific and rapid inhibition of fibrinolytic proteases. Active PAI-1 is inherently unstable and readily converts to a latent, inactive form. The binding of vitronectin and other ligands influences stability of active PAI-1. Our laboratory recently observed reciprocal effects on the stability of active PAI-1 in the presence of transition metals, such as copper, depending on the whether vitronectin was also present (Thompson et al. Protein Sci 20:353–365, 2011). To better understand the molecular basis for these copper effects on PAI-1, we have developed a gel-based copper sensitivity assay that can be used to assess the copper concentrations that accelerate the conversion of active PAI-1 to a latent form. The copper sensitivity of wild-type PAI-1 was compared with variants lacking N-terminal histidine residues hypothesized to be involved in copper binding. In these PAI-1 variants, we observed significant differences in copper sensitivity, and these data were corroborated by latency conversion kinetics and thermodynamics of copper binding by isothermal titration calorimetry. These studies identified a copper-binding site involving histidines at positions 2 and 3 that confers a remarkable stabilization of PAI-1 beyond what is observed with vitronectin alone. A second site, independent from the two histidines, binds metal and increases the rate of the latency conversion.
Collapse
Affiliation(s)
- Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.,Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Carlee S McClintock
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
| | - Yuzhuo Chu
- Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Gregory L Ware
- Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kayla D McConnell
- Department of Chemistry, Mississippi State University, Box 1115, Starkville, MS, 39762, USA
| | - Joseph P Emerson
- Department of Chemistry, Mississippi State University, Box 1115, Starkville, MS, 39762, USA
| | - Cynthia B Peterson
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA. .,Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
7
|
Petersen M, Madsen JB, Jørgensen TJD, Trelle MB. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry. Sci Rep 2017; 7:6636. [PMID: 28747729 PMCID: PMC5529462 DOI: 10.1038/s41598-017-06290-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/12/2017] [Indexed: 11/25/2022] Open
Abstract
Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1 as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment.
Collapse
Affiliation(s)
- Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Jeppe B Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Morten B Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark.
| |
Collapse
|
8
|
Nguyen Quang N, Perret G, Ducongé F. Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers. Pharmaceuticals (Basel) 2016; 9:ph9040076. [PMID: 27973417 PMCID: PMC5198051 DOI: 10.3390/ph9040076] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS.
Collapse
Affiliation(s)
- Nam Nguyen Quang
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
| | - Gérald Perret
- LFB Biotechnologies, 3 avenue des Tropiques, 91958 Courtaboeuf CEDEX, France.
| | - Frédéric Ducongé
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
| |
Collapse
|
9
|
Fortenberry YM, Brandal SM, Carpentier G, Hemani M, Pathak AP. Intracellular Expression of PAI-1 Specific Aptamers Alters Breast Cancer Cell Migration, Invasion and Angiogenesis. PLoS One 2016; 11:e0164288. [PMID: 27755560 PMCID: PMC5068744 DOI: 10.1371/journal.pone.0164288] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/22/2016] [Indexed: 02/07/2023] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1) is elevated in various cancers, where it has been shown to effect cell migration and invasion and angiogenesis. While, PAI-1 is a secreted protein, its intercellular levels are increased in cancer cells. Consequently, intracellular PAI-1 could contribute to cancer progression. While various small molecule inhibitors of PAI-1 are currently being investigated, none specifically target intracellular PAI-1. A class of inhibitors, termed aptamers, has been used effectively in several clinical applications. We previously generated RNA aptamers that target PAI-1 and demonstrated their ability to inhibit extracellular PAI-1. In the current study we explored the effect of these aptamers on intracellular PAI-1. We transiently transfected the PAI-1 specific aptamers into both MDA-MB-231 human breast cancer cells, and human umbilical vein endothelial cells (HUVECs) and studied their effects on cell migration, invasion and angiogenesis. Aptamer expressing MDA-MB-231 cells exhibited a decrease in cell migration and invasion. Additionally, intracellular PAI-1 and urokinase plasminogen activator (uPA) protein levels decreased, while the PAI-1/uPA complex increased. Moreover, a significant decrease in endothelial tube formation in HUVECs transfected with the aptamers was observed. In contrast, conditioned media from aptamer transfected MDA-MB-231 cells displayed a slight pro-angiogenic effect. Collectively, our study shows that expressing functional aptamers inside breast and endothelial cells is feasible and may exhibit therapeutic potential.
Collapse
Affiliation(s)
- Yolanda M Fortenberry
- Department of Pediatric Hematology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.,Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Stephanie M Brandal
- Department of Pediatric Hematology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Gilles Carpentier
- Laboratoire CRRET, Faculté des Sciences et Technologie, Université Paris-Est Créteil, 61 avenue du général De Gaulle, 94010 Créteil, France
| | - Malvi Hemani
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Arvind P Pathak
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| |
Collapse
|
10
|
Bucci JC, Trelle MB, McClintock CS, Qureshi T, Jørgensen TJD, Peterson CB. Copper(II) Ions Increase Plasminogen Activator Inhibitor Type 1 Dynamics in Key Structural Regions That Govern Stability. Biochemistry 2016; 55:4386-98. [DOI: 10.1021/acs.biochem.6b00256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel C. Bucci
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
- Department
of Biological Sciences, Louisiana State University, A221 Life
Sciences Annex, Baton Rouge, Louisiana 70803, United States
| | - Morten Beck Trelle
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 55 Campusvej, 5000 Odense M, Denmark
| | - Carlee S. McClintock
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Tihami Qureshi
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 55 Campusvej, 5000 Odense M, Denmark
| | - Cynthia B. Peterson
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
- Department
of Biological Sciences, Louisiana State University, A221 Life
Sciences Annex, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
11
|
Madsen JB, Andersen LM, Dupont DM, Trelle MB, Johansen JS, Jensen JK, Jørgensen TJD, Andreasen PA. An RNA Aptamer Inhibits a Mutation-Induced Inactivating Misfolding of a Serpin. Cell Chem Biol 2016; 23:700-8. [PMID: 27265748 DOI: 10.1016/j.chembiol.2016.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 12/17/2022]
Abstract
Most serpins are fast and specific inhibitors of extracellular serine proteases controlling biological processes such as blood coagulation, fibrinolysis, tissue remodeling, and inflammation. The inhibitory activity of serpins is based on a conserved metastable structure and their conversion to a more stable state during reaction with the target protease. However, the metastable state also makes serpins vulnerable to mutations, resulting in disease caused by inactive and misfolded monomeric or polymeric forms ("serpinopathy"). Misfolding can occur either intracellularly (type-I serpinopathies) or extracellularly (type-II serpinopathies). We have isolated a 2'-fluoropyrimidine-modified RNA aptamer, which inhibits a mutation-induced inactivating misfolding of the serpin α1-antichymotrypsin. It is the first agent able to stabilize a type-II mutation of a serpin without interfering with the inhibitory mechanism, thereby presenting a solution for the long-standing challenge of preventing pathogenic misfolding without compromising the inhibitory function.
Collapse
Affiliation(s)
- Jeppe B Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Lisbeth M Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Morten B Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper S Johansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Jan K Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.
| |
Collapse
|
12
|
Bjerregaard N, Andreasen PA, Dupont DM. Expected and unexpected features of protein-binding RNA aptamers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:744-757. [PMID: 27173731 DOI: 10.1002/wrna.1360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022]
Abstract
RNA molecules with high affinity to specific proteins can be isolated from libraries of up to 1016 different RNA sequences by systematic evolution of ligands by exponential enrichment (SELEX). These so-called protein-binding RNA aptamers are often interesting, e.g., as modulators of protein function for therapeutic use, for probing the conformations of proteins, for studies of basic aspects of nucleic acid-protein interactions, etc. Studies on the interactions between RNA aptamers and proteins display a number of expected and unexpected features, including the chemical nature of the interacting RNA-protein surfaces, the conformation of protein-bound aptamer versus free aptamer, the conformation of aptamer-bound protein versus free protein, and the effects of aptamers on protein function. Here, we review current insights into the details of RNA aptamer-protein interactions. WIREs RNA 2016, 7:744-757. doi: 10.1002/wrna.1360 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
13
|
Dupont DM, Bjerregaard N, Verpaalen B, Andreasen PA, Jensen JK. Building a Molecular Trap for a Serine Protease from Aptamer and Peptide Modules. Bioconjug Chem 2016; 27:918-26. [PMID: 26926041 DOI: 10.1021/acs.bioconjchem.6b00007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug development, molecular intervention strategies are usually based on interference with a single protein function, such as enzyme activity or receptor binding. However, in many cases, protein drug targets are multifunctional, with several molecular functions contributing to their pathophysiological actions. Aptamers and peptides are interesting synthetic building blocks for the design of multivalent molecules capable of modulating multiple functions of a target protein. Here, we report a molecular trap with the ability to interfere with the activation, catalytic activity, receptor binding, etc. of the serine protease urokinase-type plasminogen activator (uPA) by a rational combination of two RNA aptamers and a peptide with different inhibitory properties. The assembly of these artificial inhibitors into one molecule enhanced the inhibitory activity between 10- and 10,000-fold toward several functions of uPA. The study highlights the potential of multivalent designs and illustrates how they can easily be constructed from aptamers and peptides using nucleic acid engineering, chemical synthesis, and bioconjugation chemistry. By aptamer to aptamer and aptamer to peptide conjugation, we created, to the best of our knowledge, the first trivalent molecule which combines three artificial inhibitors binding to three different sites in a protein target. We hypothesize that by simultaneously preventing all of the functional interactions and activities of the target protein, this approach may represent an alternative to siRNA technology for a functional knockout.
Collapse
Affiliation(s)
- Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Ben Verpaalen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Aarhus University , Gustav Wieds Vej 10C, 8000 Aarhus, Denmark
| |
Collapse
|
14
|
Dupont DM, Larsen N, Jensen JK, Andreasen PA, Kjems J. Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools. Nucleic Acids Res 2015; 43:e139. [PMID: 26163061 PMCID: PMC4666376 DOI: 10.1093/nar/gkv700] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/30/2015] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid aptamer selection by systematic evolution of ligands by exponential enrichment (SELEX) has shown great promise for use in the development of research tools, therapeutics and diagnostics. Typically, aptamers are identified from libraries containing up to 1016 different RNA or DNA sequences by 5–10 rounds of affinity selection towards a target of interest. Such library screenings can result in complex pools of many target-binding aptamers. New high-throughput sequencing techniques may potentially revolutionise aptamer selection by allowing quantitative assessment of the dynamic changes in the pool composition during the SELEX process and by facilitating large-scale post-SELEX characterisation. In the present study, we demonstrate how high-throughput sequencing of SELEX pools, before and after a single round of branched selection for binding to different target variants, can provide detailed information about aptamer binding sites, preferences for specific target conformations, and functional effects of the aptamers. The procedure was applied on a diverse pool of 2′-fluoropyrimidine-modified RNA enriched for aptamers specific for the serpin plasminogen activator inhibitor-1 (PAI-1) through five rounds of standard selection. The results demonstrate that it is possible to perform large-scale detailed characterisation of aptamer sequences directly in the complex pools obtained from library selection methods, thus without the need to produce individual aptamers.
Collapse
Affiliation(s)
- Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Niels Larsen
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark iNANO Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| |
Collapse
|
15
|
Goodwin S, Gade AM, Byrom M, Herrera B, Spears C, Anslyn EV, Ellington AD. Next-generation sequencing as input for chemometrics in differential sensing routines. Angew Chem Int Ed Engl 2015; 54:6339-42. [PMID: 25826754 PMCID: PMC4426058 DOI: 10.1002/anie.201501822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 12/21/2022]
Abstract
Differential sensing (DS) methods traditionally use spatially arrayed receptors and optical signals to create score plots from multivariate data which classify individual analytes or complex mixtures. Herein, a new approach is described, in which nucleic acid sequences and sequence counts are used as the multivariate data without the necessity of a spatial array. To demonstrate this approach to DS, previously selected aptamers, identified from the literature, were used as semi-specific receptors, Next-Gen DNA sequencing was used to generate data, and cell line differentiation was the test-bed application. The study of a principal component analysis loading plot revealed cross-reactivity between the aptamers. The technique generates high-dimensionality score plots, and should be applicable to any mixture of complex and subtly different analytes for which nucleic acid-based receptors exist.
Collapse
Affiliation(s)
- Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (USA)
| | - Alexandra M Gade
- Department of Chemistry A1590, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Michelle Byrom
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Baine Herrera
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Camille Spears
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Eric V Anslyn
- Department of Chemistry A1590, The University of Texas at Austin, Austin, TX 78712 (USA).
| | - Andrew D Ellington
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA).
| |
Collapse
|
16
|
Bjerregaard N, Bøtkjær KA, Helsen N, Andreasen PA, Dupont DM. Tissue-type plasminogen activator-binding RNA aptamers inhibiting low-density lipoprotein receptor family-mediated internalisation. Thromb Haemost 2015; 114:139-49. [PMID: 25855589 DOI: 10.1160/th14-08-0686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/10/2015] [Indexed: 01/29/2023]
Abstract
Recombinant tissue-type plasminogen activator (tPA, trade name Alteplase), currently the only drug approved by the US Food and Drug Administration and the European Medicines Agency for the treatment of cerebral ischaemic stroke, has been implicated in a number of adverse effects reportedly mediated by interactions with the low-density lipoprotein (LDL) family receptors, including neuronal cell death and an increased risk of cerebral haemorrhage. The tissue-type plasminogen activator is the principal initiator of thrombolysis in human physiology, an effect that is mediated directly via localised activation of the plasmin zymogen plasminogen at the surface of fibrin clots in the vascular lumen. Here, we sought to identify a ligand to tPA capable of inhibiting the relevant LDL family receptors without interfering with the fibrinolytic activity of tPA. Systematic evolution of ligands by exponential enrichment (SELEX) was employed to isolate tPA-binding RNA aptamers, which were characterised in biochemical assays of tPA association to low density lipoprotein receptor-related protein-1 (LRP-1, an LDL receptor family member); tPA-mediated in vitro and ex vivo clot lysis; and tPA-mediated plasminogen activation in the absence and presence of a stimulating soluble fibrin fragment. Two aptamers, K18 and K32, had minimal effects on clot lysis, but were able to efficiently inhibit tPA-LRP-1 association and LDL receptor family-mediated endocytosis in human vascular endothelial cells and astrocytes. These observations suggest that coadministration alongside tPA may be a viable strategy to improve the safety of thrombolytic treatment of cerebral ischaemic stroke by restricting tPA activity to the vascular lumen.
Collapse
Affiliation(s)
- Nils Bjerregaard
- Nils Bjerregaard, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, Tel.: +45 87 15 49 07, Fax: +45 86 12 31 78, E-mail:
| | | | | | | | | |
Collapse
|
17
|
Goodwin S, Gade AM, Byrom M, Herrera B, Spears C, Anslyn EV, Ellington AD. Next-Generation Sequencing as Input for Chemometrics in Differential Sensing Routines. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
18
|
Damare J, Brandal S, Fortenberry YM. Inhibition of PAI-1 antiproteolytic activity against tPA by RNA aptamers. Nucleic Acid Ther 2014; 24:239-49. [PMID: 24922319 DOI: 10.1089/nat.2013.0475] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1; SERPINE1) inhibits the plasminogen activators: tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA). Elevated levels of PAI-1 have been correlated with an increased risk for cardiovascular disease. Pharmacologically suppressing PAI-1 might prevent, or successfully treat PAI-1 related vascular diseases. This can potentially be accomplished by using small RNA molecules (aptamers). This study's goal is to develop RNA aptamers to a region of PAI-1 that will prevent the ability of PAI-1 to interact with the plasminogen activators. The aptamers were generated through a systematic evolution of ligands via exponential enrichment approach that ensures the creation of RNA molecules that bind to our target protein, PAI-1. In vitro assays were used to determine the effect of these aptamers on PAI-1's inhibitory activity. Three aptamers that bind to PAI-1 with affinities in the nanomolar range were isolated. The aptamer clones R10-4 and R10-2 inhibited PAI-1's antiproteolytic activity against tPA and disrupted PAI-1's ability to form a stable covalent complex with tPA. Increasing aptamer concentrations correlated positively with an increase in cleaved PAI-1. To the best of our knowledge, this is the first report of RNA molecules that inhibit the antiproteolytic activity of PAI-1.
Collapse
Affiliation(s)
- Jared Damare
- 1 Department of Pediatric Hematology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | | | | |
Collapse
|
19
|
Trelle MB, Dupont DM, Madsen JB, Andreasen PA, Jørgensen TJD. Dissecting the effect of RNA aptamer binding on the dynamics of plasminogen activator inhibitor 1 using hydrogen/deuterium exchange mass spectrometry. ACS Chem Biol 2014; 9:174-82. [PMID: 24138169 DOI: 10.1021/cb400619v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA aptamers, selected from large synthetic libraries, are attracting increasing interest as protein ligands, with potential uses as prototype pharmaceuticals, conformational probes, and reagents for specific quantification of protein levels in biological samples. Very little is known, however, about their effects on protein conformation and dynamics. We have employed hydrogen/deuterium exchange (HDX) mass spectrometry to study the effect of RNA aptamers on the structural flexibility of the serpin plasminogen activator inhibitor-1 (PAI-1). The aptamers have characteristic effects on the biochemical properties of PAI-1. In particular, they are potent inhibitors of the structural transition of PAI-1 from the active state to the inactive, so-called latent state. This transition is one of the largest conformational changes of a folded protein domain without covalent modification. Binding of the aptamers to PAI-1 is associated with substantial and widespread protection against deuterium uptake in PAI-1. The aptamers induce protection against exchange with the solvent both in the protein-aptamer interface as well as in other specific areas. Interestingly, the aptamers induce substantial protection against exchange in α-helices B, C and I. This observation substantiates the relevance of structural instability in this region for transition to the latent state and argues for involvement of flexibility in regions not commonly associated with regulation of latency transition in serpins.
Collapse
Affiliation(s)
- Morten B. Trelle
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Daniel M. Dupont
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Jeppe B. Madsen
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Peter A. Andreasen
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| |
Collapse
|
20
|
Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013; 53:883-7. [DOI: 10.1002/anie.201309160] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Indexed: 11/06/2022]
|
21
|
Buratto J, Colombo C, Stupfel M, Dawson SJ, Dolain C, Langlois d'Estaintot B, Fischer L, Granier T, Laguerre M, Gallois B, Huc I. Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201309160] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Lin Z, Jensen JK, Hong Z, Shi X, Hu L, Andreasen PA, Huang M. Structural insight into inactivation of plasminogen activator inhibitor-1 by a small-molecule antagonist. ACTA ACUST UNITED AC 2013; 20:253-61. [PMID: 23438754 DOI: 10.1016/j.chembiol.2013.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 12/24/2012] [Accepted: 12/27/2012] [Indexed: 12/19/2022]
Abstract
Plasminogen activator inhibitor-1 (PAI-1), a serpin, is the physiological inhibitor of tissue-type and urokinase-type plasminogen activators and thus also an inhibitor of fibrinolysis and tissue remodeling. It is a potential therapeutic target in many pathological conditions, including thrombosis and cancer. Several types of PAI-1 antagonist have been developed, but the structural basis for their action has remained largely unknown. Here we report X-ray crystal structure analysis of PAI-1 in complex with a small-molecule antagonist, embelin. We propose a mechanism for embelin-induced rapid conversion of PAI-1 into a substrate for its target proteases and the subsequent slow conversion of PAI-1 into an irreversibly inactivated form. Our work provides structural clues to an understanding of PAI-1 inactivation by small-molecule antagonists and an important step toward the design of drugs targeting PAI-1.
Collapse
Affiliation(s)
- Zhonghui Lin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | | | | | | | | | | | | |
Collapse
|
23
|
Fortenberry YM. Plasminogen activator inhibitor-1 inhibitors: a patent review (2006-present). Expert Opin Ther Pat 2013; 23:801-15. [PMID: 23521527 DOI: 10.1517/13543776.2013.782393] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Plasminogen activator inhibitor-1 (PAI-1), the serine protease inhibitor (serpin), binds to and inhibits the plasminogen activators-tissue-type plasminogen activator (tPA) and the urokinase-type plasminogen activator (uPA). This results in both a decrease in plasmin production and a decrease in the dissolution of fibrin clots. Elevated levels of PAI-1 are correlated with an increased risk for cardiovascular disease and have been linked to obesity and metabolic syndrome. Consequently, the pharmacological suppression of PAI-1 might prevent or treat vascular disease. AREAS COVERED This article provides an overview of the patenting activity on PAI-1 inhibitors. Patents filed by pharmaceutical companies or individual research groups are described, and the biological and biochemical evaluation of the inhibitors, including in vitro and in vivo studies, is discussed. An overview of patents pertaining to using these inhibitors for treating various diseases is also included. EXPERT OPINION Although there is still no PAI-1 inhibitor being evaluated in a clinical setting or approved for human therapy, research in this field has progressed, and promising new compounds have been designed. Most research has focused on improving the pharmacological profile of these compounds, which will hopefully allow them to proceed to clinical studies. Despite the need for further testing and research, the potential use of PAI-1 inhibitors for treating cardiovascular disease appears quite promising.
Collapse
Affiliation(s)
- Yolanda M Fortenberry
- Johns Hopkins University School of Medicine, Division of Hematology/Department of Pediatrics, 720 Rutland Avenue Ross 1120, Baltimore, MD 21205, USA.
| |
Collapse
|
24
|
Bager R, Kristensen TK, Jensen JK, Szczur A, Christensen A, Andersen LM, Johansen JS, Larsen N, Baatrup E, Huang M, Ploug M, Andreasen PA. Urokinase-type plasminogen activator-like proteases in teleosts lack genuine receptor-binding epidermal growth factor-like domains. J Biol Chem 2012; 287:27526-36. [PMID: 22733817 DOI: 10.1074/jbc.m112.369207] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasminogen activation catalyzed by urokinase-type plasminogen activator (uPA) plays an important role in normal and pathological tissue remodeling processes. Since its discovery in the mid-1980s, the cell membrane-anchored urokinase-type plasminogen activator receptor (uPAR) has been believed to be central to the functions of uPA, as uPA-catalyzed plasminogen activation activity appeared to be confined to cell surfaces through the binding of uPA to uPAR. However, a functional uPAR has so far only been identified in mammals. We have now cloned, recombinantly produced, and characterized two zebrafish proteases, zfuPA-a and zfuPA-b, which by several criteria are the fish orthologs of mammalian uPA. Thus, both proteases catalyze the activation of fish plasminogen efficiently and both proteases are inhibited rapidly by plasminogen activator inhibitor-1 (PAI-1). But zfuPA-a differs from mammalian uPA by lacking the exon encoding the uPAR-binding epidermal growth factor-like domain; zfuPA-b differs from mammalian uPA by lacking two cysteines of the epidermal growth factor-like domain and a uPAR-binding sequence comparable with that found in mammalian uPA. Accordingly, no zfuPA-b binding activity could be found in fish white blood cells or fish cell lines. We therefore propose that the current consensus of uPA-catalyzed plasminogen activation taking place on cell surfaces, derived from observations with mammals, is too narrow. Fish uPAs appear incapable of receptor binding in the manner known from mammals and uPA-catalyzed plasminogen activation in fish may occur mainly in solution. Studies with nonmammalian vertebrate species are needed to obtain a comprehensive understanding of the mechanism of plasminogen activation.
Collapse
Affiliation(s)
- René Bager
- Department of Molecular Biology and Genetics, Aarhus University, 10 Gustav Wieds Vej, 8000 Aarhus C, Denmark
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
| |
Collapse
|
26
|
Brandal S, Blake CM, Sullenger BA, Fortenberry YM. Effects of plasminogen activator inhibitor-1-specific RNA aptamers on cell adhesion, motility, and tube formation. Nucleic Acid Ther 2011; 21:373-81. [PMID: 22103403 PMCID: PMC3279719 DOI: 10.1089/nat.2011.0320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 10/09/2011] [Indexed: 11/12/2022] Open
Abstract
The serine protease inhibitor (serpin) plasminogen activator inhibitor-1 (PAI-1) is associated with the pathophysiology of several diseases, including cancer and cardiovascular disease. The extracellular matrix protein vitronectin increases at sites of vessel injury and is also present in fibrin clots. Integrins present on the cell surface bind to vitronectin and anchor the cell to the extracellular matrix. However, the binding of PAI-1 to vitronectin prevents this interaction, thereby decreasing both cell adhesion and migration. We previously developed PAI-1-specific RNA aptamers that bind to (or in the vicinity of) the vitronectin binding site of PAI-1. These aptamers prevented cancer cells from detaching from vitronectin in the presence of PAI-1, resulting in an increase in cell adhesion. In the current study, we used in vitro assays to investigate the effects that these aptamers have on human aortic smooth muscle cell (HASMC) and human umbilical vein endothelial cell (HUVEC) migration, adhesion, and proliferation. The PAI-1-specific aptamers (SM20 and WT15) increased attachment of HASMCs and HUVECs to vitronectin in the presence of PAI-1 in a dose-dependent manner. Whereas PAI-1 significantly inhibited cell migration through its interaction with vitronectin, both SM20 and WT15 restored cell migration. The PAI-1 vitronectin binding mutant (PAI-1AK) did not facilitate cell detachment or have an effect on cell migration. The effect on cell proliferation was minimal. Additionally, both SM20 and WT15 promoted tube formation on matrigel that was supplemented with vitronectin, thereby reversing the PAI-1's inhibition of tube formation. Collectively, results from this study show that SM20 and WT15 bind to the PAI-1's vitronectin binding site and interfere with its effect on cell migration, adhesion, and tube formation. By promoting smooth muscle and endothelial cell migration, these aptamers can potentially eliminate the adverse effects of elevated PAI-1 levels in the pathogenesis of vascular disease.
Collapse
Affiliation(s)
- Stephanie Brandal
- Department of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charlene M. Blake
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Bruce A. Sullenger
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Yolanda M. Fortenberry
- Department of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
27
|
Schmitt M, Harbeck N, Brünner N, Jänicke F, Meisner C, Mühlenweg B, Jansen H, Dorn J, Nitz U, Kantelhardt EJ, Thomssen C. Cancer therapy trials employing level-of-evidence-1 disease forecast cancer biomarkers uPA and its inhibitor PAI-1. Expert Rev Mol Diagn 2011; 11:617-34. [PMID: 21745015 DOI: 10.1586/erm.11.47] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clinical research on cancer biomarkers is essential in understanding recent discoveries in cancer biology and heterogeneity of the cancer disease. However, there are only a few examples of clinically useful studies that have identified cancer biomarkers with clinical benefit. Urokinase-type plasminogen activator (uPA) and its inhibitor plasminogen activator inhibitor type 1 (PAI-1) are two of the few tumor tissue-associated cancer biomarkers that have been evaluated successfully and extensively in many preclinical and clinical studies for their clinical utility. Most of the studies have been conducted in early breast cancer to demonstrate the prognostic and predictive value for this malignancy. As a result of these investigations, uPA and PAI-1 have reached the highest level of clinical evidence, level of evidence 1. This article sheds light on the current status of major clinical Phase II and III breast cancer therapy trials (Chemo-N0, NNBC-3 and Plan B), and introduces ongoing clinical trials targeting uPA in advanced cancers of the breast and pancreas, employing synthetic small-size drugs to counteract uPA activity (WX-UK1, Mesupron(®)). The therapeutic effect of a uPA-derived small-size synthetic peptide (Å6) is tested in advanced ovarian cancer patients.
Collapse
Affiliation(s)
- Manfred Schmitt
- Clinical Research Unit, Department of Obstetrics and Gynecology (Frauenklinik), Klinikum rechts der Isar of the Technical University of Munich, Ismaninger Strasse 22, D-81675 Munich, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Schmitt M, Mengele K, Napieralski R, Magdolen V, Reuning U, Gkazepis A, Sweep F, Brünner N, Foekens J, Harbeck N. Clinical utility of level-of-evidence-1 disease forecast cancer biomarkers uPA and its inhibitor PAI-1. Expert Rev Mol Diagn 2011; 10:1051-67. [PMID: 21080821 DOI: 10.1586/erm.10.71] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The prognostic and/or predictive value of the cancer biomarkers, urokinase-type plasminogen activator (uPA) and its inhibitor (plasminogen activator inhibitor [PAI]-1), determined by ELISA in tumor-tissue extracts, was demonstrated for several cancer types in numerous clinically relevant retrospective or prospective studies, including a multicenter breast cancer therapy trial (Chemo-N0). Consequently, for the first time ever for any cancer biomarker for breast cancer, uPA and PAI-1 have reached the highest level of evidence, level-of-evidence-1. At present, two other breast cancer therapy trials, NNBC-3 and Plan B, also incorporating uPA and PAI-1 as treatment-assignment tools are in effect. Furthermore, small synthetic molecules targeting uPA are currently in Phase II clinical trials in patients afflicted with advanced cancer of the ovary, breast or pancreas.
Collapse
Affiliation(s)
- Manfred Schmitt
- Frauenklinik der Technischen Universitaet Muenchen, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
Serpins (serine protease inhibitors) have traditionally been grouped together based on structural homology. They share common structural features of primary sequence, but not all serpins require binding to cofactors in order to achieve maximal protease inhibition. In order to obtain physiologically relevant rates of inhibition of target proteases, some serpins utilize the unbranched sulfated polysaccharide chains known as glycosaminoglycans (GAGs) to enhance inhibition. These GAG-binding serpins include antithrombin (AT), heparin cofactor II (HCII), and protein C inhibitor (PCI). The GAGs heparin and heparan sulfate have been shown to bind AT, HCII, and PCI, while HCII is also able to utilize dermatan sulfate as a cofactor. Other serpins such as PAI-1, kallistatin, and α(1)-antitrypsin also interact with GAGs with different endpoints, some accelerating protease inhibition while others inhibit it. There are many serpins that bind or carry ligands that are unrelated to GAGs, which are described elsewhere in this work. For most GAG-binding serpins, binding of the GAG occurs in a conserved region of the serpin near or involving helix D, with the exception of PCI, which utilizes helix H. The binding of GAG to serpin can lead to a conformational change within the serpin, which can lead to increased or tighter binding to the protease, and can accelerate the rates of inhibition up to 10,000-fold compared to the unbound native serpin. In this chapter, we will discuss three major GAG-binding serpins with known physiological roles in modulating coagulation: AT (SERPINC1), HCII (SERPIND1), and PCI (SERPINA5). We will review methodologies implemented to study the structure of these serpins and those used to study their interactions with GAG's. We discuss novel techniques to examine the serpin-GAG interaction and finally we review the biological roles of these serpins by describing the mouse models used to study them.
Collapse
Affiliation(s)
- Chantelle M Rein
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | |
Collapse
|
30
|
Abstract
Plasminogen activator inhibitor-1 (PAI-1) belongs to the serine protease inhibitor super family (serpin) and is the primary inhibitor of both the tissue-type (tPA) and urokinase-type (uPA) plasminogen activators. PAI-1 has been implicated in a wide range of pathological processes where it may play a direct role in a variety of diseases. These observations have made PAI-1 an attractive target for small molecule drug development. However, PAI-1's structural plasticity and its capacity to interact with multiple ligands have made the identification and development of such small molecule PAI-1 inactivating agents challenging. In the following pages, we discuss the difficulties associated with screening for small molecule inactivators of PAI-1, in particular, and of serpins, in general. We discuss strategies for high-throughput screening (HTS) of chemical and natural product libraries, and validation steps necessary to confirm identified hits. Finally, we describe steps essential to confirm specificity of active compounds, and strategies to examine potential mechanisms of compound action.
Collapse
|
31
|
Dupont DM, Madsen JB, Hartmann RK, Tavitian B, Ducongé F, Kjems J, Andreasen PA. Serum-stable RNA aptamers to urokinase-type plasminogen activator blocking receptor binding. RNA (NEW YORK, N.Y.) 2010; 16:2360-2369. [PMID: 20962041 PMCID: PMC2995398 DOI: 10.1261/rna.2338210] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 08/30/2010] [Indexed: 05/30/2023]
Abstract
The serine proteinase urokinase-type plasminogen activator (uPA) is widely recognized as a potential target for anticancer therapy. Its association with cell surfaces through the uPA receptor (uPAR) is central to its function and plays an important role in cancer invasion and metastasis. In the current study, we used systematic evolution of ligands by exponential enrichment (SELEX) to select serum-stable 2'-fluoro-pyrimidine-modified RNA aptamers specifically targeting human uPA and blocking the interaction to its receptor at low nanomolar concentrations. In agreement with the inhibitory function of the aptamers, binding was found to be dependent on the presence of the growth factor domain of uPA, which mediates uPAR binding. One of the most potent uPA aptamers, upanap-12, was analyzed in more detail and could be reduced significantly in size without severe loss of its inhibitory activity. Finally, we show that the uPA-scavenging effect of the aptamers can reduce uPAR-dependent endocytosis of the uPA-PAI-1 complex and cell-surface associated plasminogen activation in cell culture experiments. uPA-scavenging 2'-fluoro-pyrimidine-modified RNA aptamers represent a novel promising principle for interfering with the pathological functions of the uPA system.
Collapse
Affiliation(s)
- Daniel Miotto Dupont
- Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark.
| | | | | | | | | | | | | |
Collapse
|
32
|
Marton S, Reyes-Darias JA, Sánchez-Luque FJ, Romero-López C, Berzal-Herranz A. In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules. Molecules 2010; 15:4610-38. [PMID: 20657381 PMCID: PMC6257598 DOI: 10.3390/molecules15074610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/17/2010] [Accepted: 06/24/2010] [Indexed: 02/05/2023] Open
Abstract
It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids.
Collapse
Affiliation(s)
- Soledad Marton
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, P.T. Ciencias de la Salud, Av. del Conocimiento s/n, Armilla, 18100 Granada, Spain.
| | | | | | | | | |
Collapse
|