1
|
Abstract
The systematic evolution of ligands by exponential enrichment (SELEX) enables the identification of ssDNA or RNA sequences binding to different target molecules, highly specific and with high affinity. In this chapter, we describe a selection strategy with ssDNA for a histidine-tagged protein that could be either performed hands-on manually or fully automated by an appropriate robotic selection platform.
Collapse
Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany.
| |
Collapse
|
2
|
Shraim AS, Abdel Majeed BA, Al-Binni M, Hunaiti A. Therapeutic Potential of Aptamer-Protein Interactions. ACS Pharmacol Transl Sci 2022; 5:1211-1227. [PMID: 36524009 PMCID: PMC9745894 DOI: 10.1021/acsptsci.2c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between 25 and 100 nucleotides which fold into three-dimensional structures capable of binding to target molecules. Specific aptamers can be isolated against a large variety of targets through efficient and relatively cheap methods, and they demonstrate target-binding affinities that sometimes surpass those of antibodies. Consequently, interest in aptamers has surged over the past three decades, and their application has shown promise in advancing knowledge in target analysis, designing therapeutic interventions, and bioengineering. With emphasis on their therapeutic applications, aptamers are emerging as a new innovative class of therapeutic agents with promising biochemical and biological properties. Aptamers have the potential of providing a feasible alternative to antibody- and small-molecule-based therapeutics given their binding specificity, stability, low toxicity, and apparent non-immunogenicity. This Review examines the general properties of aptamers and aptamer-protein interactions that help to understand their binding characteristics and make them important therapeutic candidates.
Collapse
Affiliation(s)
- Ala’a S. Shraim
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Bayan A. Abdel Majeed
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Maysaa’
Adnan Al-Binni
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| | - Abdelrahim Hunaiti
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| |
Collapse
|
3
|
Keretsu S, Bhujbal SP, Cho SJ. Docking and 3D-QSAR Studies of Hydrazone and Triazole Derivatives for Selective Inhibition of GRK2 over ROCK2. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190618105320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction:
G protein-coupled receptor kinase 2 (GRK2) is known to be implicated in
heart failure, and therefore serves as an important drug target. GRK2 belongs to the protein kinase A,
G, and C family and shares high sequence similarity with its closely related protein, the Rhoassociated
coiled-coil protein kinase 2 (ROCK2). Therefore, selective inhibition of GRK2 over
ROCK2 is considered crucial for heart failure therapy.
Objective:
To understand the structural factors for enhancing the inhibitory activity for GRK2 and
selectivity over ROCK2, we analyzed and compared molecular interactions using the same set of
ligands against both receptors.
Methods:
We have performed molecular docking and three-dimensional quantitative structure
activity relationship (3D-QSAR) studies on a series of hydrazone and triazole derivatives.
Results:
The presence of hydrophobic substituents at the triazole ring, electronegative substituents
between the pyridine and triazole ring and hydrophobic substituents near the benzene ring increases
the activity of both kinases. Whereas, having non-bulky substituents near the triazole ring, bulky and
hydrophobic substations at the benzene ring and electronegative and H-bond acceptor substituents at
the triazole ring showed a higher inhibitory preference for GRK2 over ROCK2.
Conclusion:
The outcome of this study may be used in the future development of potent GRK2
inhibitors having ROCK2 selectivity.
Collapse
Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea
| | | | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, Gwangju 501-759, Korea
| |
Collapse
|
4
|
Shraim AS, Hunaiti A, Awidi A, Alshaer W, Ababneh NA, Abu-Irmaileh B, Odeh F, Ismail S. Developing and Characterization of Chemically Modified RNA Aptamers for Targeting Wild Type and Mutated c-KIT Receptor Tyrosine Kinases. J Med Chem 2019; 63:2209-2228. [PMID: 31369705 DOI: 10.1021/acs.jmedchem.9b00868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The c-KIT receptor represents an attractive target for cancer therapy. Aptamers are emerging as a new promising class of nucleic acid therapeutics. In this study, a conventional SELEX approach was applied against the kinase domain of a group of c-KIT proteins (c-KITWT, c-KITD816V, and c-KITD816H) to select aptamers from a random RNA pool that can bind to the kinase domain of each target with high affinity and can selectively interfere with their kinase activities. Interestingly, our data indicated that one candidate aptamer, called V15, can specifically inhibit the in vitro kinase activity of mutant c-KITD816V with an IC50 value that is 9-fold more potent than the sunitinib drug tested under the same conditions. Another aptamer, named as H5/V36, showed the potential to distinguish between the c-KIT kinases by modulating the phosphorylation activity of each in a distinct mechanism of action and in a different potency.
Collapse
Affiliation(s)
- Ala'a S Shraim
- Department of Biological Sciences, School of Science, The University of Jordan, Amman JO 11942, Jordan.,Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman JO 19328, Jordan
| | - Abdelrahim Hunaiti
- Department of Clinical Laboratory Sciences, School of Science, The University of Jordan, Amman JO 11942, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Nidaa A Ababneh
- Cell Therapy Center, The University of Jordan, Amman JO 11942, Jordan
| | - Bashaer Abu-Irmaileh
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman JO 11942, Jordan
| | - Fadwa Odeh
- Department of Chemistry, School of Science, The University of Jordan, Amman JO 11942, Jordan
| | - Said Ismail
- Department of Biochemistry and Physiology, School of Medicine, The University of Jordan, Amman JO 11942, Jordan.,Qatar Genome Project, Qatar Foundation, Doha, Qatar
| |
Collapse
|
5
|
Abstract
G protein-coupled receptors (GPCRs) are critical cellular sensors that mediate numerous physiological processes. In the heart, multiple GPCRs are expressed on various cell types, where they coordinate to regulate cardiac function by modulating critical processes such as contractility and blood flow. Under pathological settings, these receptors undergo aberrant changes in expression levels, localization and capacity to couple to downstream signalling pathways. Conventional therapies for heart failure work by targeting GPCRs, such as β-adrenergic receptor and angiotensin II receptor antagonists. Although these treatments have improved patient survival, heart failure remains one of the leading causes of mortality worldwide. GPCR kinases (GRKs) are responsible for GPCR phosphorylation and, therefore, desensitization and downregulation of GPCRs. In this Review, we discuss the GPCR signalling pathways and the GRKs involved in the pathophysiology of heart disease. Given that increased expression and activity of GRK2 and GRK5 contribute to the loss of contractile reserve in the stressed and failing heart, inhibition of overactive GRKs has been proposed as a novel therapeutic approach to treat heart failure.
Collapse
|
6
|
Breuers S, Bryant LL, Legen T, Mayer G. Robotic assisted generation of 2'-deoxy-2'-fluoro-modifed RNA aptamers - High performance enabling strategies in aptamer selection. Methods 2019; 161:3-9. [PMID: 31152781 PMCID: PMC6599171 DOI: 10.1016/j.ymeth.2019.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/10/2019] [Accepted: 05/26/2019] [Indexed: 01/07/2023] Open
Abstract
Aptamer selection is a laborious procedure, requiring expertise and significant resources. These characteristics limit the accessibility of researchers to these molecular tools. We describe a selection procedure, making use of a robotic system that allows the fully automated selection of RNA and 2'deoxy-2'-fluoro pyrimidine RNA aptamers. The platform offers a rapid access to aptamers for basic research and development, therefore opening the path to aptamer-based systemic analysis of proteomes in biological settings.
Collapse
Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Laura Lledo Bryant
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Tjasa Legen
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany.
| |
Collapse
|
7
|
Murga C, Arcones AC, Cruces-Sande M, Briones AM, Salaices M, Mayor F. G Protein-Coupled Receptor Kinase 2 (GRK2) as a Potential Therapeutic Target in Cardiovascular and Metabolic Diseases. Front Pharmacol 2019; 10:112. [PMID: 30837878 PMCID: PMC6390810 DOI: 10.3389/fphar.2019.00112] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
G protein-coupled receptor kinase 2 (GRK2) is a central signaling node involved in the modulation of many G protein-coupled receptors (GPCRs) and also displaying regulatory functions in other cell signaling routes. GRK2 levels and activity have been reported to be enhanced in patients or in preclinical models of several relevant pathological situations, such as heart failure, cardiac hypertrophy, hypertension, obesity and insulin resistance conditions, or non-alcoholic fatty liver disease (NAFLD), and to contribute to disease progression by a variety of mechanisms related to its multifunctional roles. Therefore, targeting GRK2 by different strategies emerges as a potentially relevant approach to treat cardiovascular disease, obesity, type 2 diabetes, or NAFLD, pathological conditions which are frequently interconnected and present as co-morbidities.
Collapse
Affiliation(s)
- Cristina Murga
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Alba C Arcones
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Marta Cruces-Sande
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| | - Ana M Briones
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Farmacología, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Mercedes Salaices
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Farmacología, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Federico Mayor
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria La Princesa, Madrid, Spain
| |
Collapse
|
8
|
De Majo F, De Windt LJ. RNA therapeutics for heart disease. Biochem Pharmacol 2018; 155:468-478. [DOI: 10.1016/j.bcp.2018.07.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022]
|
9
|
Yu S, Sun L, Jiao Y, Lee LTO. The Role of G Protein-coupled Receptor Kinases in Cancer. Int J Biol Sci 2018; 14:189-203. [PMID: 29483837 PMCID: PMC5821040 DOI: 10.7150/ijbs.22896] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/17/2017] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of plasma membrane receptors. Emerging evidence demonstrates that signaling through GPCRs affects numerous aspects of cancer biology such as vascular remolding, invasion, and migration. Therefore, development of GPCR-targeted drugs could provide a new therapeutic strategy to treating a variety of cancers. G protein-coupled receptor kinases (GRKs) modulate GPCR signaling by interacting with the ligand-activated GPCR and phosphorylating its intracellular domain. This phosphorylation initiates receptor desensitization and internalization, which inhibits downstream signaling pathways related to cancer progression. GRKs can also regulate non-GPCR substrates, resulting in the modulation of a different set of pathophysiological pathways. In this review, we will discuss the role of GRKs in modulating cell signaling and cancer progression, as well as the therapeutic potential of targeting GRKs.
Collapse
Affiliation(s)
- Shan Yu
- Centre of Reproduction Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Litao Sun
- Department of Ultrasound, The Secondary Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yufei Jiao
- Department of Pathology, The Secondary Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Leo Tsz On Lee
- Centre of Reproduction Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| |
Collapse
|
10
|
Cannavo A, Komici K, Bencivenga L, D'amico ML, Gambino G, Liccardo D, Ferrara N, Rengo G. GRK2 as a therapeutic target for heart failure. Expert Opin Ther Targets 2017; 22:75-83. [PMID: 29166798 DOI: 10.1080/14728222.2018.1406925] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION G protein-coupled receptor (GPCR) kinase-2 (GRK2) is a regulator of GPCRs, in particular β-adrenergic receptors (ARs), and as demonstrated by decades of investigation, it has a pivotal role in the development and progression of cardiovascular disease, like heart failure (HF). Indeed elevated levels and activity of this kinase are able to promote the dysfunction of both cardiac and adrenal α- and β-ARs and to dysregulate other protective signaling pathway, such as sphingosine 1-phospate and insulin. Moreover, recent discoveries suggest that GRK2 can signal independently from GPCRs, in a 'non-canonical' manner, via interaction with non-GPCR molecule or via its mitochondrial localization. Areas covered: Based on this premise, GRK2 inhibition or its genetic deletion has been tested in several disparate animal models of cardiovascular disease, showing to protect the heart from adverse remodeling and dysfunction. Expert opinion: HF is one of the leading cause of death worldwide with enormous health care costs. For this reason, the identification of new therapeutic targets like GRK2 and strategies such as its inhibition represents a new hope in the fight against HF development and progression. Herein, we will update the readers about the 'state-of-art' of GRK2 inhibition as a potent therapeutic strategy in HF.
Collapse
Affiliation(s)
- Alessandro Cannavo
- a Center for Translational Medicine , Temple University Lewis Katz School of Medicine , Philadelphia , PA , USA.,b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy
| | - Klara Komici
- b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy
| | - Leonardo Bencivenga
- b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy
| | - Maria Loreta D'amico
- c Istituti Clinici Scientifici Maugeri SpA Società Benefit , Telese Terme Institute , Benevento , Italy
| | - Giuseppina Gambino
- c Istituti Clinici Scientifici Maugeri SpA Società Benefit , Telese Terme Institute , Benevento , Italy
| | - Daniela Liccardo
- b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy
| | - Nicola Ferrara
- b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy.,c Istituti Clinici Scientifici Maugeri SpA Società Benefit , Telese Terme Institute , Benevento , Italy
| | - Giuseppe Rengo
- b Dpt Translational Medical Sciences , Federico II University of Naples , Naples , Italy.,c Istituti Clinici Scientifici Maugeri SpA Società Benefit , Telese Terme Institute , Benevento , Italy
| |
Collapse
|
11
|
Sorriento D, Ciccarelli M, Cipolletta E, Trimarco B, Iaccarino G. "Freeze, Don't Move": How to Arrest a Suspect in Heart Failure - A Review on Available GRK2 Inhibitors. Front Cardiovasc Med 2016; 3:48. [PMID: 27999776 PMCID: PMC5138235 DOI: 10.3389/fcvm.2016.00048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022] Open
Abstract
Cardiovascular disease and heart failure (HF) still collect the largest toll of death in western societies and all over the world. A growing number of molecular mechanisms represent possible targets for new therapeutic strategies, which can counteract the metabolic and structural changes observed in the failing heart. G protein-coupled receptor kinase 2 (GRK2) is one of such targets for which experimental and clinical evidence are established. Indeed, several strategies have been carried out in place to interface with the known GRK2 mechanisms of action in the failing heart. This review deals with results from basic and preclinical studies. It shows different strategies to inhibit GRK2 in HF in vivo (βARK-ct gene therapy, treatment with gallein, and treatment with paroxetine) and in vitro (RNA aptamer, RKIP, and peptide-based inhibitors). These strategies are based either on the inhibition of the catalytic activity of the kinase (“Freeze!”) or the prevention of its shuttling within the cell (“Don’t Move!”). Here, we review the peculiarity of each strategy with regard to the ability to interact with the multiple tasks of GRK2 and the perspective development of eventual clinical use.
Collapse
Affiliation(s)
- Daniela Sorriento
- Department of Advanced Biomedical Sciences, University of Naples Federico II , Naples , Italy
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno , Baronissi, SA , Italy
| | - Ersilia Cipolletta
- Department of Advanced Biomedical Sciences, University of Naples Federico II , Naples , Italy
| | - Bruno Trimarco
- Department of Advanced Biomedical Sciences, University of Naples Federico II , Naples , Italy
| | - Guido Iaccarino
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno , Baronissi, SA , Italy
| |
Collapse
|
12
|
Abstract
Only a few of the aptamers designed to selectively target proteins have been structurally characterized, such as those that target thrombin, von Willebrand factor, Plasmodium falciparum lactate dehydrogenase, interleukin 6, and platelet-derived growth factor B. Most of these aptamers are composed of DNA and were designed as therapeutics/diagnostics for targets found in human plasma. Recently, the crystal structure of a complex between an RNA aptamer and an intracellular target, G protein-coupled receptor kinase 2, was determined. Herein is described the overall approach used to isolate crystals that would allow the identification of the key interactions between aptamer and kinase. These strategies may be useful in structural characterization of other SELEX-generated RNA aptamer complexes.
Collapse
Affiliation(s)
- John J G Tesmer
- Departments of Pharmacology and Biological Chemistry, University of Michigan, Room 3435, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.
| |
Collapse
|
13
|
Guccione M, Ettari R, Taliani S, Da Settimo F, Zappalà M, Grasso S. G-Protein-Coupled Receptor Kinase 2 (GRK2) Inhibitors: Current Trends and Future Perspectives. J Med Chem 2016; 59:9277-9294. [PMID: 27362616 DOI: 10.1021/acs.jmedchem.5b01939] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G-protein-coupled receptor kinase 2 (GRK2) is a G-protein-coupled receptor kinase that is ubiquitously expressed in many tissues and regulates various intracellular mechanisms. The up- or down-regulation of GRK2 correlates with several pathological disorders. GRK2 plays an important role in the maintenance of heart structure and function; thus, this kinase is involved in many cardiovascular diseases. GRK2 up-regulation can worsen cardiac ischemia; furthermore, increased kinase levels occur during the early stages of heart failure and in hypertensive subjects. GRK2 up-regulation can lead to changes in the insulin signaling cascade, which can translate to insulin resistance. Increased GRK2 levels also correlate with the degree of cognitive impairment that is typically observed in Alzheimer's disease. This article reviews the most potent and selective GRK2 inhibitors that have been developed. We focus on their mechanism of action, inhibition profile, and structure-activity relationships to provide insight into the further development of GRK2 inhibitors as drug candidates.
Collapse
Affiliation(s)
- Manuela Guccione
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina , Viale Annunziata, 98168 Messina, Italy
| | - Roberta Ettari
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina , Viale Annunziata, 98168 Messina, Italy
| | - Sabrina Taliani
- Dipartimento di Farmacia, Università di Pisa , Via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Dipartimento di Farmacia, Università di Pisa , Via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Maria Zappalà
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina , Viale Annunziata, 98168 Messina, Italy
| | - Silvana Grasso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina , Viale Annunziata, 98168 Messina, Italy
| |
Collapse
|
14
|
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
|
15
|
Waldschmidt HV, Homan KT, Cruz-Rodríguez O, Cato MC, Waninger-Saroni J, Larimore KL, Cannavo A, Song J, Cheung JY, Koch WJ, Tesmer JJG, Larsen SD, Larsen SD. Structure-Based Design, Synthesis, and Biological Evaluation of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors. J Med Chem 2016; 59:3793-807. [PMID: 27050625 PMCID: PMC4890168 DOI: 10.1021/acs.jmedchem.5b02000] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are central to many physiological processes. Regulation of this superfamily of receptors is controlled by GPCR kinases (GRKs), some of which have been implicated in heart failure. GSK180736A, developed as a Rho-associated coiled-coil kinase 1 (ROCK1) inhibitor, was identified as an inhibitor of GRK2 and co-crystallized in the active site. Guided by its binding pose overlaid with the binding pose of a known potent GRK2 inhibitor, Takeda103A, a library of hybrid inhibitors was developed. This campaign produced several compounds possessing high potency and selectivity for GRK2 over other GRK subfamilies, PKA, and ROCK1. The most selective compound, 12n (CCG-224406), had an IC50 for GRK2 of 130 nM, >700-fold selectivity over other GRK subfamilies, and no detectable inhibition of ROCK1. Four of the new inhibitors were crystallized with GRK2 to give molecular insights into the binding and kinase selectivity of this class of inhibitors.
Collapse
Affiliation(s)
- Helen V. Waldschmidt
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Kristoff T. Homan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Osvaldo Cruz-Rodríguez
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,PhD Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Marilyn C. Cato
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jessica Waninger-Saroni
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109,Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, 48109
| | - Kelly L. Larimore
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Alessandro Cannavo
- Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania, 19140
| | - Jianliang Song
- Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania, 19140
| | - Joseph Y. Cheung
- Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania, 19140
| | - Walter J. Koch
- Center for Translational Medicine, Temple University, Philadelphia, Pennsylvania, 19140
| | - John J. G. Tesmer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Scott D. Larsen
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, 48109,Departments of Medicinal Chemistry, Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109,Corresponding Author: Scott D. Larsen, , (734) 615 - 0454
| | | |
Collapse
|
16
|
Gomez-Monterrey I, Carotenuto A, Cipolletta E, Sala M, Vernieri E, Limatola A, Bertamino A, Musella S, Grieco P, Trimarco B, Novellino E, Iaccarino G, Campiglia P. SAR study and conformational analysis of a series of novel peptide G protein-coupled receptor kinase 2 inhibitors. Biopolymers 2016; 101:121-8. [PMID: 23733420 DOI: 10.1002/bip.22295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/22/2013] [Accepted: 05/22/2013] [Indexed: 01/09/2023]
Abstract
G protein-coupled receptor kinase 2 (GRK2) plays a central role in the cellular transduction network. In particular, during chronic heart failure GRK2 is upregulated and believed to contribute to disease progression. Thereby, its inhibition offers a potential therapeutic solution to several pathological conditions. In the present study, we performed a SAR study and a NMR conformational analysis of peptides derived from HJ loop of GRK2 and able to selectively inhibit GRK2. From Ala-scan and D-Ala point replacement, we found that Arg residues don't affect the inhibitory properties, while a D-amino acid at position 5 is key to the activity. Conformational analysis identified two β-turns that involve N-terminal residues, followed by a short extended region. These information can help the design of peptides and peptido-mimetics with enhanced GRK2 inhibition properties.
Collapse
|
17
|
Abstract
Heightened cardiac adrenergic nervous system (ANS) activity and progression of left ventricular (LV) remodeling are temporally related in patients with systolic heart failure. Whether cardiac ANS activation directly contributes to or merely accompanies LV remodeling remains an unresolved issue. Human and experimental data that directly link cardiac ANS activation to LV remodeling and worsening heart failure are first reviewed, including cardiac norepinephrine spillover. Alterations of beta adrenergic receptor signaling pathways are then addressed with emphasis on the mechanisms that may mediate the beneficial effect of beta adrenergic receptor blockade on LV remodeling. Lastly, alternative approaches to beta adrenergic receptor blockade for lessening cardiac ANS activation and reversing cardiac ANS-induced LV remodeling are discussed. A large body of work now links LV remodeling to cardiac ANS activation. However, the precise mechanisms that link cardiac ANS activation to LV remodeling are still to be fully understood. Fully understanding of these mechanisms may uncover new therapeutic approaches.
Collapse
|
18
|
Opazo F, Eiden L, Hansen L, Rohrbach F, Wengel J, Kjems J, Mayer G. Modular Assembly of Cell-targeting Devices Based on an Uncommon G-quadruplex Aptamer. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e251. [PMID: 26325628 PMCID: PMC4877450 DOI: 10.1038/mtna.2015.25] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/22/2015] [Indexed: 11/26/2022]
Abstract
Aptamers are valuable tools that provide great potential to develop cost-effective diagnostics and therapies in the biomedical field. Here, we report a novel DNA aptamer that folds into an unconventional G-quadruplex structure able to recognize and enter specifically into human Burkitt's lymphoma cells. We further optimized this aptamer to a highly versatile and stable minimized version. The minimized aptamer can be easily equipped with different functionalities like quantum dots, organic dyes, or even a second different aptamer domain yielding a bi-paratopic aptamer. Although the target molecule of the aptamer remains unknown, our microscopy and pharmacological studies revealed that the aptamer hijacks the clathrin-mediated endocytosis pathway for its cellular internalization. We conclude that this novel class of aptamers can be used as a modular tool to specifically deliver different cargoes into malignant cells. This work provides a thorough characterization of the aptamer and we expect that our strategy will pave the path for future therapeutic applications.
Collapse
Affiliation(s)
- Felipe Opazo
- Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Göttingen, Germany
| | - Laura Eiden
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Line Hansen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Falk Rohrbach
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Odense M, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| |
Collapse
|
19
|
Larsen MJ, Larsen SD, Fribley A, Grembecka J, Homan K, Mapp A, Haak A, Nikolovska-Coleska Z, Stuckey JA, Sun D, Sherman DH. The role of HTS in drug discovery at the University of Michigan. Comb Chem High Throughput Screen 2015; 17:210-30. [PMID: 24409957 DOI: 10.2174/1386207317666140109121546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/05/2013] [Accepted: 01/07/2014] [Indexed: 12/17/2022]
Abstract
High throughput screening (HTS) is an integral part of a highly collaborative approach to drug discovery at the University of Michigan. The HTS lab is one of four core centers that provide services to identify, produce, screen and follow-up on biomedical targets for faculty. Key features of this system are: protein cloning and purification, protein crystallography, small molecule and siRNA HTS, medicinal chemistry and pharmacokinetics. Therapeutic areas that have been targeted include anti-bacterial, metabolic, neurodegenerative, cardiovascular, anti-cancer and anti-viral. The centers work in a coordinated, interactive environment to affordably provide academic investigators with the technology, informatics and expertise necessary for successful drug discovery. This review provides an overview of these centers at the University of Michigan, along with case examples of successful collaborations with faculty.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - David H Sherman
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
20
|
Homan KT, Tesmer JJG. Molecular basis for small molecule inhibition of G protein-coupled receptor kinases. ACS Chem Biol 2015; 10:246-56. [PMID: 24984143 PMCID: PMC4301174 DOI: 10.1021/cb5003976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Small molecules that inhibit the protein kinase A, G, and C (AGC) family of serine/threonine kinases can exert profound effects on cell homeostasis and thereby regulate fundamental processes such as heart rate, blood pressure, and metabolism, but there is not yet a clinically approved drug in the United States selective for a member of this family. One subfamily of AGC kinases, the G protein-coupled receptor (GPCR) kinases (GRKs), initiates the desensitization of active GPCRs. Of these, GRK2 has been directly implicated in the progression of heart failure. Thus, there is great interest in the identification of GRK2-specific chemical probes that can be further developed into therapeutics. Herein, we compare crystal structures of small molecule inhibitors in complex with GRK2 to those of highly selective compounds in complex with Rho-associated coiled-coil containing kinase 1 (ROCK1), a closely related AGC kinase. This analysis suggests that reduced hydrogen-bond formation with the hinge of the kinase domain, occupation of the hydrophobic subsite, and, consequently, higher buried surface area are key drivers of potency and selectivity among GRK inhibitors.
Collapse
Affiliation(s)
- Kristoff T. Homan
- Life Sciences Institute,
Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John J. G. Tesmer
- Life Sciences Institute,
Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
21
|
Lennarz S, Heider E, Blind M, Mayer G. An aptamer to the MAP kinase insert region. ACS Chem Biol 2015; 10:320-7. [PMID: 25184543 DOI: 10.1021/cb5005756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Targeting functional, non-catalytic domains of protein kinases or other proteins is an emerging field in chemical biology research. Non-ATP competitive kinase inhibitors allow for the investigation of active-site independent functions, e.g., the biological role of protein-protein interactions. These inhibitors also serve as a starting point for developing novel therapeutic strategies. However, the identification of such inhibitors by means of conventional low molecular weight compounds represents a great challenge in modern drug discovery. Employing the mitogen-activated protein (MAP) kinase Erk2, we show that RNA aptamers have the capacity to be a novel, promising class of protein kinase inhibitors that can be applied to target individual subdomains and block domain specific functions without affecting kinase activity per se.
Collapse
Affiliation(s)
- Sabine Lennarz
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Elena Heider
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Michael Blind
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| |
Collapse
|
22
|
Tolle F, Wilke J, Wengel J, Mayer G. By-product formation in repetitive PCR amplification of DNA libraries during SELEX. PLoS One 2014; 9:e114693. [PMID: 25490402 PMCID: PMC4260880 DOI: 10.1371/journal.pone.0114693] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 11/12/2014] [Indexed: 11/20/2022] Open
Abstract
The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.
Collapse
Affiliation(s)
- Fabian Tolle
- LIMES Institute, University of Bonn, Bonn, Germany
| | - Julian Wilke
- LIMES Institute, University of Bonn, Bonn, Germany
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Günter Mayer
- LIMES Institute, University of Bonn, Bonn, Germany
- * E-mail:
| |
Collapse
|
23
|
Erdem A, Congur G. Voltammetric aptasensor combined with magnetic beads assay developed for detection of human activated protein C. Talanta 2014; 128:428-33. [PMID: 25059182 DOI: 10.1016/j.talanta.2014.04.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/25/2014] [Accepted: 04/29/2014] [Indexed: 01/08/2023]
Abstract
A sensitive and selective label free voltammetric aptasensor based on magnetic beads assay was performed for the first time in our study for monitoring of human activated protein C (APC), which is a serine protease (i.e., key enzyme of the protein C pathway). An amino modified DNA aptamer (DNA APT) was covalently immobilized onto the surface of carboxylated magnetic beads (MBs), and then, the specific interaction between DNA APT and its cognate protein, APC, was performed at the surface of MBs. Similarly a biotinylated DNA APT was immobilized onto the surface of streptavidin coated MBs. Before and after interaction process, the oxidation signal of guanine was measured at disposable pencil graphite electrode (PGE) surface in combination with differential pulse voltammetry (DPV) technique and accordingly, the decrease at the guanine signal was evaluated. The biomolecular recognition of APC was successfully achieved with a low detection limit found as 2.35 µg mL(-1) by using MB-COOH based assay. Moreover, the selectivity of this aptasensor assay was tested in the presence of numerous proteins and other biomolecules: protein C (PC), thrombin (THR), bovine serum albumin (BSA), factor Va (FVa) and chromogenic substrate (KS).
Collapse
Affiliation(s)
- Arzum Erdem
- Ege University, Faculty of Pharmacy, Analytical Chemistry Department, Bornova, 35100 Izmir, Turkey; Ege University, Graduate School of Natural and Applied Science, Biotechnology Department, Bornova, 35100 Izmir, Turkey.
| | - Gulsah Congur
- Ege University, Faculty of Pharmacy, Analytical Chemistry Department, Bornova, 35100 Izmir, Turkey; Ege University, Graduate School of Natural and Applied Science, Biotechnology Department, Bornova, 35100 Izmir, Turkey
| |
Collapse
|
24
|
Meyer C, Berg K, Eydeler-Haeder K, Lorenzen I, Grötzinger J, Rose-John S, Hahn U. Stabilized Interleukin-6 receptor binding RNA aptamers. RNA Biol 2013; 11:57-65. [PMID: 24440854 DOI: 10.4161/rna.27447] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Interleukin-6 (IL-6) is a multifunctional cytokine that is involved in the progression of various inflammatory diseases, such as rheumatoid arthritis and certain cancers; for example, multiple myeloma or hepatocellular carcinoma. To interfere with IL-6-dependent diseases, targeting IL-6 receptor (IL-6R)-presenting tumor cells using aptamers might be a valuable strategy to broaden established IL-6- or IL-6R-directed treatment regimens. Recently, we reported on the in vitro selection of RNA aptamers binding to the human IL-6 receptor (IL-6R) with nanomolar affinity. One aptamer, namely AIR-3A, was 19 nt in size and able to deliver bulky cargos into IL-6R-presenting cells. As AIR-3A is a natural RNA molecule, its use for in vivo applications might be limited due to its susceptibility to ubiquitous ribonucleases. Aiming at more robust RNA aptamers targeting IL-6R, we now report on the generation of stabilized RNA aptamers for potential in vivo applications. The new 2'-F-modified RNA aptamers bind to IL-6R via its extracellular portion with low nanomolar affinity comparable to the previously identified unmodified counterpart. Aptamers do not interfere with the IL-6 receptor complex formation. The work described here represents one further step to potentially apply stabilized IL-6R-binding RNA aptamers in IL-6R-connected diseases, like multiple myeloma and hepatocellular carcinoma.
Collapse
Affiliation(s)
- Cindy Meyer
- Laboratory of RNA Molecular Biology; Howard Hughes Medical Institute; The Rockefeller University; New York, NY USA
| | - Katharina Berg
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Katja Eydeler-Haeder
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute of Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| |
Collapse
|
25
|
Structural insights into G protein-coupled receptor kinase function. Curr Opin Cell Biol 2013; 27:25-31. [PMID: 24680427 DOI: 10.1016/j.ceb.2013.10.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/20/2022]
Abstract
The atomic structure of a protein can greatly advance our understanding of molecular recognition and catalysis, properties of fundamental importance in signal transduction. However, a single structure is incapable of fully describing how a protein functions, particularly when allostery is involved. Recent advances in the structure and function of G protein-coupled receptor (GPCR) kinases (GRKs) have concentrated on the mechanism of their inhibition by small and large molecules. These studies have generated a wealth of new information on the conformational flexibility of these enzymes, which opens new avenues for the development of selective chemical probes and provides deeper insights into the molecular basis for activation of these enzymes by GPCRs and phospholipids.
Collapse
|
26
|
Cannavo A, Liccardo D, Koch WJ. Targeting cardiac β-adrenergic signaling via GRK2 inhibition for heart failure therapy. Front Physiol 2013; 4:264. [PMID: 24133451 PMCID: PMC3783981 DOI: 10.3389/fphys.2013.00264] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/06/2013] [Indexed: 12/23/2022] Open
Abstract
Cardiac cells, like those of the other tissues, undergo regulation through membrane-bound proteins known as G protein-coupled receptors (GPCRs). β-adrenergic receptors (βARs) are key GPCRs expressed on cardiomyocytes and their role is crucial in cardiac physiology since they regulate inotropic and chronotropic responses of the sympathetic nervous system (SNS). In compromised conditions such as heart failure (HF), chronic βAR hyperstimulation occurs via SNS activation resulting in receptor dysregulation and down-regulation and consequently there is a marked reduction of myocardial inotropic reserve and continued loss of pump function. Data accumulated over the last two decades indicates that a primary culprit in initiating and maintain βAR dysfunction in the injured and stressed heart is GPCR kinase 2 (GRK2), which was originally known as βARK1 (for βAR kinase). GRK2 is up-regulated in the failing heart due to chronic SNS activity and targeting this kinase has emerged as a novel therapeutic strategy in HF. Indeed, its inhibition or genetic deletion in several disparate animal models of HF including a pre-clinical pig model has shown that GRK2 targeting improves functional and morphological parameters of the failing heart. Moreover, non-βAR properties of GRK2 appear to also contribute to its pathological effects and thus, its inhibition will likely complement existing therapies such as βAR blockade. This review will explore recent research regarding GRK2 inhibition; in particular it will focus on the GRK2 inhibitor peptide known as βARKct, which represents new hope in the treatment against HF progression.
Collapse
Affiliation(s)
- Alessandro Cannavo
- Center for Translational Medicine, Department of Pharmacology, Temple UniversityPhiladelphia, PA, USA
| | - Daniela Liccardo
- Division of Geriatrics, Department of Translational Medical Sciences, Federico II University of NaplesNaples, Italy
| | - Walter J. Koch
- Center for Translational Medicine, Department of Pharmacology, Temple UniversityPhiladelphia, PA, USA
| |
Collapse
|
27
|
Carotenuto A, Cipolletta E, Gomez-Monterrey I, Sala M, Vernieri E, Limatola A, Bertamino A, Musella S, Sorriento D, Grieco P, Trimarco B, Novellino E, Iaccarino G, Campiglia P. Design, synthesis and efficacy of novel G protein-coupled receptor kinase 2 inhibitors. Eur J Med Chem 2013; 69:384-92. [PMID: 24077529 DOI: 10.1016/j.ejmech.2013.08.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/19/2013] [Accepted: 08/22/2013] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptor kinase 2 (GRK2) is a relevant signaling node of the cellular transduction network, playing major roles in the physiology of various organs/tissues including the heart and blood vessels. Emerging evidence suggests that GRK2 is up regulated in pathological situations such as heart failure, hypertrophy and hypertension, and its inhibition offers a potential therapeutic solution to these diseases. We explored the GRK2 inhibitory activity of a library of cyclic peptides derived from the HJ loop of G protein-coupled receptor kinases 2 (GRK2). The design of these cyclic compounds was based on the conformation of the HJ loop within the X-ray structure of GRK2. One of these compounds, the cyclic peptide 7, inhibited potently and selectively the GRK2 activity, being more active than its linear precursor. In a cellular system, this peptide confirms the beneficial signaling properties of a potent GRK2 inhibitor. Preferred conformations of the most potent analog were investigated by NMR spectroscopy.
Collapse
|
28
|
Magbanua E, Zivkovic T, Hansen B, Beschorner N, Meyer C, Lorenzen I, Grötzinger J, Hauber J, Torda AE, Mayer G, Rose-John S, Hahn U. d(GGGT) 4 and r(GGGU) 4 are both HIV-1 inhibitors and interleukin-6 receptor aptamers. RNA Biol 2013; 10:216-27. [PMID: 23235494 PMCID: PMC3594281 DOI: 10.4161/rna.22951] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aptamers are oligonucleotides that bind targets with high specificity and affinity. They have become important tools for biosensing, target detection, drug delivery and therapy. We selected the quadruplex-forming 16-mer DNA aptamer AID-1 [d(GGGT) 4] with affinity for the interleukin-6 receptor (IL-6R) and identified single nucleotide variants that showed no significant loss of binding ability. The RNA counterpart of AID-1 [r(GGGU) 4] also bound IL-6R as quadruplex structure. AID-1 is identical to the well-known HIV inhibitor T30923, which inhibits both HIV infection and HIV-1 integrase. We also demonstrated that IL-6R specific RNA aptamers not only bind HIV-1 integrase and inhibit its 3' processing activity in vitro, but also are capable of preventing HIV de novo infection with the same efficacy as the established inhibitor T30175. All these aptamer target interactions are highly dependent on formation of quadruplex structure.
Collapse
Affiliation(s)
- Eileen Magbanua
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Tijana Zivkovic
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Björn Hansen
- Centre for Bioinformatics; Hamburg University; Hamburg, Germany
| | - Niklas Beschorner
- Heinrich Pette Institute; Leibnitz Institute for Experimental Virology; Hamburg, Germany
| | - Cindy Meyer
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Hauber
- Heinrich Pette Institute; Leibnitz Institute for Experimental Virology; Hamburg, Germany
| | - Andrew E. Torda
- Centre for Bioinformatics; Hamburg University; Hamburg, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute; University of Bonn; Bonn, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
- Correspondence to: Ulrich Hahn,
| |
Collapse
|
29
|
Thal DM, Homan KT, Chen J, Wu EK, Hinkle PM, Huang ZM, Chuprun JK, Song J, Gao E, Cheung JY, Sklar LA, Koch WJ, Tesmer JJ. Paroxetine is a direct inhibitor of g protein-coupled receptor kinase 2 and increases myocardial contractility. ACS Chem Biol 2012; 7:1830-9. [PMID: 22882301 DOI: 10.1021/cb3003013] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptor kinase 2 (GRK2) is a well-established therapeutic target for the treatment of heart failure. Herein we identify the selective serotonin reuptake inhibitor (SSRI) paroxetine as a selective inhibitor of GRK2 activity both in vitro and in living cells. In the crystal structure of the GRK2·paroxetine-Gβγ complex, paroxetine binds in the active site of GRK2 and stabilizes the kinase domain in a novel conformation in which a unique regulatory loop forms part of the ligand binding site. Isolated cardiomyocytes show increased isoproterenol-induced shortening and contraction amplitude in the presence of paroxetine, and pretreatment of mice with paroxetine before isoproterenol significantly increases left ventricular inotropic reserve in vivo with no significant effect on heart rate. Neither is observed in the presence of the SSRI fluoxetine. Our structural and functional results validate a widely available drug as a selective chemical probe for GRK2 and represent a starting point for the rational design of more potent and specific GRK2 inhibitors.
Collapse
Affiliation(s)
- David M. Thal
- Life Sciences
Institute and
the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristoff T. Homan
- Life Sciences
Institute and
the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jun Chen
- Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque,
New Mexico 87131, United States
| | - Emily K. Wu
- Life Sciences
Institute and
the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Patricia M. Hinkle
- Department of Pharmacology and
Physiology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Z. Maggie Huang
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - J. Kurt Chuprun
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - Jianliang Song
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - Erhe Gao
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - Joseph Y. Cheung
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - Larry A. Sklar
- Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque,
New Mexico 87131, United States
| | - Walter J. Koch
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia,
Pennsylvania 19140, United States
| | - John J.G. Tesmer
- Life Sciences
Institute and
the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
30
|
Mondragon E, Maher L. An Ace in the Hole... Structure 2012; 20:1285-6. [DOI: 10.1016/j.str.2012.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
31
|
Tesmer VM, Lennarz S, Mayer G, Tesmer JJG. Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer. Structure 2012; 20:1300-9. [PMID: 22727813 DOI: 10.1016/j.str.2012.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 04/17/2012] [Accepted: 05/02/2012] [Indexed: 11/27/2022]
Abstract
Cardiovascular homeostasis is maintained in part by the rapid desensitization of activated heptahelical receptors that have been phosphorylated by G protein-coupled receptor kinase 2 (GRK2). However, during chronic heart failure GRK2 is upregulated and believed to contribute to disease progression. We have determined crystallographic structures of GRK2 bound to an RNA aptamer that potently and selectively inhibits kinase activity. Key to the mechanism of inhibition is the positioning of an adenine nucleotide into the ATP-binding pocket and interactions with the basic αF-αG loop region of the GRK2 kinase domain. Constraints imposed on the RNA by the terminal stem of the aptamer also play a role. These results highlight how a high-affinity aptamer can be used to selectively trap a novel conformational state of a protein kinase.
Collapse
Affiliation(s)
- Valerie M Tesmer
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA.
| | | | | | | |
Collapse
|
32
|
Meyer C, Eydeler K, Magbanua E, Zivkovic T, Piganeau N, Lorenzen I, Grötzinger J, Mayer G, Rose-John S, Hahn U. Interleukin-6 receptor specific RNA aptamers for cargo delivery into target cells. RNA Biol 2012; 9:67-80. [PMID: 22258147 PMCID: PMC3342945 DOI: 10.4161/rna.9.1.18062] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aptamers represent an emerging strategy to deliver cargo molecules, including dyes, drugs, proteins or even genes, into specific target cells. Upon binding to specific cell surface receptors aptamers can be internalized, for example by macropinocytosis or receptor mediated endocytosis. Here we report the in vitro selection and characterization of RNA aptamers with high affinity (Kd = 20 nM) and specificity for the human IL-6 receptor (IL-6R). Importantly, these aptamers trigger uptake without compromising the interaction of IL-6R with its natural ligands the cytokine IL-6 and glycoprotein 130 (gp130). We further optimized the aptamers to obtain a shortened, only 19-nt RNA oligonucleotide retaining all necessary characteristics for high affinity and selective recognition of IL-6R on cell surfaces. Upon incubation with IL-6R presenting cells this aptamer was rapidly internalized. Importantly, we could use our aptamer, to deliver bulky cargos, exemplified by fluorescently labeled streptavidin, into IL-6R presenting cells, thereby setting the stage for an aptamer-mediated escort of drug molecules to diseased cell populations or tissues.
Collapse
Affiliation(s)
- Cindy Meyer
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Katja Eydeler
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Eileen Magbanua
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Tijana Zivkovic
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Nicolas Piganeau
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| | - Inken Lorenzen
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Joachim Grötzinger
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute; University of Bonn; Bonn, Germany
| | - Stefan Rose-John
- Institute of Biochemistry; Medical Faculty; Christian-Albrechts-University; Kiel, Germany
| | - Ulrich Hahn
- Institute for Biochemistry and Molecular Biology; Chemistry Department; MIN-Faculty; Hamburg University; Hamburg, Germany
| |
Collapse
|
33
|
Abstract
Aptamers that target a specific cell subpopulation within composite mixtures represent invaluable tools in biomedical research and in the development of cell-specific therapeutics. Here we describe a detailed protocol for a modular and generally applicable scheme to select aptamers that target the subpopulations of cells in which you are interested. A fluorescence-activated cell-sorting device is used to simultaneously differentiate and separate those subpopulations of cells having bound and unbound aptamers. There are fewer false positives when using this approach in comparison with other cell-selection approaches in which unspecific binding of nucleic acids to cells with reduced membrane integrity or their unselective uptake by dead cells occurs more often. The protocol provides a state-of-the-art approach for identifying aptamers that selectively target virtually any cell type under investigation. As an example, we provide the step-by-step protocol targeting CD19(+) Burkitt's lymphoma cells, starting from the pre-SELEX (systematic evolution of ligands by exponential amplification) measurements to establish suitable SELEX conditions and ending at completion of the SELEX procedure, which reveals the enriched single-stranded DNA library.
Collapse
|
34
|
Penela P, Murga C, Ribas C, Lafarga V, Mayor F. The complex G protein-coupled receptor kinase 2 (GRK2) interactome unveils new physiopathological targets. Br J Pharmacol 2010; 160:821-32. [PMID: 20590581 DOI: 10.1111/j.1476-5381.2010.00727.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
GRK2 is a ubiquitous member of the G protein-coupled receptor kinase (GRK) family that appears to play a central, integrative role in signal transduction cascades. GRKs participate together with arrestins in the regulation of G protein-coupled receptors (GPCR), a family of hundreds of membrane proteins of key physiological and pharmacological importance, by triggering receptor desensitization from G proteins and GPCR internalization, and also by helping assemble macromolecular signalosomes in the receptor environment acting as agonist-regulated adaptor scaffolds, thus contributing to signal propagation. In addition, emerging evidence indicates that GRK2 can phosphorylate a growing number of non-GPCR substrates and associate with a variety of proteins related to signal transduction, thus suggesting that this kinase could also have diverse 'effector' functions. We discuss herein the increasing complexity of such GRK2 'interactome', with emphasis on the recently reported roles of this kinase in cell migration and cell cycle progression and on the functional impact of the altered GRK2 levels observed in several relevant cardiovascular, inflammatory or tumour pathologies. Deciphering how the different networks of potential GRK2 functional interactions are orchestrated in a stimulus, cell type or context-specific way is critical to unveil the contribution of GRK2 to basic cellular processes, to understand how alterations in GRK2 levels or functionality may participate in the onset or development of several cardiovascular, tumour or inflammatory diseases, and to assess the feasibility of new therapeutic strategies based on the modulation of the activity, levels or specific interactions of GRK2.
Collapse
Affiliation(s)
- Petronila Penela
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Universidad Autónoma, Madrid, Spain
| | | | | | | | | |
Collapse
|
35
|
Lünse CE, Michlewski G, Hopp CS, Rentmeister A, Cáceres JF, Famulok M, Mayer G. An aptamer targeting the apical-loop domain modulates pri-miRNA processing. Angew Chem Int Ed Engl 2010; 49:4674-7. [PMID: 20533473 DOI: 10.1002/anie.200906919] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Christina E Lünse
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Strasse 1, Bonn, Germany
| | | | | | | | | | | | | |
Collapse
|
36
|
Lünse C, Michlewski G, Hopp C, Rentmeister A, Cáceres J, Famulok M, Mayer G. Modulation der pri-miRNA-Reifung durch ein die apikale Schleife bindendes Aptamer. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
37
|
Ahmed MSL, Mayer G. Evolution of specific RNA motifs derived from pan-protein interacting precursors. Bioorg Med Chem Lett 2010; 20:3793-6. [PMID: 20471261 DOI: 10.1016/j.bmcl.2010.04.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 11/24/2022]
Abstract
In vitro evolution of nucleic acid aptamers is a powerful tool to investigate the structure-function relationship of natural occurring RNA-protein interaction motifs. Otherwise, it also allows the identification of novel RNA-based ligands that can be used to investigate a target's function in its native environment. However, artifacts have been described during in vitro selection procedures hampering the successful enrichment of aptamers. Here we describe a novel observation, namely the enrichment of pan-protein binding RNA sequences. We demonstrate that evolution of specific target binding sequences originating from a pan-protein binding RNA precursor is possible in general. Our data demonstrate that the mutual co-variation of an ancestor molecule can be applied for the evolution of specific target binding RNA sequences. These results might have implications in the context of the RNA world theory, exemplifying a possible evolutionary route towards protein-specific RNA molecules from a common ancestor.
Collapse
Affiliation(s)
- Marie-Sophie L Ahmed
- Strathclyde Institute for Pharmacy and Biological Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | | |
Collapse
|
38
|
Murga C, Penela P, Ribas C, Mayor F. G protein-coupled receptor kinases: Specific phosphorylation of 7TM receptors and beyond. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e1-e94. [PMID: 24103684 DOI: 10.1016/j.ddtec.2010.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
39
|
Mayer G, Lohberger A, Butzen S, Pofahl M, Blind M, Heckel A. From selection to caged aptamers: identification of light-dependent ssDNA aptamers targeting cytohesin. Bioorg Med Chem Lett 2009; 19:6561-4. [PMID: 19854646 DOI: 10.1016/j.bmcl.2009.10.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/07/2009] [Accepted: 10/07/2009] [Indexed: 11/25/2022]
Abstract
Caged aptamers represent valuable tools for the spatiotemporal control of protein function by light. Here we describe a general route starting with the de novo selection process targeting cytohesin-1 and aiming at the synthesis of caged aptamers without the prior knowledge of detailed structural determinants of aptamer-target binding.
Collapse
Affiliation(s)
- Günter Mayer
- Strathclyde Institute for Pharmacy and Biological Sciences, University of Strathclyde, Glasgow G4 0NR, Scotland, United Kingdom.
| | | | | | | | | | | |
Collapse
|
40
|
Hunsicker A, Steber M, Mayer G, Meitert J, Klotzsche M, Blind M, Hillen W, Berens C, Suess B. An RNA aptamer that induces transcription. ACTA ACUST UNITED AC 2009; 16:173-80. [PMID: 19246008 DOI: 10.1016/j.chembiol.2008.12.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/12/2008] [Accepted: 12/15/2008] [Indexed: 11/16/2022]
Abstract
We identified an RNA aptamer that induces TetR-controlled gene expression in Escherichia coli when expressed in the cell. The aptamer was found by a combined approach of in vitro selection for TetR binding and in vivo screening for TetR induction. The smallest active aptamer folds into a stem-loop with an internal loop interrupting the stem. Mutational analysis in vivo and in-line probing in vitro reveal this loop to be the protein binding site. The TetR-inducing activity of the aptamer directly correlates with its stability and the best construct is as efficient as the natural inducer tetracycline. Because of its small size, high induction efficiency, and the stability of the TetR aptamer under in vivo conditions, it is well suited to be an alternative RNA-based inducer of TetR-controlled gene expression.
Collapse
Affiliation(s)
- Anke Hunsicker
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Erdem A, Karadeniz H, Mayer G, Famulok M, Caliskan A. Electrochemical Sensing of Aptamer-Protein Interactions Using a Magnetic Particle Assay and Single-Use Sensor Technology. ELECTROANAL 2009. [DOI: 10.1002/elan.200804557] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
42
|
Abstract
Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.
Collapse
Affiliation(s)
- Günter Mayer
- Life and Medical Sciences, Prog. Unit Chemical Biology and Medicinal Chemistry, University of Bonn c/o Kekulé-Institute for Organic Chemistry and Biochemistry, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| |
Collapse
|
43
|
|
44
|
Mayer G, Höver T. In vitro selection of ssDNA aptamers using biotinylated target proteins. Methods Mol Biol 2009; 535:19-32. [PMID: 19377986 DOI: 10.1007/978-1-59745-557-2_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aptamers are single-stranded nucleic acids that bind specifically to a target molecule and thus often inhibit target-associated biological functions. Aptamers have been described for a series of target molecules including peptides, proteins, and even living cells. Besides RNA and 20-modified RNA molecules also ssDNA molecules can be subjected to in vitro selection protocols aiming at the enrichment of ssDNA aptamers. ssDNA aptamers can be selected using the SELEX procedure (systematic enrichment of ligands by exponential amplification) from libraries of randomized single-stranded DNA with a diversity of up to 10(16) different molecules. In repetitive selection cycles, the library is incubated with the target of choice and separation of non-binding sequences from bound sequences is achieved by distinct separation methods. The bound molecules are specifically eluted and amplified, thus representing the starting library for the next cycle. Thereby, an enriched population of aptamers is evolved. Here we describe a generalized in vitro selection experiment aiming at the enrichment of ssDNA aptamers using biotinylated target molecules. This procedure allows the application of streptavidin-biotin chemistry to separate bound from unbound DNA species during the selection process.
Collapse
|