Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer.

Published on Oct 17, 2018in Nucleic Acids Research11.147
· DOI :10.2210/pdb6evv/pdb
Romualdo Troisi2
Estimated H-index: 2
(University of Naples Federico II),
Valeria Napolitano3
Estimated H-index: 3
(University of Naples Federico II)
+ 2 AuthorsFilomena Sica25
Estimated H-index: 25
(University of Naples Federico II)
: Despite aptamers are very promising alternative to antibodies, very few of them are under clinical trials or are used as drugs. Among them, NU172 is currently in Phase II as anticoagulant in heart disease treatments. It inhibits thrombin activity much more effectively than TBA, the best-known thrombin binding aptamer. The crystal structure of thrombin-NU172 complex reveals a bimodular duplex/quadruplex architecture for the aptamer, which binds thrombin exosite I through a highly complementary surface involving all three loops of the G-quadruplex module. Although the duplex domain does not interact directly with thrombin, the features of the duplex/quadruplex junction and the solution data on two newly designed NU172 mutants indicate that the duplex moiety is important for the optimization of the protein-ligand interaction and for the inhibition of the enzyme activity. Our work discloses the structural features determining the inhibition of thrombin by NU172 and put the basis for the design of mutants with improved properties.
  • References (51)
  • Citations (3)
📖 Papers frequently viewed together
20112.78PLOS ONE
28 Citations
64 Citations
20132.78PLOS ONE
12 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#1Rafał Dolot (PAN: Polish Academy of Sciences)H-Index: 6
#2Curtis H. LamH-Index: 10
Last. Xianbin YangH-Index: 14
view all 8 authors...
: Thrombin-binding aptamer (TBA) is a DNA 15-mer of sequence 5'-GGT TGG TGT GGT TGG-3' that folds into a G-quadruplex structure linked by two T-T loops located on one side and a T-G-T loop on the other. These loops are critical for post-SELEX modification to improve TBA target affinity. With this goal in mind we synthesized a T analog, 5-(indolyl-3-acetyl-3-amino-1-propenyl)-2'-deoxyuridine (W) to substitute one T or a pair of Ts. Subsequently, the affinity for each analog was determined by biol...
6 CitationsSource
#1Ali A. Mokdad (UW: University of Washington)H-Index: 100
#2Katherine Ballestros (UW: University of Washington)H-Index: 1
Last. Christopher Margono (UW: University of Washington)H-Index: 175
view all 115 authors...
Introduction Several studies have measured health outcomes in the United States, but none have provided a comprehensive assessment of patterns of health by state. Objective To use the results of the Global Burden of Disease Study (GBD) to report trends in the burden of diseases, injuries, and risk factors at the state level from 1990 to 2016. Design and Setting A systematic analysis of published studies and available data sources estimates the burden of disease by age, sex, geography, and year. ...
146 CitationsSource
#1Irene Russo Krauss (University of Naples Federico II)H-Index: 16
#2Valeria Napolitano (University of Naples Federico II)H-Index: 3
Last. Filomena Sica (University of Naples Federico II)H-Index: 25
view all 7 authors...
Abstract Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesize...
9 CitationsSource
Progress in understanding and treatment of thrombotic diseases requires new effective methods for the easy, rapid, and reversible control of coagulation processes. In this framework, the use of aptamers, and particularly of the thrombin binding aptamer (TBA), has aroused strong interest, due to its enormous therapeutic potential, associated with a large number of possible applications in biotechnological and bioanalytical fields. Here, we describe a new TBA analogue (named tris-mTBA), carrying t...
12 CitationsSource
Nucleic acid aptamers offer several advantages over traditional antibodies, but their clinical translation has been delayed by several factors, including insufficient potency, lack of safety data and high production costs. Here, Zhou and Rossi provide an overview of aptamer generation, focusing on recent technological advances and clinical development, as well as challenges and lessons learned.
260 CitationsSource
#1Andrea Pica (University of Naples Federico II)H-Index: 14
#2Irene Russo Krauss (University of Naples Federico II)H-Index: 16
Last. Filomena Sica (University of Naples Federico II)H-Index: 25
view all 8 authors...
Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two tern...
16 CitationsSource
Aptamers are single-stranded nucleic acid molecules that bind to and inhibit proteins and are commonly produced by systematic evolution of ligands by exponential enrichment (SELEX). Aptamers undergo extensive pharmacological revision, which alters affinity, specificity, and therapeutic half-life, tailoring each drug for a specific clinical need. The first therapeutic aptamer was described 25 years ago. Thus far, one aptamer has been approved for clinical use, and numerous others are in preclinic...
64 CitationsSource
#1Juan David Ospina-Villa (IPN: Instituto Politécnico Nacional)H-Index: 7
#2Absalom Zamorano-Carrillo (IPN: Instituto Politécnico Nacional)H-Index: 6
Last. Laurence A. Marchat (IPN: Instituto Politécnico Nacional)H-Index: 17
view all 5 authors...
Abstract Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptam...
5 CitationsSource
#1Elena Zavyalova (MSU: Moscow State University)H-Index: 8
#2N. B. UstinovH-Index: 2
Last. Alexey KopylovH-Index: 13
view all 5 authors...
Thrombin is a key enzyme of blood coagulation system which has multiple functions including pro- and anticoagulant, platelet aggregating and inflammatory activities. Unsurprisingly, this enzyme has been a target for anticoagulant drug development for decades. Among the most interesting direct thrombin inhibitors with intravenous administration route are the following ones: 1) hirudins, proteins with bivalent binding mode to the thrombin, 2) bivalirudin, the peptide with bivalent binding mode to ...
11 CitationsSource
#1Aaron M. Wendelboe (University of Oklahoma Health Sciences Center)H-Index: 19
#2Gary E. Raskob (University of Oklahoma Health Sciences Center)H-Index: 75
Thromboembolic conditions were estimated to account for 1 in 4 deaths worldwide in 2010 and are the leading cause of mortality. Thromboembolic conditions are divided into arterial and venous thrombotic conditions. Ischemic heart disease and ischemic stroke comprise the major arterial thromboses and deep-vein thrombosis and pulmonary embolism comprise venous thromboembolism. Atrial fibrillation is a major risk factor for stroke and systemic arterial thromboembolism. Estimates of the global burden...
64 CitationsSource
Cited By3
#1Claudia Riccardi (University of Naples Federico II)H-Index: 8
#2Albert Meyer (University of Montpellier)H-Index: 22
Last. Daniela Montesarchio (University of Naples Federico II)H-Index: 25
view all 7 authors...
Abstract A small library of cyclic TBA analogues (named cycTBA I-IV), obtained by covalently connecting its 5′- and 3′-ends with flexible linkers, has been synthesized with the aim of improving its chemical and enzymatic stability, as well as its anticoagulant properties. Two chemical procedures have been exploited to achieve the desired cyclization, based on the oxime ligation method (providing cycTBA I and II) or on Cu(I)-assisted azide-alkyne cycloaddition (CuAAC) protocols (for cycTBA III an...
2 CitationsSource
#1S. K. Haßel (University of Bonn)H-Index: 1
#2G. Mayer (University of Bonn)H-Index: 1
Aptamers are synthetic DNA or RNA oligonucleotide ligands with great potential for therapeutic applications. A vast number of disease-related targets have been used to identify agonistic, antagonistic, or inhibitory aptamers, or aptamer-based targeting ligands. However, only a few aptamers have reached late-stage clinical trials so far and the commercial infrastructure is still far behind that of other therapeutic agents such as monoclonal antibodies. The desirable properties of aptamers such as...
1 CitationsSource
#1Claudia Riccardi (University of Naples Federico II)H-Index: 8
#2Albert Meyer (University of Montpellier)H-Index: 22
Last. Daniela Montesarchio (University of Naples Federico II)H-Index: 25
view all 9 authors...
: With the aim of developing a new approach to obtain improved aptamers, a cyclic thrombin-binding aptamer (TBA) analogue (cycTBA) has been prepared by exploiting a copper(I)-assisted azide-alkyne cycloaddition. The markedly increased serum resistance and exceptional thermal stability of the G-quadruplex versus TBA were associated with halved thrombin inhibition, which suggested that some flexibility in the TBA structure was necessary for protein recognition.
1 CitationsSource