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He Q, Wei Y, Qian Y, Zhong M. Pathophysiological dynamics in the contact, coagulation, and complement systems during sepsis: Potential targets for nafamostat mesilate. JOURNAL OF INTENSIVE MEDICINE 2024; 4:453-467. [PMID: 39310056 PMCID: PMC11411436 DOI: 10.1016/j.jointm.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 09/25/2024]
Abstract
Sepsis is a life-threatening syndrome resulting from a dysregulated host response to infection. It is the primary cause of death in the intensive care unit, posing a substantial challenge to human health and medical resource allocation. The pathogenesis and pathophysiology of sepsis are complex. During its onset, pro-inflammatory and anti-inflammatory mechanisms engage in intricate interactions, possibly leading to hyperinflammation, immunosuppression, and long-term immune disease. Of all critical outcomes, hyperinflammation is the main cause of early death among patients with sepsis. Therefore, early suppression of hyperinflammation may improve the prognosis of these patients. Nafamostat mesilate is a serine protease inhibitor, which can inhibit the activation of the complement system, coagulation system, and contact system. In this review, we discuss the pathophysiological changes occurring in these systems during sepsis, and describe the possible targets of the serine protease inhibitor nafamostat mesilate in the treatment of this condition.
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Affiliation(s)
- Qiaolan He
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yilin Wei
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiqi Qian
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Zhong
- Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Lung Inflammation and Injury, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
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2
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Xu X, Herdendorf TJ, Duan H, Rohlik DL, Roy S, Zhou H, Alkhateeb H, Khandelwal S, Zhou Q, Li P, Arepally GM, Walker JK, Garcia BL, Geisbrecht BV. Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl)Pyridine-3-Carboximidamide and Chemical Analogs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:689-701. [PMID: 38149922 PMCID: PMC10872613 DOI: 10.4049/jimmunol.2300630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The classical pathway (CP) is a potent mechanism for initiating complement activity and is a driver of pathology in many complement-mediated diseases. The CP is initiated via activation of complement component C1, which consists of the pattern recognition molecule C1q bound to a tetrameric assembly of proteases C1r and C1s. Enzymatically active C1s provides the catalytic basis for cleavage of the downstream CP components, C4 and C2, and is therefore an attractive target for therapeutic intervention in CP-driven diseases. Although an anti-C1s mAb has been Food and Drug Administration approved, identifying small-molecule C1s inhibitors remains a priority. In this study, we describe 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide (A1) as a selective, competitive inhibitor of C1s. A1 was identified through a virtual screen for small molecules that interact with the C1s substrate recognition site. Subsequent functional studies revealed that A1 dose-dependently inhibits CP activation by heparin-induced immune complexes, CP-driven lysis of Ab-sensitized sheep erythrocytes, CP activation in a pathway-specific ELISA, and cleavage of C2 by C1s. Biochemical experiments demonstrated that A1 binds directly to C1s with a Kd of ∼9.8 μM and competitively inhibits its activity with an inhibition constant (Ki) of ∼5.8 μM. A 1.8-Å-resolution crystal structure revealed the physical basis for C1s inhibition by A1 and provided information on the structure-activity relationship of the A1 scaffold, which was supported by evaluating a panel of A1 analogs. Taken together, our work identifies A1 as a new class of small-molecule C1s inhibitor and lays the foundation for development of increasingly potent and selective A1 analogs for both research and therapeutic purposes.
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Affiliation(s)
- Xin Xu
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Timothy J. Herdendorf
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Huiquan Duan
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Denise L. Rohlik
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Sourav Roy
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Hinman Zhou
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
| | - Haya Alkhateeb
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
| | - Sanjay Khandelwal
- Division of Hematology, Duke University Medical Center; Durham, NC 27710 U.S.A
| | - Qilong Zhou
- Department of Chemistry, Kansas State University; Manhattan, KS 66506 U.S.A
| | - Ping Li
- Department of Chemistry, Kansas State University; Manhattan, KS 66506 U.S.A
| | | | - John K. Walker
- Department of Pharmacology, School of Medicine, St. Louis University; St. Louis, MO 63104 U.S.A
- Department of Chemistry, St. Louis University; St. Louis, MO 63103 U.S.A
| | - Brandon L. Garcia
- Department of Microbiology & Immunology, Brody School of Medicine East Carolina University; Greenville, NC 27834 U.S.A
| | - Brian V. Geisbrecht
- Department of Biochemistry & Molecular Biophysics, Kansas State University; Manhattan, KS 66506 U.S.A
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3
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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4
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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Ziemka-Nalecz M, Pawelec P, Ziabska K, Zalewska T. Sex Differences in Brain Disorders. Int J Mol Sci 2023; 24:14571. [PMID: 37834018 PMCID: PMC10572175 DOI: 10.3390/ijms241914571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
A remarkable feature of the brain is its sexual dimorphism. Sexual dimorphism in brain structure and function is associated with clinical implications documented previously in healthy individuals but also in those who suffer from various brain disorders. Sex-based differences concerning some features such as the risk, prevalence, age of onset, and symptomatology have been confirmed in a range of neurological and neuropsychiatric diseases. The mechanisms responsible for the establishment of sex-based differences between men and women are not fully understood. The present paper provides up-to-date data on sex-related dissimilarities observed in brain disorders and highlights the most relevant features that differ between males and females. The topic is very important as the recognition of disparities between the sexes might allow for the identification of therapeutic targets and pharmacological approaches for intractable neurological and neuropsychiatric disorders.
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Affiliation(s)
| | | | | | - Teresa Zalewska
- NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5, A. Pawinskiego Str., 02-106 Warsaw, Poland; (M.Z.-N.); (P.P.); (K.Z.)
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6
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Lu S, Fowler CR, Ream B, Waugh SM, Russell TM, Rohloff JC, Gold L, Cleveland JP, Stoll S. Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers. ACS Sens 2023; 8:2219-2227. [PMID: 37300508 DOI: 10.1021/acssensors.3c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.
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Affiliation(s)
- Shutian Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Brian Ream
- SomaLogic, Boulder, Colorado 80301, United States
| | | | | | | | - Larry Gold
- SomaLogic, Boulder, Colorado 80301, United States
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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7
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Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK. Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules 2023; 28:4645. [PMID: 37375202 PMCID: PMC10303109 DOI: 10.3390/molecules28124645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to human society through its high virulence, infectivity, and genomic mutations, which reduced the efficacy of vaccines. Here, we report the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a pivotal role in host cell entry of the virus through interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2). To develop highly effective aptamers and to understand their mechanism in inhibiting viral infection, we determined the three-dimensional (3D) structures of aptamer/receptor-binding domain (RBD) complexes using cryogenic electron microscopy (cryo-EM). Moreover, we developed bivalent aptamers targeting two distinct regions of the RBD in the spike protein that directly interact with ACE2. One aptamer interferes with the binding of ACE2 by blocking the ACE2-binding site in RBD, and the other aptamer allosterically inhibits ACE2 by binding to a distinct face of RBD. Using the 3D structures of aptamer-RBD complexes, we minimized and optimized these aptamers. By combining the optimized aptamers, we developed a bivalent aptamer that showed a stronger inhibitory effect on virus infection than the component aptamers. This study confirms that the structure-based aptamer-design approach has a high potential in developing antiviral drugs against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Md Shafiqur Rahman
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Min Jung Han
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Sang Won Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Seong Mu Kang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Bo Ri Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Heesun Kim
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Chang Jun Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Jung Eun Noh
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Hanseong Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Jie-Oh Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea; (M.S.R.); (M.J.H.); (S.W.K.)
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
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Laich A, Patel H, Zarantonello A, Sim R, Inal J. C2 by-pass: cross-talk between the complement classical and alternative pathways. Immunobiology 2022; 227:152225. [DOI: 10.1016/j.imbio.2022.152225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
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Pundir M, Papagerakis S, De Rosa MC, Chronis N, Kurabayashi K, Abdulmawjood S, Prince MEP, Lobanova L, Chen X, Papagerakis P. Emerging biotechnologies for evaluating disruption of stress, sleep, and circadian rhythm mechanism using aptamer-based detection of salivary biomarkers. Biotechnol Adv 2022; 59:107961. [DOI: 10.1016/j.biotechadv.2022.107961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2022] [Accepted: 04/09/2022] [Indexed: 12/26/2022]
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10
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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