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He A, Wan L, Zhang Y, Yan Z, Guo P, Han D, Tan W. Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization. Proc Natl Acad Sci U S A 2024; 121:e2404060121. [PMID: 38985770 PMCID: PMC11260122 DOI: 10.1073/pnas.2404060121] [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: 02/26/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures. Moreover, the experimentally determined 3D structures of DNA molecules with exquisite functions remain scarce. These factors impede our comprehension and optimization of some important DNA aptamers. Here, we performed a streamlined solution NMR-based structural investigation on the 41-nt sgc8c, a prominent DNA aptamer used to target membrane protein tyrosine kinase 7, for cancer theranostics. We show that sgc8c prefolds into an intricate three-way junction (3WJ) structure stabilized by long-range tertiary interactions and extensive base-base stackings. Delineated by NMR chemical shift perturbations, site-directed mutagenesis, and 3D structural information, we identified essential nucleotides constituting the key functional elements of sgc8c that are centralized at the core of 3WJ. Leveraging the well-established structure-function relationship, we efficiently engineered two sgc8c variants by modifying the apical loop and introducing L-DNA base pairs to simultaneously enhance thermostability, biostability, and binding affinity for both protein and cell targets, a feat not previously attained despite extensive efforts. This work showcases a simplified NMR-based approach to comprehend and optimize sgc8c without acquiring the complex structure, and offers principles for the sophisticated structure-function organization of DNA molecules.
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Affiliation(s)
- Axin He
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Liqi Wan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Yuchao Zhang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Zhenzhen Yan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
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2
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Laface C, Ricci AD, Vallarelli S, Ostuni C, Rizzo A, Ambrogio F, Centonze M, Schirizzi A, De Leonardis G, D’Alessandro R, Lotesoriere C, Giannelli G. Autotaxin-Lysophosphatidate Axis: Promoter of Cancer Development and Possible Therapeutic Implications. Int J Mol Sci 2024; 25:7737. [PMID: 39062979 PMCID: PMC11277072 DOI: 10.3390/ijms25147737] [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: 05/30/2024] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Autotaxin (ATX) is a member of the ectonucleotide pyrophosphate/phosphodiesterase (ENPP) family; it is encoded by the ENPP2 gene. ATX is a secreted glycoprotein and catalyzes the hydrolysis of lysophosphatidylcholine to lysophosphatidic acid (LPA). LPA is responsible for the transduction of various signal pathways through the interaction with at least six G protein-coupled receptors, LPA Receptors 1 to 6 (LPAR1-6). The ATX-LPA axis is involved in various physiological and pathological processes, such as angiogenesis, embryonic development, inflammation, fibrosis, and obesity. However, significant research also reported its connection to carcinogenesis, immune escape, metastasis, tumor microenvironment, cancer stem cells, and therapeutic resistance. Moreover, several studies suggested ATX and LPA as relevant biomarkers and/or therapeutic targets. In this review of the literature, we aimed to deepen knowledge about the role of the ATX-LPA axis as a promoter of cancer development, progression and invasion, and therapeutic resistance. Finally, we explored its potential application as a prognostic/predictive biomarker and therapeutic target for tumor treatment.
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Affiliation(s)
- Carmelo Laface
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
| | - Angela Dalia Ricci
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
| | - Simona Vallarelli
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
| | - Carmela Ostuni
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
| | - Alessandro Rizzo
- Medical Oncology, IRCCS Istituto Tumori “Giovanni Paolo II”, Viale Orazio Flacco 65, 70124 Bari, Italy
| | - Francesca Ambrogio
- Section of Dermatology and Venereology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Matteo Centonze
- Personalized Medicine Laboratory, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy;
| | - Annalisa Schirizzi
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, “IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.)
| | - Giampiero De Leonardis
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, “IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.)
| | - Rosalba D’Alessandro
- Laboratory of Experimental Oncology, National Institute of Gastroenterology, “IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (A.S.); (G.D.L.)
| | - Claudio Lotesoriere
- Medical Oncology Unit, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
| | - Gianluigi Giannelli
- Scientific Direction, National Institute of Gastroenterology, IRCCS “S. de Bellis” Research Hospital, 70013 Castellana Grotte, Italy
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3
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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4
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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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Hanazaki H, Yokota H, Yamagami S, Nakamura Y, Nagaoka T. The Effect of Anti-Autotaxin Aptamers on the Development of Proliferative Vitreoretinopathy. Int J Mol Sci 2023; 24:15926. [PMID: 37958909 PMCID: PMC10647324 DOI: 10.3390/ijms242115926] [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: 09/11/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
This study investigated the effect of anti-autotaxin (ATX) aptamers on the development of proliferative vitreoretinopathy (PVR) in both in vivo and in vitro PVR swine models. For the in vitro study, primary retinal pigment epithelial (RPE) cells were obtained from porcine eyes and cultured for cell proliferation and migration assays. For the in vivo study, a swine PVR model was established by inducing retinal detachment and injecting cultured RPE cells (2.0 × 106). Concurrently, 1 week after RPE cell injection, the anti-ATX aptamer, RBM-006 (10 mg/mL, 0.1 mL), was injected twice into the vitreous cavity. Post-injection effects of the anti-ATX aptamer on PVR development in the in vivo swine PVR model were investigated. For the in vitro evaluation, the cultured RPE cell proliferation and migration were significantly reduced at anti-ATX aptamer concentrations of 0.5-0.05 mg and at only 0.5 mg, respectively. Intravitreal administration of the anti-ATX aptamer also prevented tractional retinal detachment caused by PVR in the in vivo PVR model. We observed that the anti-ATX aptamer, RBM-006, inhibited PVR-related RPE cell proliferation and migration in vitro and inhibited the progression of PVR in the in vivo model, suggesting that the anti-ATX aptamer may be effective in preventing PVR.
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Affiliation(s)
- Hirotsugu Hanazaki
- Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (H.H.); (H.Y.); (S.Y.)
| | - Harumasa Yokota
- Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (H.H.); (H.Y.); (S.Y.)
| | - Satoru Yamagami
- Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (H.H.); (H.Y.); (S.Y.)
| | - Yoshikazu Nakamura
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan;
- RIBOMIC Inc., Minato-ku, Tokyo 108-0071, Japan
| | - Taiji Nagaoka
- Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (H.H.); (H.Y.); (S.Y.)
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6
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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: 5] [Impact Index Per Article: 5.0] [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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7
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Yang L, Shu P, Wu N, Hu M, Luo Z. Pharmacokinetics, pharmacodynamics, safety and tolerability of FTP-198, a novel, selective Autotaxin inhibitor, in healthy subjects: A phase I randomized placebo-controlled trial. Eur J Pharm Sci 2023; 189:106552. [PMID: 37532064 DOI: 10.1016/j.ejps.2023.106552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Autotaxin (ATX) and lysophosphatidic acid (LPA) play an important role in pathogenesis of idiopathic pulmonary fibrosis (IPF). FTP-198 is an oral, novel and selective ATX inhibitor indicated for treating IPF. The study aimed to investigate the pharmacokinetics, pharmacodynamics, safety and tolerability of FTP-198 in healthy subjects. METHODS A single-center, randomized, double-blind, placebo-controlled, single ascending-dose Phase I study was performed. Pharmacokinetics, pharmacodynamics, food effect on pharmacokinetics, elimination, safety and tolerability of FTP-198 were evaluated. RESULTS A total of 30 subjects were enrolled and completed the study. After oral administration of single ascending-dose of 100 mg, 300 mg and 400 mg FTP-198 under fasted condition, FTP-198 was absorbed with median time to reach peak concentration (Tmax) of 1.75, 2.75 and 3.5 h, respectively and eliminated with mean elimination half-life (t1/2) of 8.77, 10.58 and 10.57 h, respectively. Peak concentration (Cmax), plasma area under concentration-time curve from time 0 to the last measurable concentration (AUC0-t) and to infinity (AUC0-∞) increased in dose-proportional manner for 100 mg to 400 mg FTP-198. Food intake slightly increased the Cmax, AUC0-t and AUC0-∞ and prolonged Tmax, but not affecting t1/2 of FTP-198 compared with fasted state. The pharmacodynamic biomarker plasma lysophosphatidic acid (LPA) 18:2 decreased significantly for 100 mg to 400 mg FTP-198, with inhibition rate from baseline reaching approximately 80% at 24 h post dosing, and higher dose of FTP-198 increased the time to maintain inhibitory plateau. FTP-198 was eliminated from the body almost with no unchanged drug excreted in urine and a small amount of unchanged drug detected in feces of human. Moreover, FTP-198 exhibited favorable safety and tolerability in healthy subjects. CONCLUSION Pharmacokinetics, pharmacodynamics, safety and tolerability of FTP-198 support further subsequent clinical development of FTP -198 in IPF patients.
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Affiliation(s)
- Ling Yang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, Sichuan, 610044, China; Clinical Trial Center, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, Sichuan, 610044, China
| | - Pei Shu
- Clinical Trial Center, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, Sichuan, 610044, China
| | - Nan Wu
- Haisco Pharmaceutical Group Co., LtPd., Chengdu, China
| | - Mengyue Hu
- Haisco Pharmaceutical Group Co., LtPd., Chengdu, China
| | - Zhu Luo
- Clinical Trial Center, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, Sichuan, 610044, China.
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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Anti-TGF-β1 aptamer enhances therapeutic effect of tyrosine kinase inhibitor, gefitinib, on non-small cell lung cancer in xenograft model. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:969-978. [PMID: 36189081 PMCID: PMC9481871 DOI: 10.1016/j.omtn.2022.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 06/07/2022] [Indexed: 11/30/2022]
Abstract
Transforming growth factor β (TGF-β) is a multifunctional cytokine that plays crucial pathophysiological roles in various diseases, such as cancer and fibrosis. However, the disease modulation by targeting TGF-β1 isoform remains to be established, regardless of several studies employed with limited antibodies. Here, we developed an RNA aptamer to human active TGF-β1, named APT-β1, and characterized its properties in vitro and in vivo. APT-β1 bound to human and mouse active TGF-β1 proteins with high affinity and specificity and strongly inhibited TGF-β1-induced downstream signaling and cell morphology with 50% inhibition concentration (IC50) values at picomolar concentrations. In a xenograft mouse model of non-small cell lung cancer, APT-β1 alone showed no appreciable effect on tumor growth, while it greatly enhanced the anti-tumor effect of gefitinib, an approved tyrosine kinase inhibitor. These findings strongly suggest that the anti-TGF-β1 medication may be a promising cancer therapy to suppress repopulation of lung cancer in combination with certain anti-cancer drugs, such as gefitinib.
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10
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Seeliger B, Carleo A, Wendel-Garcia PD, Fuge J, Montes-Warboys A, Schuchardt S, Molina-Molina M, Prasse A. Changes in serum metabolomics in idiopathic pulmonary fibrosis and effect of approved antifibrotic medication. Front Pharmacol 2022; 13:837680. [PMID: 36059968 PMCID: PMC9428132 DOI: 10.3389/fphar.2022.837680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive disease with significant mortality and morbidity. Approval of antifibrotic therapy has ameliorated disease progression, but therapy response is heterogeneous and to date, adequate biomarkers predicting therapy response are lacking. In recent years metabolomic technology has improved and is broadly applied in cancer research thus enabling its use in other fields. Recently both aberrant metabolic and lipidomic pathways have been described to influence profibrotic responses. We thus aimed to characterize the metabolomic and lipidomic changes between IPF and healthy volunteers (HV) and analyze metabolomic changes following treatment with nintedanib and pirfenidone. We collected serial serum samples from two IPF cohorts from Germany (n = 122) and Spain (n = 21) and additionally age-matched healthy volunteers (n = 16). Metabolomic analysis of 630 metabolites covering 14 small molecule and 12 different lipid classes was carried out using flow injection analysis tandem mass spectrometry for lipids and liquid chromatography tandem mass spectrometry for small molecules. Levels were correlated with survival and disease severity. We identified 109 deregulated analytes in IPF compared to HV in cohort 1 and 112 deregulated analytes in cohort 2. Metabolites which were up-regulated in both cohorts were mainly triglycerides while the main class of down-regulated metabolites were phosphatidylcholines. Only a minority of de-regulated analytes were small molecules. Triglyceride subclasses were inversely correlated with baseline disease severity (GAP-score) and a clinical compound endpoint of lung function decline or death. No changes in the metabolic profiles were observed following treatment with pirfenidone. Nintedanib treatment induced up-regulation of triglycerides and phosphatidylcholines. Patients in whom an increase in these metabolites was observed showed a trend towards better survival using the 2-years composite endpoint (HR 2.46, p = 0.06). In conclusion, we report major changes in metabolites in two independent cohorts testing a large number of patients. Specific lipidic metabolite signatures may serve as biomarkers for disease progression or favorable treatment response to nintedanib.
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Affiliation(s)
- Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Alfonso Carleo
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | | | - Jan Fuge
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Ana Montes-Warboys
- ILD Multidisciplinary Unit, Hospital Universitari Bellvitge, IDIBELL, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Maria Molina-Molina
- ILD Multidisciplinary Unit, Hospital Universitari Bellvitge, IDIBELL, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
- Centro Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Antje Prasse
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
- *Correspondence: Antje Prasse,
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Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking. PLoS One 2022; 17:e0264701. [PMID: 35320268 PMCID: PMC8942228 DOI: 10.1371/journal.pone.0264701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/15/2022] [Indexed: 02/07/2023] Open
Abstract
Aptamers are single-stranded oligonucleotides, formerly evolved by Systematic Evolution of Ligands by EXponential enrichment (SELEX), that fold into functional three-dimensional structures. Such conformation is crucial for aptamers' ability to bind to a target with high affinity and specificity. Unnatural nucleotides have been used to develop nucleic acid mimic (NAM) aptamers with increased performance, such as biological stability. Prior knowledge of aptamer-target interactions is critical for applying post-SELEX modifications with unnatural nucleotides since it can affect aptamers' structure and performance. Here, we describe an easy-to-apply in silico workflow using free available software / web servers to predict the tertiary conformation of NAM, DNA and RNA aptamers, as well as the docking with the target molecule. Representative 2'-O-methyl (2'OMe), locked nucleic acid (LNA), DNA and RNA aptamers, with experimental data deposited in Protein Data Bank, were selected to validate the workflow. All aptamers' tertiary structure and docking models were successfully predicted with good structural similarity to the experimental data. Thus, this workflow will boost the development of aptamers, particularly NAM aptamers, by assisting in the rational modification of specific nucleotides and avoiding trial-and-error approaches.
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12
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Hoshino Y, Okuno T, Saigusa D, Kano K, Yamamoto S, Shindou H, Aoki J, Uchida K, Yokomizo T, Ito N. Lysophosphatidic acid receptor 1/3 antagonist inhibits the activation of satellite glial cells and reduces acute nociceptive responses. FASEB J 2022; 36:e22236. [PMID: 35218596 DOI: 10.1096/fj.202101678r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 02/06/2023]
Abstract
Lysophosphatidic acid (LPA) exerts various biological activities through six characterized G protein-coupled receptors (LPA1-6 ). While LPA-LPA1 signaling contributes toward the demyelination and retraction of C-fiber and induces neuropathic pain, the effects of LPA-LPA1 signaling on acute nociceptive pain is uncertain. This study investigated the role of LPA-LPA1 signaling in acute nociceptive pain using the formalin test. The pharmacological inhibition of the LPA-LPA1 axis significantly attenuated formalin-induced nociceptive behavior. The LPA1 mRNA was expressed in satellite glial cells (SGCs) in dorsal root ganglion (DRG) and was particularly abundant in SGCs surrounding large DRG neurons, which express neurofilament 200. Treatment with LPA1/3 receptor (LPA1/3 ) antagonist inhibited the upregulation of glial markers and inflammatory cytokines in DRG following formalin injection. The LPA1/3 antagonist also attenuated phosphorylation of extracellular signal-regulated kinase, especially in SGCs and cyclic AMP response element-binding protein in the dorsal horn following formalin injection. LPA amounts after formalin injection to the footpad were quantified by liquid chromatography/tandem mass spectrometry, and LPA levels were found to be increased in the innervated DRGs. Our results indicate that LPA produced in the innervated DRGs promotes the activation of SGCs through LPA1 , increases the sensitivity of primary neurons, and modulates pain behavior. These results facilitate our understanding of the pathology of acute nociceptive pain and demonstrate the possibility of the LPA1 on SGCs as a novel target for acute pain control.
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Affiliation(s)
- Yoko Hoshino
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Okuno
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan.,Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shota Yamamoto
- Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hideo Shindou
- Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan.,Department of Lipid Medical Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kanji Uchida
- Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuko Ito
- Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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13
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Murakami K, Izuo N, Bitan G. Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases. J Biol Chem 2022; 298:101478. [PMID: 34896392 PMCID: PMC8728582 DOI: 10.1016/j.jbc.2021.101478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are oligonucleotides selected from large pools of random sequences based on their affinity for bioactive molecules and are used in similar ways to antibodies. Aptamers provide several advantages over antibodies, including their small size, facile, large-scale chemical synthesis, high stability, and low immunogenicity. Amyloidogenic proteins, whose aggregation is relevant to neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion diseases, are among the most challenging targets for aptamer development due to their conformational instability and heterogeneity, the same characteristics that make drug development against amyloidogenic proteins difficult. Recently, chemical tethering of aptagens (equivalent to antigens) and advances in high-throughput sequencing-based analysis have been used to overcome some of these challenges. In addition, internalization technologies using fusion to cellular receptors and extracellular vesicles have facilitated central nervous system (CNS) aptamer delivery. In view of the development of these techniques and resources, here we review antiamyloid aptamers, highlighting preclinical application to CNS therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Naotaka Izuo
- Laboratory of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA.
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14
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Ozturk M, Nilsen-Hamilton M, Ilgu M. Aptamer Applications in Neuroscience. Pharmaceuticals (Basel) 2021; 14:1260. [PMID: 34959661 PMCID: PMC8709198 DOI: 10.3390/ph14121260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.
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Affiliation(s)
- Meric Ozturk
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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15
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Oliveira R, Pinho E, Sousa AL, DeStefano JJ, Azevedo NF, Almeida C. Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches. Trends Biotechnol 2021; 40:549-563. [PMID: 34756455 DOI: 10.1016/j.tibtech.2021.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are structural single-stranded oligonucleotides generated in vitro to bind to a specific target molecule. Aptamers' versatility can be enhanced with nucleic acid mimics (NAMs) during or after a selection process, also known as systematic evolution of ligands by exponential enrichment (SELEX). We address advantages and limitations of the technologies used to generate NAM aptamers, especially the applicability of existing engineered polymerases to replicate NAMs and methodologies to improve aptamers after SELEX. We also discuss the limitations of existing methods for sequencing NAM sequences and bioinformatic tools to predict NAM aptamer structures. As a conclusion, we suggest that NAM aptamers might successfully compete with molecular tools based on proteins such as antibodies for future application.
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Affiliation(s)
- Ricardo Oliveira
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Eva Pinho
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal
| | - Ana Luísa Sousa
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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16
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Heredia FL, Roche-Lima A, Parés-Matos EI. A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PLoS Comput Biol 2021; 17:e1009247. [PMID: 34343165 PMCID: PMC8362955 DOI: 10.1371/journal.pcbi.1009247] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/13/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucleotide-specific molecule. Usually, 10 to 20 steps are required for SELEX to be completed. Throughout this process it is necessary to discriminate between true DNA aptamers and unspecified DNA-binding sequences. Thus, a novel machine learning-based approach was developed to support and simplify the early steps of the SELEX process, to help discriminate binding between DNA aptamers from those unspecified targets of DNA-binding sequences. An Artificial Intelligence (AI) approach to identify aptamers were implemented based on Natural Language Processing (NLP) and Machine Learning (ML). NLP method (CountVectorizer) was used to extract information from the nucleotide sequences. Four ML algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, Support Vector Machines) were trained using data from the NLP method along with sequence information. The best performing model was Support Vector Machines because it had the best ability to discriminate between positive and negative classes. In our model, an Accuracy (A) of 0.995, the fraction of samples that the model correctly classified, and an Area Under the Receiving Operating Curve (AUROC) of 0.998, the degree by which a model is capable of distinguishing between classes, were observed. The developed AI approach is useful to identify potential DNA aptamers to reduce the amount of rounds in a SELEX selection. This new approach could be applied in the design of DNA libraries and result in a more efficient and faster process for DNA aptamers to be chosen during SELEX. In this manuscript authors explain the development and validation of a novel artificial intelligence approach to support and simplify the early steps of the process from SELEX, to help discriminate binding between deoxynucleotide aptamers from those unspecified targets of DNA-binding sequences. The approach was implemented based on Natural Language Processing and Machine Learning. CountVectorizer, a Natural Language Processing method, was used to extract information from nucleotide sequences. Four Machine Learning algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, and Support Vector Machines) were trained using data from the Natural Language Processing method along with sequence information. From these four trained machine learning algorithms, the best performance and selected model was Support Vectors Machines, because it had the best discriminatory metrics (i.e., Accuracy (A) = 0.995; AUROC (AU) = 0.998). In general, all models showed good metric results for predicting DNA aptamer sequences. The Machine Learning model complexity and difficult interpretation may hinder its application into the standard practice. For this reason, the development of a web-app is already taking place to facilitate the interpretation and application of the obtained results.
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Affiliation(s)
- Frances L. Heredia
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Elsie I. Parés-Matos
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
- * E-mail:
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Tsukakoshi K, Yamagishi Y, Kanazashi M, Nakama K, Oshikawa D, Savory N, Matsugami A, Hayashi F, Lee J, Saito T, Sode K, Khunathai K, Kuno H, Ikebukuro K. G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res 2021; 49:6069-6081. [PMID: 34095949 PMCID: PMC8216272 DOI: 10.1093/nar/gkab388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 04/25/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023] Open
Abstract
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin's peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair.
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Affiliation(s)
- Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasuko Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mana Kanazashi
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kenta Nakama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daiki Oshikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jinhee Lee
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Taiki Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | | | - Hitoshi Kuno
- DENSO CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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18
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Lin J, Shi A, Zheng Z, Huang L, Wang Y, Lin H, Lin X. Simultaneous Quantification of Ampicillin and Kanamycin in Water Samples Based on Lateral Flow Aptasensor Strip with an Internal Line. Molecules 2021; 26:molecules26133806. [PMID: 34206584 PMCID: PMC8270245 DOI: 10.3390/molecules26133806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/17/2022] Open
Abstract
In this work, a simple and rapid method based on the lateral flow assay (LFA) has been developed for the detection of dual antibiotics. To achieve the quantitative assay and to reduce the non-specific adsorption, an internal system has been developed. A non-specific DNA was exploited as an internal standard and could be recognized by the DNA marker that was coated at the internal line. Two different kinds of aptamers were applied to recognize ampicillin (AMP) and kanamycin (KAM), and the distance between the detection line and conjugate pad was then optimized. Under the optimum conditions, the quantitative assays of AMP (R2 = 0.984) and KAM (R2 = 0.990) were achieved with dynamic ranges of 0.50 to 500.0 ng/L, and of 0.50 to 1000.0 ng/L, respectively. The LOQs of AMP and KAM were 0.06 ng/L and 0.015 ng/L, respectively. Finally, the proposed method has been successfully applied to analyze aquaculture water, tap water, and lake water, and hospital wastewater, indicating the established method could be used to monitor the environment.
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Affiliation(s)
- Jinbiao Lin
- Provincial Key Laboratory of Naval Architecture & Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (J.L.); (A.S.); (Z.Z.); (H.L.)
| | - Ang Shi
- Provincial Key Laboratory of Naval Architecture & Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (J.L.); (A.S.); (Z.Z.); (H.L.)
| | - Ziwu Zheng
- Provincial Key Laboratory of Naval Architecture & Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (J.L.); (A.S.); (Z.Z.); (H.L.)
| | - Long Huang
- CNTAC Testing Services Co., Ltd., Quanzhou 362700, China
- Correspondence: (L.H.); (X.L.)
| | - Yixin Wang
- Shanghai WEIPU Chemical Technology Service Co., Ltd., Shanghai 200000, China;
| | - Honggui Lin
- Provincial Key Laboratory of Naval Architecture & Ocean Engineering, Marine Engineering College, Jimei University, Xiamen 361021, China; (J.L.); (A.S.); (Z.Z.); (H.L.)
| | - Xuexia Lin
- Department of Chemical Engineering & Pharmaceutical Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
- Correspondence: (L.H.); (X.L.)
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19
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Zhang X, Li M, Yin N, Zhang J. The Expression Regulation and Biological Function of Autotaxin. Cells 2021; 10:cells10040939. [PMID: 33921676 PMCID: PMC8073485 DOI: 10.3390/cells10040939] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
Autotaxin (ATX) is a secreted glycoprotein and functions as a key enzyme to produce extracellular lysophosphatidic acid (LPA). LPA interacts with at least six G protein-coupled receptors, LPAR1-6, on the cell membrane to activate various signal transduction pathways through distinct G proteins, such as Gi/0, G12/13, Gq/11, and Gs. The ATX-LPA axis plays an important role in physiological and pathological processes, including embryogenesis, obesity, and inflammation. ATX is one of the top 40 most unregulated genes in metastatic cancer, and the ATX-LPA axis is involved in the development of different types of cancers, such as colorectal cancer, ovarian cancer, breast cancer, and glioblastoma. ATX expression is under multifaceted controls at the transcription, post-transcription, and secretion levels. ATX and LPA in the tumor microenvironment not only promote cell proliferation, migration, and survival, but also increase the expression of inflammation-related circuits, which results in poor outcomes for patients with cancer. Currently, ATX is regarded as a potential cancer therapeutic target, and an increasing number of ATX inhibitors have been developed. In this review, we focus on the mechanism of ATX expression regulation and the functions of ATX in cancer development.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Correspondence: ; Tel.: +86-10-58802137; Fax: +86-10-58807720
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20
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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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21
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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22
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Zulfikar S, Mulholland S, Adamali H, Barratt SL. Inhibitors of the Autotaxin-Lysophosphatidic Acid Axis and Their Potential in the Treatment of Interstitial Lung Disease: Current Perspectives. Clin Pharmacol 2020; 12:97-108. [PMID: 32765123 PMCID: PMC7367740 DOI: 10.2147/cpaa.s228362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a progressive fibrosing interstitial lung disease for which there is no known cure. Currently available therapeutic options have been shown at best to slow the progression of the disease and thus there remains an urgent unmet need to identify new therapies. In this article, we will discuss the mechanisms of action, pre-clinical and clinical trial data surrounding inhibitors of the autotaxin-lysophosphatidic acid axis, which show promise as emerging novel therapies for fibrotic lung disease.
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Affiliation(s)
- Sabrina Zulfikar
- Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Bristol, UK
| | - Sarah Mulholland
- Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Bristol, UK
| | - Huzaifa Adamali
- Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Bristol, UK
| | - Shaney L Barratt
- Bristol Interstitial Lung Disease Service, North Bristol NHS Trust, Bristol, UK
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Oteng EK, Gu W, McKeague M. High-efficiency enrichment enables identification of aptamers to circulating Plasmodium falciparum-infected erythrocytes. Sci Rep 2020; 10:9706. [PMID: 32546848 PMCID: PMC7298056 DOI: 10.1038/s41598-020-66537-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Plasmodium falciparum is the causative agent of the deadliest human malaria. New molecules are needed that can specifically bind to erythrocytes that are infected with P. falciparum for diagnostic purposes, to disrupt host-parasite interactions, or to deliver chemotherapeutics. Aptamer technology has the potential to revolutionize biological diagnostics and therapeutics; however, broad adoption is hindered by the high failure rate of the systematic evolution of ligands by exponential enrichment (SELEX). Here we performed parallel SELEX experiments to compare the impact of two different methods for single-strand recovery on the efficiency of aptamer enrichment. Our experimental results and analysis of SELEX publications spanning 13 years implicate the alkaline denaturation step as a significant cause for inefficient aptamer selection. Thus, we applied an exonuclease single-strand recovery step in our SELEX to direct aptamers to the surface of erythrocytes infected with P. falciparum. The selected aptamers bind with high affinity (low nanomolar Kd values) and selectivity to exposed surface proteins of both laboratory parasite strains as well isolates from patients in Asia and Africa with clinical malaria. The results obtained in this study potentially open new approaches to malaria diagnosis and surveillance.
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Affiliation(s)
- Eugene K Oteng
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, 20852, USA.
| | - Wenjuan Gu
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA
| | - Maureen McKeague
- Department of Pharmacology and Therapeutics, McGill University, 3655 Prom. Sir-William-Osler, Montreal, Quebec, H3G 1Y6, Canada.,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
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24
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Lei H, Guo M, Li X, Jia F, Li C, Yang Y, Cao M, Jiang N, Ma E, Zhai X. Discovery of Novel Indole-Based Allosteric Highly Potent ATX Inhibitors with Great In Vivo Efficacy in a Mouse Lung Fibrosis Model. J Med Chem 2020; 63:7326-7346. [DOI: 10.1021/acs.jmedchem.0c00506] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hongrui Lei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ming Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaopeng Li
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Fang Jia
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Changtao Li
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yu Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Meng Cao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Nan Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Enlong Ma
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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25
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Li X, Leng Y, Li X, Wang Y, Luo P, Zhang C, Wang Z, Yue X, Shen C, Chen L, Liu Z, Shi C, Xie L. The TβR II-targeted aptamer S58 prevents fibrosis after glaucoma filtration surgery. Aging (Albany NY) 2020; 12:8837-8857. [PMID: 32452828 PMCID: PMC7288943 DOI: 10.18632/aging.102997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
Abstract
Glaucoma filtration surgery (GFS) is an effective clinical treatment for glaucoma when intraocular pressure (IOP) control is poor. However, the occurrence of conjunctival scarring at the surgical site is the main reason for failure of the surgery. In a previous study, we isolated and developed S58, a novel nucleic acid aptamer targeting TβR II, by systematic evolution of ligands by exponential enrichment (SELEX). Here, we show how S58 sterically inhibits the TβR II interaction with TGF-β. The effects of topical S58 treatment were studied in a rabbit model of GFS. At 6 postoperative weeks, S58 reduced fibrosis and prolonged bleb survival in rabbits after GFS. Further in vitro tests showed that the levels of fibrosis in S58 treated-Human Conjunctival Fibroblasts (HConFs) were decreased and that antioxidant defense was increased. In addition, the loss of nuclear factor erythroid 2-related factor 2 (Nrf2) or the inhibition of phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) reversed the anti-fibrotic effects of S58. The present work suggests that S58 could effectively improve GFS surgical outcomes by activating the intracellular antioxidant defense PI3K/Akt/Nrf2 signaling pathway.
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Affiliation(s)
- Xueru Li
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Yu Leng
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Xiangji Li
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Yawei Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Peng Luo
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Chi Zhang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Ziwen Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Xiaofeng Yue
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Chongxing Shen
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Long Chen
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Zujuan Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Lin Xie
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
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26
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Dexamethasone Attenuates X-Ray-Induced Activation of the Autotaxin-Lysophosphatidate-Inflammatory Cycle in Breast Tissue and Subsequent Breast Fibrosis. Cancers (Basel) 2020; 12:cancers12040999. [PMID: 32325715 PMCID: PMC7226295 DOI: 10.3390/cancers12040999] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
We recently showed that radiation-induced DNA damage in breast adipose tissue increases autotaxin secretion, production of lysophosphatidate (LPA) and expression of LPA1/2 receptors. We also established that dexamethasone decreases autotaxin production and LPA signaling in non-irradiated adipose tissue. In the present study, we showed that dexamethasone attenuated the radiation-induced increases in autotaxin activity and the concentrations of inflammatory mediators in cultured human adipose tissue. We also exposed a breast fat pad in mice to three daily 7.5 Gy fractions of X-rays. Dexamethasone attenuated radiation-induced increases in autotaxin activity in plasma and mammary adipose tissue and LPA1 receptor levels in adipose tissue after 48 h. DEX treatment during five daily fractions of 7.5 Gy attenuated fibrosis by ~70% in the mammary fat pad and underlying lungs at 7 weeks after radiotherapy. This was accompanied by decreases in CXCL2, active TGF-β1, CTGF and Nrf2 at 7 weeks in adipose tissue of dexamethasone-treated mice. Autotaxin was located at the sites of fibrosis in breast tissue and in the underlying lungs. Consequently, our work supports the premise that increased autotaxin production and lysophosphatidate signaling contribute to radiotherapy-induced breast fibrosis and that dexamethasone attenuated the development of fibrosis in part by blocking this process.
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Yanagida K, Valentine WJ. Druggable Lysophospholipid Signaling Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1274:137-176. [DOI: 10.1007/978-3-030-50621-6_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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The Structural Binding Mode of the Four Autotaxin Inhibitor Types that Differentially Affect Catalytic and Non-Catalytic Functions. Cancers (Basel) 2019; 11:cancers11101577. [PMID: 31623219 PMCID: PMC6826961 DOI: 10.3390/cancers11101577] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Autotaxin (ATX) is a secreted lysophospholipase D, catalysing the conversion of lysophosphatidylcholine (LPC) to bioactive lysophosphatidic acid (LPA). LPA acts through two families of G protein-coupled receptors (GPCRs) controlling key cellular responses, and it is implicated in many physiological processes and pathologies. ATX, therefore, has been established as an important drug target in the pharmaceutical industry. Structural and biochemical studies of ATX have shown that it has a bimetallic nucleophilic catalytic site, a substrate-binding (orthosteric) hydrophobic pocket that accommodates the lipid alkyl chain, and an allosteric tunnel that can accommodate various steroids and LPA. In this review, first, we revisit what is known about ATX-mediated catalysis, crucially in light of allosteric regulation. Then, we present the known ATX catalysis-independent functions, including binding to cell surface integrins and proteoglycans. Next, we analyse all crystal structures of ATX bound to inhibitors and present them based on the four inhibitor types that are established based on the binding to the orthosteric and/or the allosteric site. Finally, in light of these data we discuss how mechanistic differences might differentially modulate the activity of the ATX-LPA signalling axis, and clinical applications including cancer.
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Pleotropic Roles of Autotaxin in the Nervous System Present Opportunities for the Development of Novel Therapeutics for Neurological Diseases. Mol Neurobiol 2019; 57:372-392. [PMID: 31364025 DOI: 10.1007/s12035-019-01719-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/23/2019] [Indexed: 12/23/2022]
Abstract
Autotaxin (ATX) is a soluble extracellular enzyme that is abundant in mammalian plasma and cerebrospinal fluid (CSF). It has two known enzymatic activities, acting as both a phosphodiesterase and a phospholipase. The majority of its biological effects have been associated with its ability to liberate lysophosphatidic acid (LPA) from its substrate, lysophosphatidylcholine (LPC). LPA has diverse pleiotropic effects in the central nervous system (CNS) and other tissues via the activation of a family of six cognate G protein-coupled receptors. These LPA receptors (LPARs) are expressed in some combination in all known cell types in the CNS where they mediate such fundamental cellular processes as proliferation, differentiation, migration, chronic inflammation, and cytoskeletal organization. As a result, dysregulation of LPA content may contribute to many CNS and PNS disorders such as chronic inflammatory or neuropathic pain, glioblastoma multiforme (GBM), hemorrhagic hydrocephalus, schizophrenia, multiple sclerosis, Alzheimer's disease, metabolic syndrome-induced brain damage, traumatic brain injury, hepatic encephalopathy-induced cerebral edema, macular edema, major depressive disorder, stress-induced psychiatric disorder, alcohol-induced brain damage, HIV-induced brain injury, pruritus, and peripheral nerve injury. ATX activity is now known to be the primary biological source of this bioactive signaling lipid, and as such, represents a potentially high-value drug target. There is currently one ATX inhibitor entering phase III clinical trials, with several additional preclinical compounds under investigation. This review discusses the physiological and pathological significance of the ATX-LPA-LPA receptor signaling axis and summarizes the evidence for targeting this pathway for the treatment of CNS diseases.
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30
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Döhler C, Zebisch M, Krinke D, Robitzki A, Sträter N. Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain. Acta Crystallogr F Struct Biol Commun 2018; 74:696-703. [PMID: 30387774 PMCID: PMC6213977 DOI: 10.1107/s2053230x18011111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 08/03/2018] [Indexed: 11/11/2022] Open
Abstract
Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI- cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit. The SMB2 domain is oriented as in NPP2, but the SMB1 domain does not interact with the PDE domain but extends further away from the PDE domain. Deletion of the SMB domains resulted in crystals that diffracted to 2.4 Å resolution and are suitable for substrate-binding studies.
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Affiliation(s)
- Christoph Döhler
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Matthias Zebisch
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
- Division of Structural Biology, Evotec, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, England
| | - Dana Krinke
- Division of Molecular Biological–Biochemical Processing Technology, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Andrea Robitzki
- Division of Molecular Biological–Biochemical Processing Technology, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
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31
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Ninou I, Kaffe E, Müller S, Budd DC, Stevenson CS, Ullmer C, Aidinis V. Pharmacologic targeting of the ATX/LPA axis attenuates bleomycin-induced pulmonary fibrosis. Pulm Pharmacol Ther 2018; 52:32-40. [DOI: 10.1016/j.pupt.2018.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/16/2018] [Indexed: 02/08/2023]
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32
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Salgado-Polo F, Fish A, Matsoukas MT, Heidebrecht T, Keune WJ, Perrakis A. Lysophosphatidic acid produced by autotaxin acts as an allosteric modulator of its catalytic efficiency. J Biol Chem 2018; 293:14312-14327. [PMID: 30026231 DOI: 10.1074/jbc.ra118.004450] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/13/2018] [Indexed: 12/18/2022] Open
Abstract
Autotaxin (ATX) is a secreted glycoprotein and the only member of the ectonucleotide pyrophosphatase/phosphodiesterase family that converts lysophosphatidylcholine (LPC) into lysophosphatidic acid (LPA). LPA controls key responses, such as cell migration, proliferation, and survival, implicating ATX-LPA signaling in various (patho)physiological processes and establishing it as a drug target. ATX structural and functional studies have revealed an orthosteric and an allosteric site, called the "pocket" and the "tunnel," respectively. However, the mechanisms in allosteric modulation of ATX's activity as a lysophospholipase D are unclear. Here, using the physiological LPC substrate, a new fluorescent substrate, and diverse ATX inhibitors, we revisited the kinetics and allosteric regulation of the ATX catalytic cycle, dissecting the different steps and pathways leading to LPC hydrolysis. We found that ATX activity is stimulated by LPA and that LPA activates ATX lysophospholipase D activity by binding to the ATX tunnel. A consolidation of all experimental kinetics data yielded a comprehensive catalytic model supported by molecular modeling simulations and suggested a positive feedback mechanism that is regulated by the abundance of the LPA products activating hydrolysis of different LPC species. Our results complement and extend the current understanding of ATX hydrolysis in light of the allosteric regulation by ATX-produced LPA species and have implications for the design and application of both orthosteric and allosteric ATX inhibitors.
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Affiliation(s)
- Fernando Salgado-Polo
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and
| | - Alex Fish
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and
| | - Minos-Timotheos Matsoukas
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and.,the Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Tatjana Heidebrecht
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and
| | - Willem-Jan Keune
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and
| | - Anastassis Perrakis
- From the Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands and
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34
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Ninou I, Magkrioti C, Aidinis V. Autotaxin in Pathophysiology and Pulmonary Fibrosis. Front Med (Lausanne) 2018; 5:180. [PMID: 29951481 PMCID: PMC6008954 DOI: 10.3389/fmed.2018.00180] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/25/2018] [Indexed: 12/17/2022] Open
Abstract
Lysophospholipid signaling is emerging as a druggable regulator of pathophysiological responses, and especially fibrosis, exemplified by the relative ongoing clinical trials in idiopathic pulmonary fibrosis (IPF) patients. In this review, we focus on ectonucleotide pyrophosphatase-phosphodiesterase 2 (ENPP2), or as more widely known Autotaxin (ATX), a secreted lysophospholipase D (lysoPLD) largely responsible for extracellular lysophosphatidic acid (LPA) production. In turn, LPA is a bioactive phospholipid autacoid, forming locally upon increased ATX levels and acting also locally through its receptors, likely guided by ATX's structural conformation and cell surface associations. Increased ATX activity levels have been detected in many inflammatory and fibroproliferative conditions, while genetic and pharmacologic studies have confirmed a pleiotropic participation of ATX/LPA in different processes and disorders. In pulmonary fibrosis, ATX levels rise in the broncheoalveolar fluid (BALF) and stimulate LPA production. LPA engagement of its receptors activate multiple G-protein mediated signal transduction pathways leading to different responses from pulmonary cells including the production of pro-inflammatory signals from stressed epithelial cells, the modulation of endothelial physiology, the activation of TGF signaling and the stimulation of fibroblast accumulation. Genetic or pharmacologic targeting of the ATX/LPA axis attenuated disease development in animal models, thus providing the proof of principle for therapeutic interventions.
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Affiliation(s)
- Ioanna Ninou
- Division of Immunology, Alexander Fleming Biomedical Sciences Research Center, Athens, Greece
| | - Christiana Magkrioti
- Division of Immunology, Alexander Fleming Biomedical Sciences Research Center, Athens, Greece
| | - Vassilis Aidinis
- Division of Immunology, Alexander Fleming Biomedical Sciences Research Center, Athens, Greece
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35
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Benesch MGK, MacIntyre ITK, McMullen TPW, Brindley DN. Coming of Age for Autotaxin and Lysophosphatidate Signaling: Clinical Applications for Preventing, Detecting and Targeting Tumor-Promoting Inflammation. Cancers (Basel) 2018; 10:cancers10030073. [PMID: 29543710 PMCID: PMC5876648 DOI: 10.3390/cancers10030073] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 12/13/2022] Open
Abstract
A quarter-century after the discovery of autotaxin in cell culture, the autotaxin-lysophosphatidate (LPA)-lipid phosphate phosphatase axis is now a promising clinical target for treating chronic inflammatory conditions, mitigating fibrosis progression, and improving the efficacy of existing cancer chemotherapies and radiotherapy. Nearly half of the literature on this axis has been published during the last five years. In cancer biology, LPA signaling is increasingly being recognized as a central mediator of the progression of chronic inflammation in the establishment of a tumor microenvironment which promotes cancer growth, immune evasion, metastasis, and treatment resistance. In this review, we will summarize recent advances made in understanding LPA signaling with respect to chronic inflammation and cancer. We will also provide perspectives on the applications of inhibitors of LPA signaling in preventing cancer initiation, as adjuncts extending the efficacy of current cancer treatments by blocking inflammation caused by either the cancer or the cancer therapy itself, and by disruption of the tumor microenvironment. Overall, LPA, a simple molecule that mediates a plethora of biological effects, can be targeted at its levels of production by autotaxin, LPA receptors or through LPA degradation by lipid phosphate phosphatases. Drugs for these applications will soon be entering clinical practice.
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Affiliation(s)
- Matthew G K Benesch
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL AlB 3V6, Canada.
- Signal Transduction Research Group, Cancer Research Institute of Northern Alberta, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada.
| | - Iain T K MacIntyre
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL AlB 3V6, Canada.
| | - Todd P W McMullen
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G7, Canada.
| | - David N Brindley
- Signal Transduction Research Group, Cancer Research Institute of Northern Alberta, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada.
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36
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Baader M, Bretschneider T, Broermann A, Rippmann JF, Stierstorfer B, Kuttruff CA, Mark M. Characterization of the properties of a selective, orally bioavailable autotaxin inhibitor in preclinical models of advanced stages of liver fibrosis. Br J Pharmacol 2018; 175:693-707. [PMID: 29197066 DOI: 10.1111/bph.14118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 11/13/2017] [Accepted: 11/21/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Autotaxin (ATX) is a secreted phospholipase which hydrolyses lysophosphatidylcholine to generate lysophosphatidic acid (LPA). The extracellular signalling molecule LPA exerts its biological actions through activation of six GPCRs expressed in various cell types including fibroblasts. Multiple preclinical studies using knockout animals, LPA receptor antagonists or ATX inhibitors have provided evidence for a potential role of the ATX/LPA axis in tissue fibrosis. Despite growing evidence for a correlation between ATX levels and the degree of fibrosis in chronic liver diseases, including viral hepatitis and hepatocellular carcinoma, the role of ATX in non-alcoholic steatohepatitis (NASH) remains unclear. EXPERIMENTAL APPROACH The relevance of ATX in the pathogenesis of liver fibrosis was investigated by oral administration of Ex_31, a selective ATX inhibitor, in a 10 week model of carbon tetrachloride-induced liver injury and in a 14 week model of choline-deficient amino acid-defined diet-induced liver injury in rats. KEY RESULTS Oral administration of Ex_31, a selective ATX inhibitor, at 15 mg·kg-1 twice daily in therapeutic intervention mode resulted in efficient ATX inhibition and more than 95% reduction in plasma LPA levels in both studies. Treatment with Ex_31 had no effect on biomarkers of liver function, inflammation, or fibrosis and did not result in histological improvements in diseased animals. CONCLUSIONS AND IMPLICATIONS Our findings question the role of ATX in the pathogenesis of hepatic fibrosis and the potential of small molecule ATX inhibitors for the treatment of patients with NASH and advanced stages of liver fibrosis.
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Affiliation(s)
- Manuel Baader
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tom Bretschneider
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andre Broermann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Joerg F Rippmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | | | | | - Michael Mark
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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37
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Nomura Y, Yamazaki K, Amano R, Takada K, Nagata T, Kobayashi N, Tanaka Y, Fukunaga J, Katahira M, Kozu T, Nakamura Y, Haishima Y, Torigoe H, Sakamoto T. Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain. J Biochem 2017; 162:431-436. [PMID: 28992043 DOI: 10.1093/jb/mvx049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
To develop a high-affinity aptamer against AML1 Runt domain, two aptamers were conjugated based on their structural information. The newly designed aptamer Apt14 was generated by the conjugation of two RNA aptamers (Apt1 and Apt4) obtained by SELEX against AML1 Runt domain, resulting in improvement in its binding performance. The residues of AML1 Runt domain in contact with Apt14 were predicted in silico and confirmed by mutation and NMR analyses. It was suggested that the conjugated internal loop renders additional contacts and is responsible for the enhancement in the binding affinity. Conjugation of two aptamers that bind to different sites of the target protein is a facile and robust strategy to develop an aptamer with higher performance.
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Affiliation(s)
- Yusuke Nomura
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan.,Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Kaori Yamazaki
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan
| | - Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kenta Takada
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichiro Tanaka
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Junichi Fukunaga
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, Ina, Saitama 362-0806, Japan
| | - Yoshikazu Nakamura
- RIBOMIC Inc, 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan.,Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuji Haishima
- Division of Medical Devices, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku 162-8601, Tokyo, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Lysophosphatidylserine suppresses IL-2 production in CD4 T cells through LPS3/GPR174. Biochem Biophys Res Commun 2017; 494:332-338. [DOI: 10.1016/j.bbrc.2017.10.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023]
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Yazdani S, Bansal R, Prakash J. Drug targeting to myofibroblasts: Implications for fibrosis and cancer. Adv Drug Deliv Rev 2017; 121:101-116. [PMID: 28720422 DOI: 10.1016/j.addr.2017.07.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/20/2017] [Accepted: 07/12/2017] [Indexed: 12/21/2022]
Abstract
Myofibroblasts are the key players in extracellular matrix remodeling, a core phenomenon in numerous devastating fibrotic diseases. Not only in organ fibrosis, but also the pivotal role of myofibroblasts in tumor progression, invasion and metastasis has recently been highlighted. Myofibroblast targeting has gained tremendous attention in order to inhibit the progression of incurable fibrotic diseases, or to limit the myofibroblast-induced tumor progression and metastasis. In this review, we outline the origin of myofibroblasts, their general characteristics and functions during fibrosis progression in three major organs: liver, kidneys and lungs as well as in cancer. We will then discuss the state-of-the art drug targeting technologies to myofibroblasts in context of the above-mentioned organs and tumor microenvironment. The overall objective of this review is therefore to advance our understanding in drug targeting to myofibroblasts, and concurrently identify opportunities and challenges for designing new strategies to develop novel diagnostics and therapeutics against fibrosis and cancer.
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Affiliation(s)
- Saleh Yazdani
- Targeted Therapeutics Division, Department of Biomaterials, Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Ruchi Bansal
- Targeted Therapeutics Division, Department of Biomaterials, Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Jai Prakash
- Targeted Therapeutics Division, Department of Biomaterials, Science and Technology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands; ScarTec Therapeutics BV, Enschede, The Netherlands.
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40
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Sakamoto T, Ennifar E, Nakamura Y. Thermodynamic study of aptamers binding to their target proteins. Biochimie 2017; 145:91-97. [PMID: 29054802 DOI: 10.1016/j.biochi.2017.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023]
Abstract
Aptamers are nucleic acids that bind to a target molecule with high affinity and specificity, which are selected from systematic evolution of ligands by exponential enrichment (SELEX). Aptamers feature high affinity and specificity to their target molecule and a large structural diversity; biophysical tools, together with structural studies, are essential to reveal the mechanism of aptamers recognition. Furthermore, understanding the mechanism of action would also contribute to their development for therapeutic applications. Isothermal titration calorimetry (ITC) is a fast and robust method to study the physical basis of molecular interactions. In a single experiment, it provides all thermodynamic parameters of a molecular interaction, including dissociation constant, Kd; Gibbs free energy change, ΔG; enthalpy change, ΔH; entropy change, ΔS; and stoichiometry, N. The development of modern microcalorimeters significantly contributed to the expansion of the ITC use in biological systems. Therefore, ITC has been applied to the development of small therapeutic agents that bind to target proteins and is increasingly being used to study aptamer-target protein interactions. This review focuses on thermodynamic approaches for understanding the molecular principles of aptamer-target interactions.
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Affiliation(s)
- Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan.
| | - Eric Ennifar
- Structure and Dynamics of Biomolecular Machines, Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, F-67000 Strasbourg, France
| | - Yoshikazu Nakamura
- RIBOMIC Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan; The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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41
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Nakamura Y. Aptamers as therapeutic middle molecules. Biochimie 2017; 145:22-33. [PMID: 29050945 DOI: 10.1016/j.biochi.2017.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/12/2017] [Indexed: 02/04/2023]
Abstract
Therapeutic molecules can be classified as low-, middle- and high-molecular weight drugs depending on their molecular masses. Antibodies represent high-molecular weight drugs and their clinical applications have been developing rapidly. Aptamers, on the other hand, are middle-molecular weight molecules that are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. Recently, therapeutic middle molecules gain considerable attention as protein-protein interaction (PPI) inhibitors. This review summarizes the recent achievements in aptamer development in our laboratory in terms of PPI and non-PPI inhibitors.
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Affiliation(s)
- Yoshikazu Nakamura
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; RIBOMIC Inc., Minato-ku, Tokyo 108-0071, Japan.
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42
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Pantsar T, Singha P, Nevalainen TJ, Koshevoy I, Leppänen J, Poso A, Niskanen JM, Pasonen-Seppänen S, Savinainen JR, Laitinen T, Laitinen JT. Design, synthesis, and biological evaluation of 2,4-dihydropyrano[2,3-c]pyrazole derivatives as autotaxin inhibitors. Eur J Pharm Sci 2017; 107:97-111. [DOI: 10.1016/j.ejps.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 01/19/2023]
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43
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Joncour A, Desroy N, Housseman C, Bock X, Bienvenu N, Cherel L, Labeguere V, Peixoto C, Annoot D, Lepissier L, Heiermann J, Hengeveld WJ, Pilzak G, Monjardet A, Wakselman E, Roncoroni V, Le Tallec S, Galien R, David C, Vandervoort N, Christophe T, Conrath K, Jans M, Wohlkonig A, Soror S, Steyaert J, Touitou R, Fleury D, Vercheval L, Mollat P, Triballeau N, van der Aar E, Brys R, Heckmann B. Discovery, Structure–Activity Relationship, and Binding Mode of an Imidazo[1,2-a]pyridine Series of Autotaxin Inhibitors. J Med Chem 2017; 60:7371-7392. [DOI: 10.1021/acs.jmedchem.7b00647] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Agnès Joncour
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Nicolas Desroy
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | | | - Xavier Bock
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Natacha Bienvenu
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Laëtitia Cherel
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | | | | | - Denis Annoot
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Luce Lepissier
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Jörg Heiermann
- Mercachem, Kerkenbos 1013, 6546 Nijmegen, The Netherlands
| | | | - Gregor Pilzak
- Mercachem, Kerkenbos 1013, 6546 Nijmegen, The Netherlands
| | - Alain Monjardet
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | | | | | | | - René Galien
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Christelle David
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Nele Vandervoort
- Galapagos NV, Generaal De Wittelaan
L11 A3, 2800 Mechelen, Belgium
| | | | - Katja Conrath
- Galapagos NV, Generaal De Wittelaan
L11 A3, 2800 Mechelen, Belgium
| | - Mia Jans
- Galapagos NV, Generaal De Wittelaan
L11 A3, 2800 Mechelen, Belgium
| | - Alexandre Wohlkonig
- VIB
Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Sameh Soror
- VIB
Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Jan Steyaert
- VIB
Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussel, Belgium
| | - Robert Touitou
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Damien Fleury
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Lionel Vercheval
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | - Patrick Mollat
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
| | | | | | - Reginald Brys
- Galapagos NV, Generaal De Wittelaan
L11 A3, 2800 Mechelen, Belgium
| | - Bertrand Heckmann
- Galapagos SASU, 102 Avenue Gaston
Roussel, 93230 Romainville, France
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44
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Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes. Int J Mol Sci 2017; 18:ijms18081683. [PMID: 28767098 PMCID: PMC5578073 DOI: 10.3390/ijms18081683] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleic acid aptamers have minimal immunogenicity, high chemical synthesis production, low cost and high chemical stability when compared with antibodies. However, the susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity hindered their development as drug candidates for therapeutic applications. In this review, we will discuss methods to conquer these challenges and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.
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45
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Morihiro K, Kasahara Y, Obika S. Biological applications of xeno nucleic acids. MOLECULAR BIOSYSTEMS 2017; 13:235-245. [PMID: 27827481 DOI: 10.1039/c6mb00538a] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
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Affiliation(s)
- Kunihiko Morihiro
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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46
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Aikawa S, Kano K, Inoue A, Wang J, Saigusa D, Nagamatsu T, Hirota Y, Fujii T, Tsuchiya S, Taketomi Y, Sugimoto Y, Murakami M, Arita M, Kurano M, Ikeda H, Yatomi Y, Chun J, Aoki J. Autotaxin-lysophosphatidic acid-LPA 3 signaling at the embryo-epithelial boundary controls decidualization pathways. EMBO J 2017; 36:2146-2160. [PMID: 28588064 PMCID: PMC5509998 DOI: 10.15252/embj.201696290] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 04/12/2017] [Accepted: 05/02/2017] [Indexed: 12/21/2022] Open
Abstract
During pregnancy, up-regulation of heparin-binding (HB-) EGF and cyclooxygenase-2 (COX-2) in the uterine epithelium contributes to decidualization, a series of uterine morphological changes required for placental formation and fetal development. Here, we report a key role for the lipid mediator lysophosphatidic acid (LPA) in decidualization, acting through its G-protein-coupled receptor LPA3 in the uterine epithelium. Knockout of Lpar3 or inhibition of the LPA-producing enzyme autotaxin (ATX) in pregnant mice leads to HB-EGF and COX-2 down-regulation near embryos and attenuates decidual reactions. Conversely, selective pharmacological activation of LPA3 induces decidualization via up-regulation of HB-EGF and COX-2. ATX and its substrate lysophosphatidylcholine can be detected in the uterine epithelium and in pre-implantation-stage embryos, respectively. Our results indicate that ATX-LPA-LPA3 signaling at the embryo-epithelial boundary induces decidualization via the canonical HB-EGF and COX-2 pathways.
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Affiliation(s)
- Shizu Aikawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kuniyuki Kano
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan.,Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan
| | - Jiao Wang
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Daisuke Saigusa
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank, Tohoku University, Sendai, Miyagi, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasushi Hirota
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Soken Tsuchiya
- Department of Pharmaceutical Biochemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Taketomi
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Center for Disease Biology and Integrative Medicine Graduate School of Medicine The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yukihiko Sugimoto
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Department of Pharmaceutical Biochemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Makoto Murakami
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.,Center for Disease Biology and Integrative Medicine Graduate School of Medicine The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Makoto Kurano
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Department of Clinical Laboratory, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Hitoshi Ikeda
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Department of Clinical Laboratory, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yutaka Yatomi
- Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan.,Department of Clinical Laboratory, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan .,Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Chiyoda-ku, Tokyo, Japan
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47
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Nikolaou A, Kokotou MG, Limnios D, Psarra A, Kokotos G. Autotaxin inhibitors: a patent review (2012-2016). Expert Opin Ther Pat 2017; 27:815-829. [DOI: 10.1080/13543776.2017.1323331] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Aikaterini Nikolaou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Maroula G. Kokotou
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitris Limnios
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasia Psarra
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kokotos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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48
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Desroy N, Housseman C, Bock X, Joncour A, Bienvenu N, Cherel L, Labeguere V, Rondet E, Peixoto C, Grassot JM, Picolet O, Annoot D, Triballeau N, Monjardet A, Wakselman E, Roncoroni V, Le Tallec S, Blanque R, Cottereaux C, Vandervoort N, Christophe T, Mollat P, Lamers M, Auberval M, Hrvacic B, Ralic J, Oste L, van der Aar E, Brys R, Heckmann B. Discovery of 2-[[2-Ethyl-6-[4-[2-(3-hydroxyazetidin-1-yl)-2-oxoethyl]piperazin-1-yl]-8-methylimidazo[1,2-a]pyridin-3-yl]methylamino]-4-(4-fluorophenyl)thiazole-5-carbonitrile (GLPG1690), a First-in-Class Autotaxin Inhibitor Undergoing Clinical Evaluation for the Treatment of Idiopathic Pulmonary Fibrosis. J Med Chem 2017; 60:3580-3590. [PMID: 28414242 DOI: 10.1021/acs.jmedchem.7b00032] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Autotaxin is a circulating enzyme with a major role in the production of lysophosphatic acid (LPA) species in blood. A role for the autotaxin/LPA axis has been suggested in many disease areas including pulmonary fibrosis. Structural modifications of the known autotaxin inhibitor lead compound 1, to attenuate hERG inhibition, remove CYP3A4 time-dependent inhibition, and improve pharmacokinetic properties, led to the identification of clinical candidate GLPG1690 (11). Compound 11 was able to cause a sustained reduction of LPA levels in plasma in vivo and was shown to be efficacious in a bleomycin-induced pulmonary fibrosis model in mice and in reducing extracellular matrix deposition in the lung while also reducing LPA 18:2 content in bronchoalveolar lavage fluid. Compound 11 is currently being evaluated in an exploratory phase 2a study in idiopathic pulmonary fibrosis patients.
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Affiliation(s)
- Nicolas Desroy
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Xavier Bock
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Agnès Joncour
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Natacha Bienvenu
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Laëtitia Cherel
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Emilie Rondet
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | | | - Olivier Picolet
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Denis Annoot
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | - Alain Monjardet
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | | | | | | | - Roland Blanque
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Celine Cottereaux
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Nele Vandervoort
- Galapagos NV , Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Patrick Mollat
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Marieke Lamers
- Charles River Laboratories , Chesterford Research Park, CB10 1XL Saffron Walden, United Kingdom
| | - Marielle Auberval
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
| | - Boska Hrvacic
- Fidelta Ltd. , Prilaz baruna Filipovića 29, Zagreb, HR-10000, Croatia
| | - Jovica Ralic
- Fidelta Ltd. , Prilaz baruna Filipovića 29, Zagreb, HR-10000, Croatia
| | - Line Oste
- Galapagos NV , Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Reginald Brys
- Galapagos NV , Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Bertrand Heckmann
- Galapagos SASU , 102 Avenue Gaston Roussel, 93230 Romainville, France
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49
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Amano R, Aoki K, Miyakawa S, Nakamura Y, Kozu T, Kawai G, Sakamoto T. NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci Rep 2017; 7:283. [PMID: 28325909 PMCID: PMC5428055 DOI: 10.1038/s41598-017-00273-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 01/20/2023] Open
Abstract
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kazuteru Aoki
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Shin Miyakawa
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Yoshikazu Nakamura
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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Banerjee S, Norman DD, Lee SC, Parrill AL, Pham TCT, Baker DL, Tigyi GG, Miller DD. Highly Potent Non-Carboxylic Acid Autotaxin Inhibitors Reduce Melanoma Metastasis and Chemotherapeutic Resistance of Breast Cancer Stem Cells. J Med Chem 2017; 60:1309-1324. [PMID: 28112925 PMCID: PMC7938327 DOI: 10.1021/acs.jmedchem.6b01270] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Autotaxin (ATX, aka. ENPP2) is the main source of the lipid mediator lysophosphatidic acid (LPA) in biological fluids. This study reports on inhibitors of ATX derived by lead optimization of the benzene-sulfonamide in silico hit compound 3. The new analogues provide a comprehensive structure-activity relationship of the benzene-sulfonamide scaffold that yielded a series of highly potent ATX inhibitors. The three most potent analogues (3a, IC50 ∼ 32 nM; 3b, IC50 ∼ 9 nM; and 14, IC50 ∼ 35 nM) inhibit ATX-dependent invasion of A2058 human melanoma cells in vitro. Two of the most potent compounds, 3b and 3f (IC50 ∼ 84 nM), lack inhibitory action on ENPP6 and ENPP7 but possess weak antagonist action specific to the LPA1 G protein-coupled receptor. In particular, compound 3b potently reduced in vitro chemotherapeutic resistance of 4T1 breast cancer stem-like cells to paclitaxel and significantly reduced B16 melanoma metastasis in vivo.
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Affiliation(s)
- Souvik Banerjee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Derek D. Norman
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Sue Chin Lee
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Abby L. Parrill
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, United States
- Computational Research on Materials Institute, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Truc Chi T. Pham
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Daniel L. Baker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, United States
| | - Gabor G. Tigyi
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Duane D. Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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