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Takeuchi S, Yamazaki T, Yamaguchi K, Komura F, Tabata T, Nishi H, Azumai S, Miura K, Hirokawa M, Ikemoto K, Kawakami K. Toward the Establishment of a Harmonized Physicochemical Profiling Platform for Therapeutic Oligonucleotides: A Case Study for Aptamers Where the Higher-Order Structure Influences Physical Properties. Mol Pharm 2024; 21:3471-3484. [PMID: 38872243 DOI: 10.1021/acs.molpharmaceut.4c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Oligonucleotides are short nucleic acids that serve as one of the most promising classes of drug modality. However, attempts to establish a physicochemical evaluation platform of oligonucleotides for acquiring a comprehensive view of their properties have been limited. As the chemical stability and the efficacy as well as the solution properties at a high concentration should be related to their higher-order structure and intra-/intermolecular interactions, their detailed understanding enables effective formulation development. Here, the higher-order structure and the thermodynamic stability of the thrombin-binding aptamer (TBA) and four modified TBAs, which have similar sequences but were expected to have different higher-order structures, were evaluated using ultraviolet spectroscopy (UV), circular dichroism (CD), differential scanning calorimetry (DSC), and nuclear magnetic resonance (NMR). Then, the relationship between the higher-order structure and the solution properties including solubility, viscosity, and stability was investigated. The impact of the higher-order structure on the antithrombin activity was also confirmed. The higher-order structure and intra-/intermolecular interactions of the oligonucleotides were affected by types of buffers because of different potassium concentrations, which are crucial for the formation of the G-quadruplex structure. Consequently, solution properties, such as solubility and viscosity, chemical stability, and antithrombin activity, were also influenced. Each instrumental analysis had a complemental role in investigating the higher-order structure of TBA and modified TBAs. The utility of each physicochemical characterization method during the preclinical developmental stages is also discussed.
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Affiliation(s)
- Shoko Takeuchi
- Analytical Development, Pharmaceutical Sciences, Takeda Pharmaceutical Co., Ltd., 26-1 Muraoka Higashi 2-Chome, Fujisawa, Kanagawa 2518555, Japan
| | - Tomohiko Yamazaki
- Medical Soft Matter Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 3050044, Japan
| | - Katsutoshi Yamaguchi
- Pharmaceutical Developability, CMC Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 3058585, Japan
| | - Fusae Komura
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba-shi, Ibaraki 3002635, Japan
| | - Takahiro Tabata
- Pharmacokinetics Group, Biological Research Development, Sawai Pharmaceutical Co., Ltd., 5-2-30 Miyahara, Yodogawa-ku, Osaka 5320003, Japan
| | - Hirotaka Nishi
- Formulation Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 1408710, Japan
| | - Satomi Azumai
- Formulation Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 1408710, Japan
| | - Kanako Miura
- Formulation Technology Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 1408710, Japan
| | - Mai Hirokawa
- Modality Pharmaceutical Research Group, CMC Modality Technology Laboratories, Production Technology & Supply Chain Management Division, Mitsubishi Tanabe Pharma Corporation, 7473-2, Onoda, Sanyo-Onoda, Yamaguchi 7560054, Japan
| | - Keisuke Ikemoto
- Modality Pharmaceutical Research Group, CMC Modality Technology Laboratories, Production Technology & Supply Chain Management Division, Mitsubishi Tanabe Pharma Corporation, 7473-2, Onoda, Sanyo-Onoda, Yamaguchi 7560054, Japan
| | - Kohsaku Kawakami
- Medical Soft Matter Group, Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 3050044, Japan
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 3058577, Japan
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Salmasi Z, Rouhi N, Safarpour H, Zebardast N, Zare H. The Recent Progress in DNAzymes-Based Aptasensors for Thrombin Detection. Crit Rev Anal Chem 2022; 54:818-839. [PMID: 35867568 DOI: 10.1080/10408347.2022.2098671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Thrombin (TB) is classified among human blood coagulation proteins with key functions in hemostasis of blood vessels, wound healing, atherosclerosis, tissue adhesion, etc. Moreover, TB is involved as the main enzyme in the conversion of the fibrinogen to fibrin. Given the importance of TB detection in the clinical area, the development of innovative methods can considerably improve TB detection. Newly, aptasensors or aptamer-based biosensors have received special attention for sensitive and facile TB detection. In addition, the aptamer/nanomaterial conjugates have presented new prospects in accurate TB detection as nanoaptasensors. DNA-based enzymes or DNAzymes, as new biocatalysts, have many advantages over protein enzymes and can be used in analytical tools. This article reviews a brief overview of significant progresses regarding the various types of DNAzymes-based aptasensors and nano aptasensors developed for thrombin detection. In the following, challenges and prospects of TB detection by DNAzymes-based aptasensors are discussed.
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Affiliation(s)
- Zahra Salmasi
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nadiyeh Rouhi
- Seafood Processing Department, Marine Science Faculty, Tarbiat Modares University, Tehran, Iran
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Nozhat Zebardast
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Hamed Zare
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
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Beyond G-Quadruplexes-The Effect of Junction with Additional Structural Motifs on Aptamers Properties. Int J Mol Sci 2021; 22:ijms22189948. [PMID: 34576112 PMCID: PMC8466185 DOI: 10.3390/ijms22189948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes constitute an important type of nucleic acid structure, which can be found in living cells and applied by cell machinery as pivotal regulatory elements. Importantly, robust development of SELEX technology and modern, nucleic acid-based therapeutic strategies targeted towards various molecules have also revealed a large group of potent aptamers whose structures are grounded in G-quadruplexes. In this review, we analyze further extension of tetraplexes by additional structural elements and investigate whether G-quadruplex junctions with duplex, hairpin, triplex, or second G-quadruplex motifs are favorable for aptamers stability and biological activity. Furthermore, we indicate the specific and pivotal role of the G-quadruplex domain and the additional structural elements in interactions with target molecules. Finally, we consider the potency of G-quadruplex junctions in future applications and indicate the emerging research area that is still waiting for development to obtain highly specific and effective nucleic acid-based molecular tools.
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