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Social Cooperation Research Program

Project Division of RNA Medical Science
RNA 医科学社会連携研究部門
Project Associate Professor
Masaki Takahashi, Ph.D.
Project Senior Assistant Professor Kaku Goto, Ph.D.

特任准教授
特任講師

博士（理学）
博士（医学）

高後橋藤理

貴覚

RNA no longer stands behind DNA or protein but stands in front of DNA andprotein. Recent achievements and discovery in biological science clearly
emphasize the importance of RNA in life: the discovery of RNA interference,molecular mimicry between protein and RNA, ribosome structure at atomic
resolution, and RNA quality control triggered by aberrant mRNAs. Moreover, thecompleted human genome project revealed, to our great surprise, the existence ofa large amount of protein-noncoding RNAs (ncRNAs). These ncRNAs can beclassified into two types: one, like antisense and microRNA, those function withsequence complementarity to the target mRNA or DNA, while the other, likeaptamer, those function independent of sequence complementarity. In ourlaboratory, we aim to create artificial aptamers to target proteins of therapeuticinterest.
The concept of using single-stranded nucleic acids (aptamers) as affinity molecules
for protein or compound binding was initially described in 1990. The concept isbased on the ability of short oligonucleotides to fold, in the presence of a target,
into unique three-dimensional (3D) structures that bind the target with high affinity
and specificity. Aptamers are generated by a process known as systematic
evolution of ligands by exponential enrichment (SELEX), which merges
combinatorial chemistry with in vitro evolution from a complex library of randomized
10 14-15 different sequences. Importantly, aptamer targets can be small (e.g.,chemical compounds) or large (e.g., proteins), and simple (e.g., purified proteins)or complex (e.g., protein complexes or cell surface receptors). Therefore, aptamers
can be used as therapeutic compounds or reagents for affinity purification or as
biosensor elements.

1.  SELEX targeting virus-like particle generates
RNA aptamers inhibiting the chikungunya virus
Kaku Goto, Ryo Amano, Akiko Ichinose1, Akiya
Michishita1, Michiaki Hamada1, Yoshikazu Nakamura2, Masaki Takahashi: 1Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan; 2RIBOMIC Inc., Tokyo108-0071, JapanNucleic acid aptamers are a promising drug modality, but it remains difficult to generate virus-neutralizing aptamers because of the lack of a robust system for the discovery of aptamers targeting virus
particles of interest. We report that a platform technology to develop virus neutralizing RNA aptamers
targeting chikungunya virus (CHIKV) as a model target by adopting our SELEX method with virus-likeparticles (VLPs), VLP-SELEX. An identified aptamer
raised against CHIKV-VLPs, Apt#1, and its truncatedderivatives showed neutralizing activity with IC50

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values in the nanomolar range in a cell-based assay
system using a pseudoviral particle of CHIKV(CHIKVpp). An antiviral-based chemical genetic approach for probing the interaction area of Apt#1
showed additive effects of Apt#1 with most assessed
antivirals, whereas potent competitiveness withsuramin, a reported interactant with domain A of E2
envelope protein (E2DA), was revealed in both cell-based and surface plasmon resonance analyses, predicting E2DA to be the Apt#1 interface. Further, Apt#1
interfered with the attachment process of CHIKVpp,
suggesting it acts as an attachment inhibitor targeting
E2DA in CHIKV in concert with certain antivirals.
These results suggest that VLP-SELEX may be a novel
feasible option for exploring virus-neutralizing agentstargeting virus-particles of interest.

Publications
1.		Daniel S Pereira, Akita K, Robert B Bhisitkul,
Nishihata T, Yusuf Ali, Nakamura E, Nakamura
Y: Safety and tolerability of intravitreal umedaptanib pegol (anti-FGF2) for neovascular age-related macular degeneration (nAMD): a phase 1,
open-label study.” Eye (Lond), 2023 Dec 1, doi:
10.1038/s41433-023-02849-6. Online ahead of print.
2.		Daniel S Pereira, Raj K Maturi, Akita K, VinayaMahesh, Robert B Bhisitkul, Nishihata T, Sakota E,Yusuf Ali, Nakamura E, Padma Bezwada, Nakamura Y.: Clinical proof of concept for anti-FGF2
therapy in exudative age-related macular degeneration (nAMD): phase 2 trials in treatment-naïve
and anti-VEGF pretreated patients. Eye (Lond),
2023 Nov 30, doi: 10.1038/s41433-023-02848-7. Online ahead of print.