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Nucleic Acid Ligands Act As a PAM and Agonist Depending on the Intrinsic Ligand Binding State of P2RY2

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Nucleic Acid Ligands Act As a PAM and Agonist Depending on the Intrinsic Ligand Binding State of P2RY2 Nucleic acid ligands act as a PAM and agonist depending on the intrinsic ligand binding state of P2RY2 Masaki Takahashia,1, Ryo Amanoa, Michiru Ozawab, Anna Martinezb, Kazumasa Akitab, and Yoshikazu Nakamuraa,b,1 aProject Division of RNA Medical Science, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; and bRIBOMIC Inc., Tokyo 108-0071, Japan Edited by Brian K. Kobilka, Stanford University School of Medicine, Stanford, CA, and approved March 31, 2021 (received for review September 16, 2020) G protein–coupled receptors (GPCRs) play diverse roles in physiolog- Nonetheless, few aptamers targeting cell-surface proteins, espe- ical processes, and hence the ligands to modulate GPCRs have cially GPCRs, have been reported because of a poor integration of served as important molecules in biological and pharmacological the technologies, despite advances in each relevant technique and approaches. However, the exploration of novel ligands for GPCR expertise. still remains an arduous challenge. In this study, we report a method As aptamers specifically recognize targets with shape comple- for the discovery of nucleic acid ligands against GPCRs by an ad- mentarity, it is vital to choose and prepare selection targets in their vanced RNA aptamer screening technology that employs a virus-like native conformation. Accordingly, although several types of selec- particle (VLP), exposing the GPCR of interest. An array of biochem- tion materials targeting cell-surface proteins (e.g., recombinant ical analyses coupled with a cell-based assay revealed that one of the aptamers raised against purinergic receptor P2Y2 (P2RY2), a proteins, membrane extract, and whole cells) have been used (13, GPCR, exhibits an activation potency to unliganded receptor and 14), the most promising source material appear to be live whole prohibits a further receptor activation by endogenous ligand, be- cells, which ensure the native target structure even in case of un- having like a partial agonist. However, the aptamer enhances the stable proteins. However, such SELEX imposes several restrictions activity of intrinsic ligand-binding P2RY2, thereby acting as a posi- on the selection process because the effects on cell viability must be tive allosteric modulator (PAM) to liganded receptor. Our findings considered for ensuring target structure and for reducing noise BIOCHEMISTRY demonstrate that the nucleic acid aptamer conditionally exerts PAM proteins arising from dead cells. Moreover, SELEX using cells and and agonist effects on GPCRs, depending on their intrinsic ligand other crude materials concomitantly give rise to various aptamers binding state. These results indicate the validity of our VLP-based bound to nontarget proteins. To address this, in addition to ana- aptamer screening targeting GPCR and reemphasize the great po- lyzing a huge number of sequences in enriched libraries, in silico tential of nucleic acid ligands for exploring the GPCR activation analysis is required to unveil concealed aptamers bound to the mechanism and therapeutic applications. target from numerous sequences. A recent study highlighted the importance of such technologies (e.g., high-throughput sequencing GPCR | nucleic acid aptamer | PAM agonist | P2RY2 and bioinformatics) to isolate aptamers bound to a specific GPCR embedded in detergent micelles that mimic the lipid bilayer (15). protein–coupled receptors (GPCRs) are involved in varied Ghuman physiological functions and are targets for one-third of currently marketed drugs (1). Besides studies on specific inhibitors Significance and activators interacting with the orthosteric ligand-binding pockets of GPCRs, recent studies shedding light on allosteric Discovery of ligands for G protein–coupled receptors (GPCRs) is of modulators have drawn attention for providing a deeper under- importance in receptor biology and pharmacology but is still a standing of the molecular mechanisms underlying GPCR activation challenging issue. Here, we propose a method for the discovery of that may be exploited for potential therapeutics (2, 3). However, ligands against GPCRs by employing a virus-like particle (VLP) and the technology for developing novel compounds targeting GPCRs show unique properties of identified nucleic acid aptamers for has inherent technical hurdles for high expression and purification GPCR. One aptamer raised against purinergic receptor P2Y2 of GPCRs in their native conformation. An innovative platform (P2RY2), a GPCR, behaves like a partial agonist to unliganded re- remains to be developed to produce any type of GPCRs abun- ceptor, whereas it exhibits a positive allosteric modulator (PAM) dantly and easily while retaining the native conformation. activity to liganded receptor. We demonstrate the validity of our Nucleic acid aptamers are single-stranded oligonucleotides that aptamer screening method targetingVLP-stabilizedGPCRanda adopt diverse conformations and recognize target epitopes with unique aptamer with dual function, agonist and PAM, for GPCR, relatively high shape complementarity (4). Aptamers are isolated depending on whether the intrinsic ligand is prebound to the in vitro from combinatorial libraries composed of approximately receptor. a quadrillion molecules that give rise to a vast set of three- dimensional (3D) structures based on their primary sequence Author contributions: M.T. designed research; M.T., R.A., M.O., A.M., and K.A. performed research; M.T. and K.A. contributed new reagents/analytic tools; M.T., R.A., and K.A. an- and chemistry. The first conceptual method is referred to as sys- alyzed data; and M.T. and Y.N. wrote the paper. tematic evolution of ligands by exponential enrichment (SELEX) Competing interest statement: M.O., A.M., K.A., and Y.N. are employees of RIBOMIC Inc. (5, 6) and has generated various experimental and pharmacolog- and hold equity in RIBOMIC Inc. ical agents (7, 8). One of the most important features of SELEX This article is a PNAS Direct Submission. (or aptamer) is that aptamers can be generated against various This open access article is distributed under Creative Commons Attribution License 4.0 targets with high affinity and specificity, regardless of the molec- (CC BY). ular weight and complexity of targets, which range from small 1To whom correspondence may be addressed. Email: [email protected] or chemical compounds to recombinant proteins, bacteria, viruses, [email protected]. and cultured cells. Along with a wide range of target tolerances, This article contains supporting information online at https://www.pnas.org/lookup/suppl/ technological advances in sequencing and bioinformatics have doi:10.1073/pnas.2019497118/-/DCSupplemental. substantially expanded the potential of aptamer discovery (9–12). Published April 28, 2021. PNAS 2021 Vol. 118 No. 18 e2019497118 https://doi.org/10.1073/pnas.2019497118 | 1of7 Downloaded by guest on September 25, 2021 However, this method is only applicable to certain GPCRs whose were further analyzed using FASTAptamer (21) to efficiently structure is highly stable, such as beta2-adrenoreceptor. discover potential sequences based on the read per million (RPM) Here, we propose a method for exploring nucleic acid aptamers and enrichment (ratio of RPM of sequences in positive to that in as ligands for GPCRs by employing virus-like particles (VLPs) and false-positive sequence data) (details in Materials and Methods and immobilization-free partitioning manner (Fig. 1). Based on this Dataset S1). SELEX method using VLPs (VLP-SELEX), we screened aptam- A subsequent heatmap analysis clearly visualized the difference ers against the purinergic receptor P2Y2 (P2RY2) as a model in the read number of each aptamer, composing the enriched li- target of GPCR and elucidated their functional properties. An brary between the target and nontarget VLPs (Fig. 2A). Fur- array of biochemical analysis coupled with cell-based assay thermore, a scatter plot based on the above-mentioned clustering revealed that one of the aptamers shows dual function depending analysis with FASTAptamer indicated eight enriched sequences on whether the intrinsic ligand, uridine triphosphates (UTP), is with the highest RPM in each of the top eight clusters (see Ma- bound to the receptor. When P2RY2 is unliganded, the aptamer terials and Methods and Fig. 2B). These eight sequences were then has activation potency and prohibits further receptor activation by subjected to motif and cluster analyses (SI Appendix,Fig.S3). The endogenous ligand UTP. In contrast, when P2RY2 is liganded, the in silico analyses highlighted the sequences c1, c11, and c37 that aptamer has a positive allosteric modulator (PAM) activity to a represent unique compositions of defined motifs, which were UTP-bound receptor. These findings suggest that the aptamer subjected to further functional analyses. binds to an allosteric site of the receptor and prevents UTP from activating an unliganded GPCR by occluding the orthosteric Functional Assessment of Isolated Aptamers. Since agonist-mediated binding pocket and/or by changing the conformation of the binding α pocket. To our knowledge, this is the first bifunctional aptamer P2RY2 activations evokes calcium signaling via the G qprotein with dual agonist and PAM activity for GPCR depending on (22), the effect of aptamer on P2RY2 function was examined by whether endogenous ligand is prebound to the receptor. Our re- measuring the second messenger, calcium ions, using an Aequorin- sults reinforce the validity of VLP-SELEX targeting
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