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Lee DH, Oh S, Lim K, Lee B, Yi GS, Kim YR, Kim KB, Lee CK, Chi SW, Lee MK. Tertiary RNA Folding-Targeted Drug Screening Strategy Using a Protein Nanopore. Anal Chem 2021; 93:2811-2819. [PMID: 33475355 DOI: 10.1021/acs.analchem.0c03941] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Bacterial riboswitch RNAs are attractive targets for novel antibiotics against antibiotic-resistant superbacteria. Their binding to cognate metabolites is essential for the regulation of bacterial gene expression. Despite the importance of RNAs as therapeutic targets, the development of RNA-targeted, small-molecule drugs is limited by current biophysical methods. Here, we monitored the specific interaction between the adenine-sensing riboswitch aptamer domain (ARS) and adenine at the single-molecule level using α-hemolysin (αHL) nanopores. During adenine-induced tertiary folding, adenine-bound ARS intermediates exhibited characteristic nanopore events, including a two-level ionic current blockade and a ∼ 5.6-fold longer dwell time than that of free RNA. In a proof-of-concept experiment, tertiary RNA folding-targeted drug screening was performed using a protein nanopore, which resulted in the discovery of three new ARS-targeting hit compounds from a natural compound library. Taken together, these results reveal that αHL nanopores are a valuable platform for ultrasensitive, label-free, and single-molecule-based drug screening against therapeutic RNA targets.
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Affiliation(s)
- Dong-Hwa Lee
- Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea.,College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sohee Oh
- Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Kyungeun Lim
- Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Boah Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea
| | - Young-Rok Kim
- Graduate School of Biotechnology & Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Chong-Kil Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, KRIBB, Daejeon 34141, Republic of Korea.,Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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Mehdizadeh Aghdam E, Barzegar A, Hejazi MS. Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction. Adv Pharm Bull 2014; 4:225-35. [PMID: 24754005 DOI: 10.5681/apb.2014.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/24/2013] [Accepted: 11/26/2013] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA), raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. METHODS Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting "A site" of 16S rRNA) to riboswitches via docking method. RESULTS There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8) hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with "16S rRNA A site". Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA "A site" suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. CONCLUSION These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Drug Applied Research Center and Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran. ; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Drug Applied Research Center and Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. ; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
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Ramisetty SR, Baranger AM. Cooperative binding of a quinoline derivative to an RNA stem loop containing a dangling end. Bioorg Med Chem Lett 2010; 20:3134-7. [DOI: 10.1016/j.bmcl.2010.03.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/23/2010] [Accepted: 03/26/2010] [Indexed: 11/25/2022]
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