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Rivera M, Ayon OS, Diaconescu-Grabari S, Pottel J, Moitessier N, Mittermaier A, McKeague M. A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states. Nucleic Acids Res 2024; 52:3164-3179. [PMID: 38375901 PMCID: PMC11014391 DOI: 10.1093/nar/gkae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
The capacity of riboswitches to undergo conformational changes in response to binding their native ligands is closely tied to their functional roles and is an attractive target for antimicrobial drug design. Here, we established a probe-based fluorescence anisotropy assay to monitor riboswitch conformational switching with high sensitivity and throughput. Using the Bacillus subtillis yitJ S-Box (SAM-I), Fusobacterium nucleatum impX RFN element of (FMN) and class-I cyclic-di-GMP from Vibrio cholerae riboswitches as model systems, we developed short fluorescent DNA probes that specifically recognize either ligand-free or -bound riboswitch conformational states. We showed that increasing concentrations of native ligands cause measurable and reproducible changes in fluorescence anisotropy that correlate with riboswitch conformational changes observed by native gel analysis. Furthermore, we applied our assay to several ligand analogues and confirmed that it can discriminate between ligands that bind, triggering the native conformational change, from those that bind without causing the conformational change. This new platform opens the possibility of high-throughput screening compound libraries to identify potential new antibiotics that specifically target functional conformational changes in riboswitches.
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Affiliation(s)
- Maira Rivera
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | - Omma S Ayon
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Joshua Pottel
- Molecular Forecaster Inc. 910-2075 Robert Bourassa, Montreal, QC H3A 2L1, Canada
| | - Nicolas Moitessier
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
- Molecular Forecaster Inc. 910-2075 Robert Bourassa, Montreal, QC H3A 2L1, Canada
| | - Anthony Mittermaier
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC H3A 0B8, Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 1Y6, Canada
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2
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Tidwell ED, Kilde IR, Leskaj S, Koutmos M. Fluorescent Ligand Equilibrium Displacement: A High-Throughput Method for Identification of FMN Riboswitch-Binding Small Molecules. Int J Mol Sci 2024; 25:735. [PMID: 38255809 PMCID: PMC11154562 DOI: 10.3390/ijms25020735] [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: 10/25/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Antibiotic resistance remains a pressing global concern, with most antibiotics targeting the bacterial ribosome or a limited range of proteins. One class of underexplored antibiotic targets is bacterial riboswitches, structured RNA elements that regulate key biosynthetic pathways by binding a specific ligand. We developed a methodology termed Fluorescent Ligand Equilibrium Displacement (FLED) to rapidly discover small molecules that bind the flavin mononucleotide (FMN) riboswitch. FLED leverages intrinsically fluorescent FMN and the quenching effect on RNA binding to create a label-free, in vitro method to identify compounds that can bind the apo population of riboswitch in a system at equilibrium. The response difference between known riboswitch ligands and controls demonstrates the robustness of the method for high-throughput screening. An existing drug discovery library that was screened using FLED resulted in a final hit rate of 0.67%. The concentration response of each hit was determined and revealed a variety of approximate effective concentration values. Our preliminary screening data support the use of FLED to identify small molecules for medicinal chemistry development as FMN riboswitch-targeted antibiotic compounds. This robust, label-free, and cell-free method offers a strong alternative to other riboswitch screening methods and can be adapted to a variety of laboratory setups.
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Affiliation(s)
| | - Ingrid R. Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Markos Koutmos
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
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3
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Velema WA. Exploring antibiotic resistance with chemical tools. Chem Commun (Camb) 2023; 59:6148-6158. [PMID: 37039397 PMCID: PMC10194278 DOI: 10.1039/d3cc00759f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Antibiotic resistance is an enormous problem that is accountable for over a million deaths annually, with numbers expected to significantly increase over the coming decades. Although some of the underlying causes leading up to antibiotic resistance are well understood, many of the molecular processes involved remain elusive. To better appreciate at a molecular level how resistance emerges, customized chemical biology tools can offer a solution. This Feature Article attempts to provide an overview of the wide variety of tools that have been developed over the last decade, by highlighting some of the more illustrative examples. These include the use of fluorescent, photoaffinity and activatable antibiotics and bacterial components to start to unravel the molecular mechanisms involved in resistance. The antibiotic crisis is an eminent global threat and requires the continuous development of creative chemical tools to dissect and ultimately counteract resistance.
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Affiliation(s)
- Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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4
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Garner AL. Contemporary Progress and Opportunities in RNA-Targeted Drug Discovery. ACS Med Chem Lett 2023; 14:251-259. [PMID: 36923915 PMCID: PMC10009794 DOI: 10.1021/acsmedchemlett.3c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The surprising discovery that RNAs are the predominant gene products to emerge from the human genome catalyzed a renaissance in RNA biology. It is now well-understood that RNAs act as more than just a messenger and comprise a large and diverse family of ribonucleic acids of differing sizes, structures, and functions. RNAs play expansive roles in the cell, contributing to the regulation and fine-tuning of nearly all aspects of gene expression and genome architecture. In line with the significance of these functions, we have witnessed an explosion in discoveries connecting RNAs with a variety of human diseases. Consequently, the targeting of RNAs, and more broadly RNA biology, has emerged as an untapped area of drug discovery, making the search for RNA-targeted therapeutics of great interest. In this Microperspective, I highlight contemporary learnings in the field and present my views on how to catapult us toward the systematic discovery of RNA-targeted medicines.
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, United States
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5
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Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
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Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
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6
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Wang GA, Wu X, Chen F, Shen C, Yang Q, Li F. Toehold-Exchange-Based Activation of Aptamer Switches Enables High Thermal Robustness and Programmability. J Am Chem Soc 2023; 145:2750-2753. [PMID: 36701187 DOI: 10.1021/jacs.2c10928] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aptamer switches are attractive nature-inspired tools for developing smart materials and nanodevices. However, the thermal robustness and programmability of current aptamer switches are often limited by their activation processes that are coupled with high reaction enthalpy. Here, we present an enthalpy-independent activation approach that harnesses toehold-exchange as a general framework to design aptamer switches. We demonstrate mathematically and experimentally that this approach is highly effective in improving thermal robustness and thus leads to better analytical performances of aptamer switches. Enhanced programmability is also demonstrated through fine-grained and dynamic tuning of effective affinities and dynamic ranges, as well as the construction of a synthetic DNA network that resembled biological signaling cascades. Our study not only enriches the current toolbox for engineering and controlling synthetic molecular switches but also offers new insights into their thermodynamic basis, which is critical for diverse synthetic biological designs and applications.
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Affiliation(s)
- Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Xinghong Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Fangfang Chen
- College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, China, 710127
| | - Chenlan Shen
- Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Qianfan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan, China, 610064.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario, Canada, L2S 3A1.,Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
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7
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Yu H, Wang S, Huang J, Fu Y, Wagner M, Weil T, Zhong F, Zhao W, Wu Y. Light-Controlled Traceless Protein Labeling via Decaging Thio- o-naphthoquinone Methide Chemistry. Org Lett 2022; 24:6816-6821. [PMID: 36099167 DOI: 10.1021/acs.orglett.2c02742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the molecular design of a novel multifunctional reagent and its application for light-controlled selective protein labeling. This molecule integrates functions of protein-ligand recognition, bioconjugation, ligand cleavage, and photoactivation by merging the photochemistries of 2-nitrophenylpropyloxycarbonyl and 3-hydroxymethyl-2-naphthol with an affinity ligand and fluorescein. Highly electrophilic o-naphthoquinone methide was photochemically released and underwent proximity-driven selective labeling with the protein of interest (e.g., carbonic anhydrases), which retains its native function after labeling.
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Affiliation(s)
- Huaibin Yu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Shuangshuang Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Jianjian Huang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Yu Fu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fangrui Zhong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China
| | - Yuzhou Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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8
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Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. A Riboswitch-Driven Era of New Antibacterials. Antibiotics (Basel) 2022; 11:antibiotics11091243. [PMID: 36140022 PMCID: PMC9495366 DOI: 10.3390/antibiotics11091243] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi, 15341 Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-997932
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