1
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Parmar S, Bume DD, Connelly CM, Boer RE, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS. Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression. Nat Commun 2024; 15:8173. [PMID: 39289353 PMCID: PMC11408619 DOI: 10.1038/s41467-024-52235-3] [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: 02/26/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024] Open
Abstract
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
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Affiliation(s)
- Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Desta Doro Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Colleen M Connelly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Robert E Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Peri R Prestwood
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | | | | | | | | | - Philip Homan
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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2
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Fullenkamp CR, Mehdi S, Jones CP, Tenney L, Pichling P, Prestwood PR, Ferré-D'Amaré AR, Tiwary P, Schneekloth JS. Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612887. [PMID: 39314358 PMCID: PMC11419147 DOI: 10.1101/2024.09.13.612887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes influence gene expression pose significant difficulties for experimental investigation. This work employs a combination of computational and experimental methods to address these challenges. By integrating structure-informed design, crystallography, and machine learning-augmented all-atom molecular dynamics simulations (MD) we synthesized, biophysically and biochemically characterized, and studied the dissociation of a library of small molecule activators of the ZTP riboswitch, a ligand-binding RNA motif that regulates bacterial gene expression. We uncovered key interaction mechanisms, revealing valuable insights into the role of ligand binding kinetics on riboswitch activation. Further, we established that ligand on-rates determine activation potency as opposed to binding affinity and elucidated RNA structural differences, which provide mechanistic insights into the interplay of RNA structure on riboswitch activation.
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Affiliation(s)
| | - Shams Mehdi
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Christopher P Jones
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Logan Tenney
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Patricio Pichling
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peri R Prestwood
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
- University of Maryland Institute for Health Computing, Bethesda, Maryland 20852, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA
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3
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Mukherjee S, Barash D. Designing RNA switches for synthetic biology using inverse-RNA-folding. Trends Biotechnol 2024; 42:517-521. [PMID: 38040620 DOI: 10.1016/j.tibtech.2023.11.005] [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] [Received: 08/22/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023]
Abstract
RNA switches respond to specific ligands to control gene expression. They are widely used in synthetic biology applications and hold potential for future RNA-based therapeutic breakthroughs. However, the crux is their precise design. Here, we will discuss how inverse-RNA-folding could be utilized for the accurate design of RNA switches.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA; Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel.
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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4
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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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5
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Bushhouse DZ, Fu J, Lucks JB. RNA folding kinetics control riboswitch sensitivity in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587317. [PMID: 38585885 PMCID: PMC10996619 DOI: 10.1101/2024.03.29.587317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is controlled is critical to understanding how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover new roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating the Clostridium beijerinckii pfl ZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures that regulate transcription and translation with ON and OFF logic demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Comparison of the most sensitized versions of these switches to equilibrium aptamer:ligand dissociation constants suggests a limit to the sensitivities achievable by kinetic RNA switches. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.
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Affiliation(s)
- David Z. Bushhouse
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Jiayu Fu
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Julius B. Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
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6
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Sun S, Gao L. Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction. Bioinformatics 2024; 40:btae155. [PMID: 38507691 PMCID: PMC11007238 DOI: 10.1093/bioinformatics/btae155] [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: 01/18/2024] [Revised: 02/23/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
MOTIVATION The diverse structures and functions inherent in RNAs present a wealth of potential drug targets. Some small molecules are anticipated to serve as leading compounds, providing guidance for the development of novel RNA-targeted therapeutics. Consequently, the determination of RNA-small molecule binding affinity is a critical undertaking in the landscape of RNA-targeted drug discovery and development. Nevertheless, to date, only one computational method for RNA-small molecule binding affinity prediction has been proposed. The prediction of RNA-small molecule binding affinity remains a significant challenge. The development of a computational model is deemed essential to effectively extract relevant features and predict RNA-small molecule binding affinity accurately. RESULTS In this study, we introduced RLaffinity, a novel deep learning model designed for the prediction of RNA-small molecule binding affinity based on 3D structures. RLaffinity integrated information from RNA pockets and small molecules, utilizing a 3D convolutional neural network (3D-CNN) coupled with a contrastive learning-based self-supervised pre-training model. To the best of our knowledge, RLaffinity was the first deep learning based method for the prediction of RNA-small molecule binding affinity. Our experimental results exhibited RLaffinity's superior performance compared to baseline methods, revealed by all metrics. The efficacy of RLaffinity underscores the capability of 3D-CNN to accurately extract both global pocket information and local neighbor nucleotide information within RNAs. Notably, the integration of a self-supervised pre-training model significantly enhanced predictive performance. Ultimately, RLaffinity was also proved as a potential tool for RNA-targeted drugs virtual screening. AVAILABILITY AND IMPLEMENTATION https://github.com/SaisaiSun/RLaffinity.
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Affiliation(s)
- Saisai Sun
- School of Computer Science and Technology, Xidian University, No.266 Xinglong Section of Xi Feng Road, Xi’an, Shaanxi, 710126, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, No.266 Xinglong Section of Xi Feng Road, Xi’an, Shaanxi, 710126, China
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7
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Parmar S, Bume DD, Conelly C, Boer R, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS. Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581746. [PMID: 38903087 PMCID: PMC11188086 DOI: 10.1101/2024.02.23.581746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
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Affiliation(s)
- Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta Doro Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen Conelly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Peri R. Prestwood
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Zhen Wang
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | | | | | - Adeline Feri
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Philip Homan
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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8
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Singh K, Reddy G. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. J Chem Theory Comput 2024; 20:421-435. [PMID: 38134376 DOI: 10.1021/acs.jctc.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.
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Affiliation(s)
- Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
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9
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Kelly SL, Strobel EJ. Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573115. [PMID: 38187752 PMCID: PMC10769408 DOI: 10.1101/2023.12.22.573115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
RNA can fold into structures that mediate diverse cellular functions. Understanding how RNA primary sequence directs the formation of functional structures requires methods that can comprehensively assess how changes in an RNA sequence affect its structure and function. Here we have developed a platform for performing high-throughput cotranscriptional RNA biochemical assays, called Transcription Elongation Complex display (TECdisplay). TECdisplay measures RNA function by fractionating a TEC library based on the activity of cotranscriptionally displayed nascent RNA. In this way, RNA function is measured as the distribution of template DNA molecules between fractions of the transcription reaction. This approach circumvents typical RNA sequencing library preparation steps that can cause technical bias. We used TECdisplay to characterize the transcription antitermination activity of 32,768 variants of the Clostridium beijerinckii pfl ZTP riboswitch designed to perturb steps within its cotranscriptional folding pathway. Our findings establish TECdisplay as an accessible platform for high-throughput RNA biochemical assays.
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Affiliation(s)
- Skyler L. Kelly
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| | - Eric J. Strobel
- Department of Biological Sciences, The University at Buffalo, Buffalo, NY 14260, USA
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10
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 173] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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11
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Arney JW, Weeks KM. RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction. Biochemistry 2022; 61:1625-1632. [PMID: 35802500 PMCID: PMC9357220 DOI: 10.1021/acs.biochem.2c00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Affiliation(s)
- J. Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
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12
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Xu S, Xiao Z, Yu S, Zeng W, Zhu Y, Zhou J. Enhanced cobalamin biosynthesis in Ensifer adhaerens by regulation of key genes with gradient promoters. Synth Syst Biotechnol 2022; 7:941-948. [PMID: 35664931 PMCID: PMC9157374 DOI: 10.1016/j.synbio.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 10/28/2022] Open
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13
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Zeller MJ, Nuthanakanti A, Li K, Aubé J, Serganov A, Weeks KM. Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. ACS Chem Biol 2022; 17:438-448. [PMID: 35060698 PMCID: PMC8938680 DOI: 10.1021/acschembio.1c00880] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 μM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity.
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Affiliation(s)
- Meredith J. Zeller
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7363
| | - Jeffrey Aubé
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7363
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290,correspondence,
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14
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Chavali SS, Mali SM, Bonn R, Saseendran A, Bennett RP, Smith HC, Fasan R, Wedekind JE. Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells. J Biol Chem 2021; 297:101390. [PMID: 34767799 DOI: 10.1016/j.jbc.2021.101390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
RNA represents a potential target for new antiviral therapies, which are urgently needed to address public health threats such as the human immunodeficiency virus (HIV). We showed previously that the interaction between the viral Tat protein and the HIV-1 trans-activation response (TAR) RNA was blocked by the cyclic peptide TB-CP-6.9a. This peptide was derived from a TAR-binding loop that emerged during lab-evolution of a TAR-binding protein (TBP) family. Here we synthesized and characterized a next-generation, cyclic-peptide library based on the TBP scaffold. We sought to identify conserved RNA-binding interactions, and the influence of cyclization linkers on RNA binding and antiviral activity. A diverse group of cyclization linkers, encompassing disulfide bonds to bicyclic aromatic staples, was used to restrain the cyclic peptide geometry. Thermodynamic profiling revealed specific arginine-rich sequences with low to sub-micromolar affinity driven by enthalpic and entropic contributions. The best compounds exhibited no appreciable off-target binding to related molecules, such as BIV TAR and human 7SK RNAs. A specific arginine-to-lysine change in the highest affinity cyclic peptide reduced TAR binding by 10-fold, suggesting that TBP-derived cyclic peptides use an arginine-fork motif to recognize the TAR major-groove while differentiating the mode of binding from other TAR-targeting molecules. Finally, we showed that HIV infectivity in cell culture was reduced in the presence of cyclic peptides constrained by methylene or naphthalene-based linkers. Our findings provide insight into the molecular determinants required for HIV-1 TAR recognition and antiviral activity. These findings are broadly relevant to the development of antivirals that target RNA molecules.
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Affiliation(s)
- Sai Shashank Chavali
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester NY 14642, USA
| | - Sachitanand M Mali
- Department of Chemistry, University of Rochester, Rochester NY 14627, USA
| | - Rachel Bonn
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester NY 14642, USA
| | | | | | - Harold C Smith
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester NY 14642, USA; OyaGen, Inc., Rochester NY 14623, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester NY 14627, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester NY 14642, USA.
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Zafferani M, Hargrove AE. Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. Cell Chem Biol 2021; 28:594-609. [PMID: 33823146 DOI: 10.1016/j.chembiol.2021.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/03/2021] [Accepted: 03/10/2021] [Indexed: 02/06/2023]
Abstract
Initial successes in developing small molecule ligands for non-coding RNAs have underscored their potential as therapeutic targets. More recently, these successes have been aided by advances in biophysical and structural techniques for identification and characterization of more complex RNA structures; these higher-level folds present protein-like binding pockets that offer opportunities to design small molecules that could achieve a degree of selectivity often hard to obtain at the primary and secondary structure level. More specifically, identification and small molecule targeting of RNA tertiary and quaternary structures have allowed researchers to probe several human diseases and have resulted in promising clinical candidates. In this review we highlight a selection of diverse and exciting successes and the experimental approaches that led to their discovery. These studies include examples of recent developments in RNA-centric assays and ligands that provide insight into the features responsible for the affinity and biological outcome of RNA-targeted chemical probes. This report highlights the potential and emerging opportunities to selectively target RNA tertiary and quaternary structures as a route to better understand and, ultimately, treat many diseases.
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16
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Huang X, Wang M, Liu Y, Gui Y. Synthesis of RNA-based gene regulatory devices for redirecting cellular signaling events mediated by p53. Am J Cancer Res 2021; 11:4688-4698. [PMID: 33754021 PMCID: PMC7978309 DOI: 10.7150/thno.55856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/12/2021] [Indexed: 11/05/2022] Open
Abstract
Rationale: The p53 gene is a well-known tumor suppressor, and its mutation often contributes to the occurrence and development of tumors. Due to the diversity and complexity of p53 mutations, there is still no effective p53 gene therapy. In this study, we designed and constructed an aptazyme switch that could effectively sense cellular wild-type p53 protein and regulate downstream gene function flexibly. The application of this artificial device in combination with Cre-LoxP and dCas9-VP64 tools achieved a precisely targeted killing effect on tumor cells. Methods: The affinity of the aptamer to p53 protein was verified by SPR. p53 aptazyme and gene circuits were chemically synthesized. The function of the gene circuit was detected by cell proliferation assay, apoptosis assay and Western blot. The nude mouse transplantation tumor experiment was used to evaluate the inhibitory effect of gene circuits on tumor cells in vivo. Results: The results of the SPR experiment showed that the p53 aptamer RNA sequence had a robust binding effect with p53 protein. The p53 aptazyme could efficiently sense wild-type p53 protein and initiate self-cleavage in cells. The Cre-p53 aptazyme gene circuit and dCas9-VP64/sgRNA mediated gene circuit designed based on p53 aptazyme significantly inhibited the growth and promoted the apoptosis of wild-type p53-deficient cancer cells in vitro. In addition, the gene circuits also had a significant inhibitory effect on tumors in vivo. Conclusion: The study developed a novel and efficient ribozyme switch for p53-specific recognition and provided a modular strategy for aptazyme binding to cellular proteins. In addition, the p53 aptazyme successfully inhibited tumor growth through a combined application with other synthetic biological tools, providing a new perspective for cancer therapy.
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