1
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Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem 2024:10.1038/s41557-024-01601-1. [PMID: 39138346 DOI: 10.1038/s41557-024-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/12/2024] [Indexed: 08/15/2024]
Abstract
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds-termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| | | | | | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | | | | | | | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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2
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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3
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Prestwood PR, Yang M, Lewis GV, Balaratnam S, Yazdani K, Schneekloth JS. Competitive Microarray Screening Reveals Functional Ligands for the DHX15 RNA G-Quadruplex. ACS Med Chem Lett 2024; 15:814-821. [PMID: 38894923 PMCID: PMC11181508 DOI: 10.1021/acsmedchemlett.3c00574] [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: 01/08/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 06/21/2024] Open
Abstract
RNAs are increasingly considered valuable therapeutic targets, and the development of methods to identify and validate both RNA targets and ligands is more important than ever. Here, we utilized a bioinformatic approach to identify a hairpin-containing RNA G-quadruplex (rG4) in the 5' untranslated region (5' UTR) of DHX15 mRNA. By using a novel competitive small molecule microarray (SMM) approach, we identified a compound that specifically binds to the DHX15 rG4 (K D = 12.6 ± 1.0 μM). This rG4 directly impacts translation of a DHX15 reporter mRNA in vitro, and binding of our compound (F1) to the structure inhibits translation up to 57% (IC50 = 22.9 ± 3.8 μM). This methodology allowed us to identify and target the mRNA of a cancer-relevant helicase with no known inhibitors. Our target identification method and the novelty of our screening approach make our work informative for future development of novel small molecule cancer therapeutics for RNA targets.
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Affiliation(s)
- Peri R. Prestwood
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Mo Yang
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Grace V. Lewis
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Sumirtha Balaratnam
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Kamyar Yazdani
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - John S. Schneekloth
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
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4
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Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024; 64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [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: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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5
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Kallert E, Almena Rodriguez L, Husmann JÅ, Blatt K, Kersten C. Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system. RSC Med Chem 2024; 15:1527-1538. [PMID: 38784459 PMCID: PMC11110755 DOI: 10.1039/d3md00696d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/16/2024] [Indexed: 05/25/2024] Open
Abstract
Targeting RNA including viral RNAs with small molecules is an emerging field. The hepatitis C virus internal ribosome entry site (HCV IRES) is a potential target for translation inhibitor development to raise drug resistance mutation preparedness. Using RNA-focused and unbiased molecule libraries, a structure-based virtual screening (VS) by molecular docking and pharmacophore analysis was performed against the HCV IRES subdomain IIa. VS hits were validated by a microscale thermophoresis (MST) binding assay and a Förster resonance energy transfer (FRET) assay elucidating ligand-induced conformational changes. Ten hit molecules were identified with potencies in the high to medium micromolar range proving the suitability of structure-based virtual screenings against RNA-targets. Hit compounds from a 2-guanidino-quinazoline series, like the strongest binder, compound 8b with an EC50 of 61 μM, show low molecular weight, moderate lipophilicity and reduced basicity compared to previously reported IRES ligands. Therefore, it can be considered as a potential starting point for further optimization by chemical derivatization.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Laura Almena Rodriguez
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Jan-Åke Husmann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Kathrin Blatt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Staudingerweg 5 55128 Mainz Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University BioZentrum I, Hanns-Dieter-Hüsch-Weg 15 55128 Mainz Germany
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6
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Li B, Wang Y, Yin Z, Xu L, Xie L, Xu X. Decision tree-based identification of important molecular fragments for protein-ligand binding. Chem Biol Drug Des 2024; 103:e14427. [PMID: 38230776 DOI: 10.1111/cbdd.14427] [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: 09/26/2023] [Revised: 11/16/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Fragment-based drug design is an emerging technology in pharmaceutical research and development. One of the key aspects of this technology is the identification and quantitative characterization of molecular fragments. This study presents a strategy for identifying important molecular fragments based on molecular fingerprints and decision tree algorithms and verifies its feasibility in predicting protein-ligand binding affinity. Specifically, the three-dimensional (3D) structures of protein-ligand complexes are encoded using extended-connectivity fingerprints (ECFP), and three decision tree models, namely Random Forest, XGBoost, and LightGBM, are used to quantitatively characterize the feature importance, thereby extracting important molecular fragments with high reliability. Few-shot learning reveals that the extracted molecular fragments contribute significantly and consistently to the binding affinity even with a small sample size. Despite the absence of location and distance information for molecular fragments in ECFP, 3D visualization, in combination with the reverse ECFP process, shows that the majority of the extracted fragments are located at the binding interface of the protein and the ligand. This alignment with the distance constraints critical for binding affinity further supports the reliability of the strategy for identifying important molecular fragments.
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Affiliation(s)
- Baiyi Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yunsong Wang
- School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Zuode Yin
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
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7
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Abstract
Although fragment-based drug discovery (FBDD) has been successfully implemented and well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the challenges associated with the selective targeting of RNA, efforts to integrate known methods of RNA binder discovery with fragment-based approaches have been fruitful, as a few bioactive ligands have been identified. Here, we review various fragment-based approaches implemented for RNA targets and provide insights into experimental design and outcomes to guide future work in the area. Indeed, investigations surrounding the molecular recognition of RNA by fragments address rather important questions such as the limits of molecular weight that confer selective binding and the physicochemical properties favorable for RNA binding and bioactivity.
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Affiliation(s)
- Blessy M. Suresh
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- UF Scripps Biomedical Research & The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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8
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Koehn JT, Felder S, Weeks KM. Innovations in targeting RNA by fragment-based ligand discovery. Curr Opin Struct Biol 2023; 79:102550. [PMID: 36863268 PMCID: PMC10023403 DOI: 10.1016/j.sbi.2023.102550] [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: 11/06/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 03/04/2023]
Abstract
A subset of functional regions within large RNAs fold into complex structures able to bind small-molecule ligands with high affinity and specificity. Fragment-based ligand discovery (FBLD) offers notable opportunities for discovery and design of potent small molecules that bind pockets in RNA. Here we share an integrated analysis of recent innovations in FBLD, emphasizing opportunities resulting from fragment elaboration via both linking and growing. Analysis of elaborated fragments emphasizes that high-quality interactions form with complex tertiary structures in RNA. FBLD-inspired small molecules have been shown to modulate RNA functions by competitively inhibiting protein binding and by selectively stabilizing dynamic RNA states. FBLD is creating a foundation to interrogate the relatively unknown structural space for RNA ligands and for discovery of RNA-targeted therapeutics.
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Affiliation(s)
- Jordan T Koehn
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290, USA
| | - Simon Felder
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290, USA.
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9
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Morishita EC. Discovery of RNA-targeted small molecules through the merging of experimental and computational technologies. Expert Opin Drug Discov 2023; 18:207-226. [PMID: 36322542 DOI: 10.1080/17460441.2022.2134852] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The field of RNA-targeted small molecules is rapidly evolving, owing to the advances in experimental and computational technologies. With the identification of several bioactive small molecules that target RNA, including the FDA-approved risdiplam, the biopharmaceutical industry is gaining confidence in the field. This review, based on the literature obtained from PubMed, aims to disseminate information about the various technologies developed for targeting RNA with small molecules and propose areas for improvement to develop drugs more efficiently, particularly those linked to diseases with unmet medical needs. AREAS COVERED The technologies for the identification of RNA targets, screening of chemical libraries against RNA, assessing the bioactivity and target engagement of the hit compounds, structure determination, and hit-to-lead optimization are reviewed. Along with the description of the technologies, their strengths, limitations, and examples of how they can impact drug discovery are provided. EXPERT OPINION Many existing technologies employed for protein targets have been repurposed for use in the discovery of RNA-targeted small molecules. In addition, technologies tailored for RNA targets have been developed. Nevertheless, more improvements are necessary, such as artificial intelligence to dissect important RNA structures and RNA-small-molecule interactions and more powerful chemical probing and structure prediction techniques.
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10
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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11
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Suresh BM, Akahori Y, Taghavi A, Crynen G, Gibaut QMR, Li Y, Disney MD. Low-Molecular Weight Small Molecules Can Potently Bind RNA and Affect Oncogenic Pathways in Cells. J Am Chem Soc 2022; 144:20815-20824. [PMID: 36322830 PMCID: PMC9930674 DOI: 10.1021/jacs.2c08770] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA is challenging to target with bioactive small molecules, particularly those of low molecular weight that bind with sufficient affinity and specificity. In this report, we developed a platform to address this challenge, affording a novel bioactive interaction. An RNA-focused small-molecule fragment collection (n = 2500) was constructed by analyzing features in all publicly reported compounds that bind RNA, the largest collection of RNA-focused fragments to date. The RNA-binding landscape for each fragment was studied by using a library-versus-library selection with an RNA library displaying a discrete structural element, probing over 12.8 million interactions, the greatest number of interactions between fragments and biomolecules probed experimentally. Mining of this dataset across the human transcriptome defined a drug-like fragment that potently and specifically targeted the microRNA-372 hairpin precursor, inhibiting its processing into the mature, functional microRNA and alleviating invasive and proliferative oncogenic phenotypes in gastric cancer cells. Importantly, this fragment has favorable properties, including an affinity for the RNA target of 300 ± 130 nM, a molecular weight of 273 Da, and quantitative estimate of drug-likeness (QED) score of 0.8. (For comparison, the mean QED of oral medicines is 0.6 ± 0.2). Thus, these studies demonstrate that a low-molecular weight, fragment-like compound can specifically and potently modulate RNA targets.
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Affiliation(s)
- Blessy M. Suresh
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yoshihiro Akahori
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Amirhossein Taghavi
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Quentin M. R. Gibaut
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute & UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL 33458, United States
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12
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:10669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Affiliation(s)
| | | | | | | | - Sangeeta Tiwari
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
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13
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Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
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14
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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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