• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4657932)   Today's Articles (3972)   Subscriber (51251)
For: Umuhire Juru A, Patwardhan NN, Hargrove AE. Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. ACS Chem Biol 2019;14:824-838. [PMID: 31042354 DOI: 10.1021/acschembio.8b00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Zhuo C, Gao J, Li A, Liu X, Zhao Y. A Machine Learning Method for RNA-Small Molecule Binding Preference Prediction. J Chem Inf Model 2024;64:7386-7397. [PMID: 39265103 DOI: 10.1021/acs.jcim.4c01324] [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: 09/14/2024]
2
Chen S, Mao Q, Cheng H, Tai W. RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals. J Med Chem 2024;67:16002-16017. [PMID: 39287926 DOI: 10.1021/acs.jmedchem.4c01330] [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: 09/19/2024]
3
Yuce M, Ates B, Yasar NI, Sungur FA, Kurkcuoglu O. A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. J Mol Graph Model 2024;131:108817. [PMID: 38976944 DOI: 10.1016/j.jmgm.2024.108817] [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: 03/22/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
4
Sinzger-D'Angelo M, Hanst M, Reinhardt F, Koeppl H. Effects of mRNA conformational switching on translational noise in gene circuits. J Chem Phys 2024;160:134108. [PMID: 38573847 DOI: 10.1063/5.0186927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024]  Open
5
Zhang L, Xiao K, Kong L. A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information. Biosystems 2024;235:105094. [PMID: 38056591 DOI: 10.1016/j.biosystems.2023.105094] [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: 09/03/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
6
Dohno C, Kimura M, Fujiwara Y, Nakatani K. Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme. Nucleic Acids Res 2023;51:9533-9541. [PMID: 37615580 PMCID: PMC10570050 DOI: 10.1093/nar/gkad690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]  Open
7
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]
8
RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study. Int J Mol Sci 2023;24:ijms24065497. [PMID: 36982570 PMCID: PMC10058308 DOI: 10.3390/ijms24065497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023]  Open
9
Peng X, Liu X, Li J, Tan L. RNA-binding of Ru(II) complexes [Ru(phen)2(7-OCH3-dppz)]2+ and [Ru(phen)2(7-NO2-dppz)]2+: The former serves as a molecular "light switch" for poly(A)•poly(U). J Inorg Biochem 2022;237:111991. [PMID: 36115329 DOI: 10.1016/j.jinorgbio.2022.111991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 01/18/2023]
10
Li N, Huang X, Chen J, Shao H. Investigating the conversion from coordination bond to electrostatic interaction on self-assembled monolayer by SECM. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
11
Li W, Liu X, Tan LF. Binding properties of [Ru(phen)2(11-R-dppz)]2+ (R = F or CN) with poly(A)•poly(U) duplex RNA. J Inorg Biochem 2022;232:111833. [DOI: 10.1016/j.jinorgbio.2022.111833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
12
Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022;12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
13
Theillet FX. In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale. Chem Rev 2022;122:9497-9570. [PMID: 35357148 DOI: 10.1021/acs.chemrev.1c00937] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
14
LeBlanc RM, Mesleh MF. A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021;37:51-60. [PMID: 34895655 DOI: 10.1016/j.ddtec.2020.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
15
Levintov L, Vashisth H. Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides. Biophys J 2021;120:5060-5073. [PMID: 34710377 PMCID: PMC8633718 DOI: 10.1016/j.bpj.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/17/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022]  Open
16
Levintov L, Vashisth H. Role of conformational heterogeneity in ligand recognition by viral RNA molecules. Phys Chem Chem Phys 2021;23:11211-11223. [PMID: 34010381 DOI: 10.1039/d1cp00679g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
17
Martin WJ, Grandi P, Marcia M. Screening strategies for identifying RNA- and ribonucleoprotein-targeted compounds. Trends Pharmacol Sci 2021;42:758-771. [PMID: 34215444 DOI: 10.1016/j.tips.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022]
18
Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules 2021;26:molecules26113384. [PMID: 34205049 PMCID: PMC8199858 DOI: 10.3390/molecules26113384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022]  Open
19
Kaiser C, Schneider J, Groher F, Suess B, Wachtveitl J. What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials. Nucleic Acids Res 2021;49:3661-3671. [PMID: 33772594 PMCID: PMC8053125 DOI: 10.1093/nar/gkab166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/25/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022]  Open
20
Falese JP, Donlic A, Hargrove AE. Targeting RNA with small molecules: from fundamental principles towards the clinic. Chem Soc Rev 2021;50:2224-2243. [PMID: 33458725 PMCID: PMC8018613 DOI: 10.1039/d0cs01261k] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
21
Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021;22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
22
Huang D, Yang W, Di D, Liu J, Wei J, Liu B. One-step preparation of hydrophilic metal-organic framework materials with bimetallic linkers and polycarboxylic acid ligands and their adsorption properties. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
23
Aldhumani AH, Hossain MI, Fairchild EA, Boesger H, Marino EC, Myers M, Hines JV. RNA sequence and ligand binding alter conformational profile of SARS-CoV-2 stem loop II motif. Biochem Biophys Res Commun 2021;545:75-80. [PMID: 33545635 PMCID: PMC7834705 DOI: 10.1016/j.bbrc.2021.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
24
Umuhire Juru A, Hargrove AE. Frameworks for targeting RNA with small molecules. J Biol Chem 2021;296:100191. [PMID: 33334887 PMCID: PMC7948454 DOI: 10.1074/jbc.rev120.015203] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022]  Open
25
Ligand-RNA interaction assay based on size-selective fluorescence core-shell nanocomposite. Anal Bioanal Chem 2020;412:7349-7356. [DOI: 10.1007/s00216-020-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
26
Costales MG, Childs-Disney JL, Haniff HS, Disney MD. How We Think about Targeting RNA with Small Molecules. J Med Chem 2020;63:8880-8900. [PMID: 32212706 PMCID: PMC7486258 DOI: 10.1021/acs.jmedchem.9b01927] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
27
Levintov L, Vashisth H. Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions. J Phys Chem Lett 2020;11:5426-5432. [PMID: 32551654 DOI: 10.1021/acs.jpclett.0c01390] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
28
Padroni G, Patwardhan NN, Schapira M, Hargrove AE. Systematic analysis of the interactions driving small molecule-RNA recognition. RSC Med Chem 2020;11:802-813. [PMID: 33479676 DOI: 10.1039/d0md00167h] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]  Open
29
Hagler LD, Bonson SE, Kocheril PA, Zimmerman SC. Assessing the feasibility and stability of uracil base flipping in RNA–small molecule complexes using molecular dynamics simulations. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
30
Guo P, Farahat AA, Paul A, Kumar A, Boykin DW, Wilson WD. Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove. Biochemistry 2020;59:1756-1768. [PMID: 32293884 DOI: 10.1021/acs.biochem.0c00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
31
Martin C, De Piccoli S, Gaysinski M, Becquart C, Azoulay S, Di Giorgio A, Duca M. Unveiling RNA‐Binding Properties of Verapamil and Preparation of New Derivatives as Inhibitors of HIV‐1 Tat‐TAR Interaction. Chempluschem 2020. [DOI: 10.1002/cplu.201900650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
32
Rizvi NF, Santa Maria JP, Nahvi A, Klappenbach J, Klein DJ, Curran PJ, Richards MP, Chamberlin C, Saradjian P, Burchard J, Aguilar R, Lee JT, Dandliker PJ, Smith GF, Kutchukian P, Nickbarg EB. Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space. SLAS DISCOVERY 2019;25:384-396. [DOI: 10.1177/2472555219885373] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA