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Kovachka S, Tong Y, Childs-Disney JL, Disney MD. Heterobifunctional small molecules to modulate RNA function. Trends Pharmacol Sci 2024; 45:449-463. [PMID: 38641489 DOI: 10.1016/j.tips.2024.03.006] [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: 03/02/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
RNA has diverse cellular functionality, including regulating gene expression, protein translation, and cellular response to stimuli, due to its intricate structures. Over the past decade, small molecules have been discovered that target functional structures within cellular RNAs and modulate their function. Simple binding, however, is often insufficient, resulting in low or even no biological activity. To overcome this challenge, heterobifunctional compounds have been developed that can covalently bind to the RNA target, alter RNA sequence, or induce its cleavage. Herein, we review the recent progress in the field of RNA-targeted heterobifunctional compounds using representative case studies. We identify critical gaps and limitations and propose a strategic pathway for future developments of RNA-targeted molecules with augmented functionalities.
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Affiliation(s)
- Sandra Kovachka
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yuquan Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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2
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [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: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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3
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Chatterjee A, Zhang K, Rao Y, Sharma N, Giammar DE, Parker KM. Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3564-3574. [PMID: 35226478 DOI: 10.1021/acs.est.1c08468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yue Rao
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Sharma
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel E Giammar
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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4
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Joseph V, Levine M. Ronald C.D. Breslow (1931-2017): A career in review. Bioorg Chem 2021; 115:104868. [PMID: 34523507 DOI: 10.1016/j.bioorg.2021.104868] [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: 02/02/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022]
Abstract
Reviewed herein are key research accomplishments of Professor Ronald Charles D. Breslow (1931-2017) throughout his more than 60 year research career. These accomplishments span a wide range of topics, most notably physical organic chemistry, medicinal chemistry, and bioorganic chemistry. These topics are reviewed, as are topics of molecular electronics and origin of chirality, which combine to make up the bulk of this review. Also reviewed briefly are Breslow's contributions to the broader chemistry profession, including his work for the American Chemical Society and his work promoting gender equity. Throughout the article, efforts are made to put Breslow's accomplishments in the context of other work being done at the time, as well as to include subsequent iterations and elaborations of the research.
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Affiliation(s)
- Vincent Joseph
- Department of Chemical Sciences, Ariel University, Israel
| | - Mindy Levine
- Department of Chemical Sciences, Ariel University, Israel.
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5
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Solís‐Muñana P, Salam J, Ren CZ, Carr B, Whitten AE, Warr GG, Chen JL. An Amphiphilic (salen)Co Complex – Utilizing Hydrophobic Interactions to Enhance the Efficiency of a Cooperative Catalyst. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pablo Solís‐Muñana
- Centre for Biomedical and Chemical Sciences School of Science Auckland University of Technology 34 St Paul St 1010 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6011 Wellington New Zealand
| | - Joanne Salam
- Centre for Biomedical and Chemical Sciences School of Science Auckland University of Technology 34 St Paul St 1010 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6011 Wellington New Zealand
| | - Chloe Z.‐J. Ren
- Centre for Biomedical and Chemical Sciences School of Science Auckland University of Technology 34 St Paul St 1010 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6011 Wellington New Zealand
| | - Bronte Carr
- Centre for Biomedical and Chemical Sciences School of Science Auckland University of Technology 34 St Paul St 1010 Auckland New Zealand
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation (ANSTO) New Illawarra Rd 2234 Lucas Heights, NSW Australia
| | - Gregory G. Warr
- School of Chemistry The University of Sydney 2006 Sydney New South Wales Australia
| | - Jack L.‐Y. Chen
- Centre for Biomedical and Chemical Sciences School of Science Auckland University of Technology 34 St Paul St 1010 Auckland New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology 6011 Wellington New Zealand
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences Università degli Studi di Siena Via Aldo Moro 53100 Siena Italy
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6
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The furanosidic scaffold of d-ribose: a milestone for cell life. Biochem Soc Trans 2020; 47:1931-1940. [PMID: 31697320 DOI: 10.1042/bst20190749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 01/15/2023]
Abstract
The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the selection of molecules to be used for relevant metabolic purposes must favor structurally well-defined molecules, the inadequacy of ribose as a preferential precursor for nucleotides synthesis is discussed. The low reliability of ribose in its furanosidic hemiacetal form must have played ab initio against the choice of d-ribose for the generation of d-ribose-5-phosphate, the fundamental precursor of the ribose moiety of nucleotides. The latter, which is instead generated through the 'pentose phosphate pathway' is strictly linked to the affordable and reliable pyranosidic structure of d-glucose.
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7
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Erxleben A. Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned? Front Chem 2019; 7:82. [PMID: 30847339 PMCID: PMC6393734 DOI: 10.3389/fchem.2019.00082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.
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Affiliation(s)
- Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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8
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Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. J Phys Chem B 2017; 121:10828-10840. [DOI: 10.1021/acs.jpcb.7b09129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via
Bonomea 265, 34136 Trieste, Italy
| | - Petra Kührová
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
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9
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Nguyen L, Luu LM, Peng S, Serrano JF, Chan HYE, Zimmerman SC. Rationally designed small molecules that target both the DNA and RNA causing myotonic dystrophy type 1. J Am Chem Soc 2015; 137:14180-9. [PMID: 26473464 DOI: 10.1021/jacs.5b09266] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Single-agent, single-target therapeutic approaches are often limited by a complex disease pathobiology. We report rationally designed, multi-target agents for myotonic dystrophy type 1 (DM1). DM1 originates in an abnormal expansion of CTG repeats (CTG(exp)) in the DMPK gene. The resultant expanded CUG transcript (CUG(exp)) identified as a toxic agent sequesters important proteins, such as muscleblind-like proteins (MBNL), undergoes repeat-associated non-ATG (RAN) translation, and potentially causes microRNA dysregulation. We report rationally designed small molecules that target the DM1 pathobiology in vitro in three distinct ways by acting simultaneously as transcription inhibitors, by inhibiting aberrant protein binding to the toxic RNA, and by acting as RNase mimics to degrade the toxic RNA. In vitro, the agents are shown to (1) bind CTG(exp) and inhibit formation of the CUG(exp) transcript, (2) bind CUG(exp) and inhibit sequestration of MBNL1, and (3) cleave CUG(exp) in an RNase-like manner. The most potent compounds are capable of reducing the levels of CUG(exp) in DM1 model cells, and one reverses two separate CUG(exp)-induced phenotypes in a DM1 Drosophila model.
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Affiliation(s)
- Lien Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Shaohong Peng
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong , Shatin N.T., Hong Kong, SAR
| | - Julio F Serrano
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - H Y Edwin Chan
- Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong , Shatin N.T., Hong Kong, SAR
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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10
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Dhawan G, Chandra R, Gupta KC, Kumar P. Facile and rapid deprotection conditions for the cleavage of synthetic oligonucleotides from 1,4-anhydroerythritol-based universal polymer support. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:149-62. [PMID: 25710353 DOI: 10.1080/15257770.2014.975244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In our previous report [Kumar, P.; Dhawan, G.; Chandra, R.; Gupta, K.C. Polyamine-assisted rapid and clean cleavage of oligonucleotides from cis-diol bearing universal support. Nucl. Acids Res. 2002, 30, e130 (1-8)], we demonstrated polyamine-mediated deprotection of oligonucleotides from cis-diol group bearing universal polymer support (I). However, vulnerability of the conventional dC(bz) to modifications under these conditions compelled us to employ dC(ac) during synthesis of oligonucleotide using conventional synthons. Here, a new set of simple and rapid deprotection conditions has been developed for the complete cleavage of oligonucleotides from the 1,4-anhydroerythritol-based universal polymer support employing conventional dC(bz) synthon. Using manganese-imidazole complex in aqueous ammonium hydroxide (∼ 30%), fully deprotected oligonucleotide sequences were obtained in 40 min, which were analyzed on reverse phase-HPLC and compared with the standard oligomers in terms of their retention time. Finally, their biological compatibility was established by analyzing PCR amplified products of npsA gene of N. meningitidis.
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Affiliation(s)
- Gagan Dhawan
- a Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology , Delhi , India
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11
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Adamala K, Engelhart AE, Szostak JW. Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension. J Am Chem Soc 2014; 137:483-9. [PMID: 25521912 PMCID: PMC4984999 DOI: 10.1021/ja511564d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The earliest genomic RNAs had to
be short enough for efficient
replication, while simultaneously serving as unfolded templates and
effective ribozymes. A partial solution to this paradox may lie in
the fact that many functional RNAs can self-assemble from multiple
fragments. Therefore, in early evolution, genomic RNA fragments could
have been significantly shorter than unimolecular functional RNAs.
Here, we show that unstable, nonfunctional complexes assembled from
even shorter 3′-truncated oligonucleotides can be stabilized
and gain function via non-enzymatic primer extension. Such short RNAs
could act as good templates due to their minimal length and complex-forming
capacity, while their minimal length would facilitate replication
by relatively inefficient polymerization reactions. These RNAs could
also assemble into nascent functional RNAs and undergo conversion
to catalytically active forms, by the same polymerization chemistry
used for replication that generated the original short RNAs. Such
phenomena could have substantially relaxed requirements for copying
efficiency in early nonenzymatic replication systems.
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Affiliation(s)
- Katarzyna Adamala
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States
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12
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Abstract
We have prepared L- and D-deoxypolypeptides (DOPPs) by selective reduction of appropriately protected polyhistidines with borane, reducing the carbonyl groups to methylenes. The result is a chiral polyamine, not amide, with a mainly protonated backbone and chirally mounted imidazolylmethylene side chains that are mostly unprotonated at neutrality because of the nearby polycationic backbone. We found that, in contrast with the D-octahistidine DOPP, the L-octahistidine DOPP is able to cooperatively bind to a D-polyuridylic acid RNA; this is consistent with results of previous studies showing that, relative to D-histidine, L-histidine is able to more strongly bind to RNA. The L-DOPP was also a better catalyst for cleaving the RNA than the D-DOPP, consistent with evidence that the L-DOPP uses its imidazole groups for catalysis, in addition to the backbone cations, but the D-DOPP does not use the imidazoles. The L-DOPP bifunctional process probably forms a phosphorane intermediate. This is a mechanism we have proposed for models of ribonuclease cleavage and for the ribonuclease A enzyme itself, based on our studies of the cleavage and isomerization of UpU catalyzed by imidazole buffers as well as other relevant studies. This mechanism contrasts with earlier, generally accepted ribonuclease cleavage mechanisms where the proton donor coordinates with the oxygen of the leaving group as the 2-hydroxyl of ribose attacks the unprotonated phosphate.
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Mochizuki S, Higuchi S, Sakurai K. ssDNA-dsRNAs are cleaved at the next to its chimera-junction point by an unknown RNase activity. Biochem Biophys Res Commun 2012; 428:433-7. [PMID: 23131557 DOI: 10.1016/j.bbrc.2012.10.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 10/16/2012] [Indexed: 11/27/2022]
Abstract
We found that there is an unknown aspect in serum RNases that cleaves ssDNA-dsRNA and ssRNA-dsRNA. In the first step, RNase cleaves the phosphodiester linkage between the first and second RNA, where the first one is connected to the single stranded RNA or DNA. In the second step, the ssRNA overhang attached siRNA is cleaved. When the 2' hydroxyl of the first RNA was replaced with methoxy, the cleavage did not occur. This RNase activity can be considered related to defense system against exogenous genetic materials.
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Affiliation(s)
- Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Kitakyushu, Fukuoka 808-0135, Japan
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14
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Synthesis of Aryl-1,2,4,5-tetrazinane-3-thiones, in vitro DNA binding studies, nuclease activity and its antimicrobial activity. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Binding and biomimetic cleavage of the RNA poly(U) by synthetic polyimidazoles. Proc Natl Acad Sci U S A 2012; 109:12884-7. [PMID: 22826260 DOI: 10.1073/pnas.1210846109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four polyimidazoles were used in the binding and cleavage studies with poly(U). The two polydisperse polyvinylimidazoles were previously described by others, while the other two new polymers of polyethyleneimines were prepared by cationic polymerization of oxazolines. The latter had imidazole units attached to each nitrogen of the polymers. They were characterized by gel permeation chromatography and had very low polydispersities. When they were partially protonated they bound to the poly(U) and catalyzed its cleavage by a process analogous to that used by the enzyme ribonuclease A. The kinetics of the cleavage were followed by an assay we had previously described using phosphodiesterase I from Crotalus venom after the cleavage processes. Cleavage of poly(U) with Zn(2+) was also examined, with and without the polymers. A scheme is described in which these cleavages could be made sequence selective with various RNAs, particularly with important targets, such as viral RNAs.
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16
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Wolfenden R. Benchmark Reaction Rates, the Stability of Biological Molecules in Water, and the Evolution of Catalytic Power in Enzymes. Annu Rev Biochem 2011; 80:645-67. [DOI: 10.1146/annurev-biochem-060409-093051] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard Wolfenden
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599;
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17
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Rhee HW, Choi SJ, Yoo SH, Jang YO, Park HH, Pinto RM, Cameselle JC, Sandoval FJ, Roje S, Han K, Chung DS, Suh J, Hong JI. A bifunctional molecule as an artificial flavin mononucleotide cyclase and a chemosensor for selective fluorescent detection of flavins. J Am Chem Soc 2009; 131:10107-12. [PMID: 19569646 DOI: 10.1021/ja9018012] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Flavins, comprising flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and riboflavin (RF, vitamin B(2)), play important roles in numerous redox reactions such as those taking place in the electron-transfer chains of mitochondria in all eukaryotes and of plastids in plants. A selective chemosensor for flavins would be useful not only in the investigation of metabolic processes but also in the diagnosis of diseases related to flavins; such a sensor is presently unavailable. Herein, we report the first bifunctional chemosensor (PTZ-DPA) for flavins. PTZ-DPA consists of bis(Zn(2+)-dipicolylamine) and phenothiazine. Bis(Zn(2+)-dipicolylamine) (referred to here as XyDPA) was found to be an excellent catalyst in the conversion of FAD into cyclic FMN (riboflavin 4',5'-cyclic phosphate, cFMN) under physiological conditions, even at pH 7.4 and 27 degrees C, with less than 1 mol % of substrate. Utilizing XyDPA's superior function as an artificial FMN cyclase and phenothiazine as an electron donor able to quench the fluorescence of an isoalloxazine ring, PTZ-DPA enabled selective fluorescent discrimination of flavins (FMN, FAD, and RF): FAD shows ON(+), FMN shows OFF(-), and RF shows NO(0) fluorescence changes upon the addition of PTZ-DPA. With this selective sensing property, PTZ-DPA is applicable to real-time fluorescent monitoring of riboflavin kinase (RF to FMN), alkaline phosphatase (FMN to RF), and FAD synthetase (FMN to FAD).
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Affiliation(s)
- Hyun-Woo Rhee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea
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18
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ZHANG Z, FU Q, HUANG X, XU J, LIU J, SHEN J. Construction of the Active Site of Metalloenzyme on Au NC Micelles. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Shao Y, Ding Y, Jia ZL, Lu XM, Ke ZH, Xu WH, Lu GY. Synthesis and DNA cleavage activity of 2-hydrazinyl-1,4,5,6-tetrahydropyrimidine containing hydroxy group. Bioorg Med Chem 2009; 17:4274-9. [DOI: 10.1016/j.bmc.2009.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/15/2009] [Accepted: 05/16/2009] [Indexed: 11/17/2022]
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20
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Self-assembled gold nanocrystal micelles act as an excellent artificial nanozyme with ribonuclease activity. J Biol Inorg Chem 2009; 14:653-62. [DOI: 10.1007/s00775-009-0478-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
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21
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Kumar R, Garneau P, Nguyen N, William Lown J, Pelletier J. Methionine Sustituted Polyamides are RNAse Mimics that Inhibit Translation. J Drug Target 2008; 12:125-34. [PMID: 15203891 DOI: 10.1080/1061186042000220728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
RNAse mimics are small molecules that can cleave RNA in a fashion similar to ribonucleases. These compounds would be very useful as gene specific reagents if their activities could be regulated and targeted. We demonstrate here that polyamides with methionine substituents show enhanced RNA cleavage activity relative to other polyamides. Conjugation of these compounds to aminoglycosides produced RNAse mimics that are capable of inhibiting eukaryotic protein synthesis. As a new class of compounds capable of interacting with nucleic acids, these novel aminoglycoside-polyamides constitute promising scaffolds for the construction of nuclease mimics with biological activity.
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Affiliation(s)
- Rohtash Kumar
- Department of Chemistry University of Alberta Edmonton Alta. Canada
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Abstract
'Two is better than one' in cooperating systems. Synthetic ditopic host molecules have been constructed from cyclodextrins and from synthetic hydrophobic cavities bridged with simple connectors or with catalytic groups. These host molecules show very strong binding of appropriate substrates, and selective catalysis. A cyclodextrin bis-imidazole shows bifunctional catalysis of the cleavage of a cyclic phosphate that is simultaneous, judged from isotopic studies. The best geometry is consistent with mechanistic evidence on the preferred mechanism for such bifunctional catalysis. Certain polar compounds bind to a still unidentified cellular receptor and induce differentiation of malignant cells. Ditopic drugs that have been designed and synthesized bind strongly to two receptor sites and induce cancer cell differentiation at low concentrations with few side-effects. Clinical results with these compounds are already promising in a few cancer patients.
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Affiliation(s)
- R Breslow
- Department of Chemistry, Columbia University, New York, NY 10027
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Mathews RA, Rossiter CS, Morrow JR, Richard JP. A minimalist approach to understanding the efficiency of mononuclear Zn(II) complexes as catalysts of cleavage of an RNA analog. Dalton Trans 2007:3804-11. [PMID: 17712447 DOI: 10.1039/b707409c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mononuclear complexes between Zn(2+) and the following four macrocycles were prepared: 1,4,7,10-tetraazacyclododecane (1), 1-oxa-4,7,10-triazacyclododecane (2), 1,5,9-triazacyclododecane (3) and 1-hydroxyethyl-1,4,7-triazacyclononane (4). The pH rate profiles of values of the observed second-order rate constant log (k(Zn))(app) for Zn(X)(OH(2))-catalyzed cleavage (X = 1, 2, 3 and 4) of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) show downward breaks centered at the pK(a) for ionization of the respective zinc bound water. At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between the catalyst and the bound transition state is 5.7, 7.4, 7.4 and 5.9 kcal mol(-1) for the reactions catalyzed by Zn(1)(OH(2)), Zn(2)(OH(2)), Zn(3)(OH(2)) and Zn(4)(OH(2)), respectively. The interactions between the metal cation and the macrocycle cause either a modest increase or reduction in transition state stabilization compared with 6.6 kcal mol(-1) stabilization for catalysis by Zn(OH(2))(6). The best Zn(II)-macrocycle catalysts are those for which the interactions between the metal ion and macrocycle are the weakest. Inhibition studies show that each of the four catalysts form complexes with phosphate and oxalate dianions with a much higher affinity than diethyl phosphate monoanion, consistent with stronger interaction of the catalysts with the transition state dianion compared with the substrate monoanion HpPNP. The pH-dependence of methyl phosphate inhibition of Zn(2) catalyzed cleavage of HpPNP shows that only the Zn(2)(OH(2)) species binds the inhibitor. This result is consistent with a mechanism that has Zn(2)(OH(2)) as the active catalytic species.
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Affiliation(s)
- Ryan A Mathews
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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Mancin F, Tecilla P. Zinc(ii) complexes as hydrolytic catalysts of phosphate diester cleavage: from model substrates to nucleic acids. NEW J CHEM 2007. [DOI: 10.1039/b703556j] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- Richard Wolfenden
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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Kato M, Tanase T, Mikuriya M. Dinuclear Copper(II) Complexes with {Cu2(μ-hydroxo)bis(μ-carboxylato)}+ Cores and Their Reactions with Sugar Phosphate Esters: A Substrate Binding Model of Fructose-1,6-bisphosphatase. Inorg Chem 2006; 45:2925-41. [PMID: 16562948 DOI: 10.1021/ic051942d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of CuX2.nH2O with the biscarboxylate ligand XDK (H2XDK = m-xylenediamine bis(Kemp's triacid imide)) in the presence of N-donor auxiliary ligands yielded a series of dicopper(II) complexes, [Cu2(mu-OH)(XDK)(L)2]X (L = N,N,N',N'-tetramethylethylenediamine (tetmen), X = NO3 (1a), Cl (1b); L = N,N,N'-trimethylethylenediamine (tmen), X = NO3 (2a), Cl (2b); L =2,2'-bipyridine (bpy), X = NO3 (3); L = 1,10-phenanthroline (phen), X = NO3 (4); L = 4,4'-dimethyl-2,2'-bipyridine (Me2bpy), X = NO3 (5); L = 4-methyl-1,10-phenanthroline (Mephen), X = NO3 (6)). Complexes 1-6 were characterized by X-ray crystallography (Cu...Cu = 3.1624(6)-3.2910(4) A), and the electrochemical and magnetic properties were also examined. Complexes 3 and 4 readily reacted with diphenyl phosphoric acid (HDPP) or bis(4-nitrophenyl) phosphoric acid (HBNPP) to give [Cu2(mu-phosphate)(XDK)(L)2]NO3 (L = bpy, phosphate = DPP (11); L = phen, phosphate = DPP (12), BNPP (13)), where the phsophate diester bridges the two copper ions in a mu-1,3-O,O' bidentate fashion (Cu...Cu = 4.268(3)-4.315(1) A). Complexes 4 and 6 with phen and Mephen have proven to be good precursors to accommodate a series of sugar monophosphate esters (Sugar-P) onto the biscarboxylate-bridged dicopper centers, yielding [Cu2(mu-Sugar-P)(XDK)(L)2] (Sugar-P = alpha-D-Glc-1-P (23a and b), D-Glc-6-P (24a and b), D-Man-6-P (25a), D-Fru-6-P (26a and b); L = phen (a), Mephen (b)) and [Cu2(mu-Gly-n-P)(XDK)(Mephen)2] (Gly-n-P = glycerol n-phosphate; n = 2 (21), 3 (22)), where Glc, Man, and Fru are glucose, mannose, and fructose, respectively. The structure of [Cu2(mu-MNPP)(XDK)(phen)2(CH3OH)] (20) was characterized as a reference compound (H2MNPP = 4-nitrophenyl phosphoric acid). Complexes 4 and 6 also reacted with d-fructose 1,6-bisphosphate (D-Fru-1,6-P2) to afford the tetranuclear copper(II) complexes formulated as [Cu4(mu-D-Fru-1,6-P2)(XDK)2(L)4] (L = phen (27a), Mephen (27b)). The detailed structure of 27a was determined by X-ray crystallography to involve two different tetranuclear complexes with alpha- and beta-anomers of D-Fru-1,6-P2, [Cu4(mu-alpha-D-Fru-1,6-P2)(XDK)2(phen)4] and [Cu4(mu-beta-D-Fru-1,6-P2)(XDK)2(phen)4], in which the D-Fru-1,6-P2 tetravalent anion bridges the two [Cu2(XDK)(phen)2]2+ units through the C1 and C6 phosphate groups in a mu-1,3-O,O' bidentate fashion (Cu...Cu = 4.042(2)-4.100(2) A). Notably, the structure with alpha-D-Fru-1,6-P2 demonstrated the presence of a strong hydrogen bond between the C2 hydroxyl group and the C1 phosphate oxygen atom, which may support the previously proposed catalytic mechanism in the active site of fructose-1,6-bisphosphatase.
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Affiliation(s)
- Merii Kato
- Department of Chemistry, Faculty of Science, Nara Women's University, Kitauoya-higashi-machi, Nara 630-8285, Japan
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Transesterification of Phosphodiester by a Zinc-Containing Cyclen Derivative: Identification of the Active Species. European J Org Chem 2006. [DOI: 10.1002/jlac.199619960611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Holmes SC, Gait MJ. Syntheses and Oligonucleotide Incorporation of Nucleoside Analogues Containing Pendant Imidazolyl or Amino Functionalities - The Search for Sequence-Specific Artificial Ribonucleases. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500413] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Delehanty JB, Stuart TC, Knight DA, Goldman ER, Thach DC, Bongard JE, Chang EL. RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex. RNA (NEW YORK, N.Y.) 2005; 11:831-836. [PMID: 15840822 PMCID: PMC1370767 DOI: 10.1261/rna.7156805] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 01/18/2005] [Indexed: 05/24/2023]
Abstract
Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.
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Affiliation(s)
- James B Delehanty
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA
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31
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Koval'ov N, Kuznetsova I, Burakova E, Sil'nikov V, Zenkova M, Vlassov V. Ribonuclease activity of cationic structures conjugated to lipophilic groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:977-81. [PMID: 15560089 DOI: 10.1081/ncn-200026050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cationic compounds containing benzene ring substituted with the bis-quaternary salt of diazabicyclo[2.2.2]octane (DABCO) bearing a polymethylene fragment at the bridge positions display ribonuclease activity. Efficacy of the catalysis is affected by geometry of the cationic structures and the size of the attached aliphatic fragment. The cleavage occurs primarily within CA sequences. The compounds do not possess tradition groups participating in the transesterification step of RNA cleavage reaction, therefore a speculative mechanism of cleavage could be inducing a conformational stress on the RNA sugar phosphate backbone providing fragility to phosphodiester bonds.
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Affiliation(s)
- N Koval'ov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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32
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Maazouzi N, Bahmed K, Chakir S, Quilès F, Bonaly R, Coulon J. Chemical modification and stability of the cell wall phosphopeptidomannans of flocculent and weakly flocculent Kluyveromyces bulgaricus cells. Process Biochem 2005. [DOI: 10.1016/j.procbio.2004.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Giraldo J, De Maria L, Wodak SJ. Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase. Proteins 2004; 56:261-76. [PMID: 15211510 DOI: 10.1002/prot.20137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The microbial ribonuclease barnase exhibits low catalytic activity toward GpN dinucleotides, where G is guanosine, p is phosphate and N represents any nucleoside. When a phosphate is added to the 3'-end, as in GpNp, substrate affinity is enhanced by one order of magnitude, and the catalytic rate by two. In order to gain insight into this phenomenon, we analyzed the nucleotide conformations and protein-nucleotide interactions of 4 ns molecular dynamics (MD) trajectories of complexes of barnase with guanylyl(3'-5') adenosine (GpA) and guanylyl(3'-5') adenosine 3'-monophosphate (GpAp), respectively, in the presence of solvent and counter ions. We found that, in a majority of the bound GpA conformations, the guanine base was firmly bound to the recognition site. The phosphate and adenosine moieties pointed into the solvent, and interactions with key catalytic residues were absent. In contrast, the bound GpAp adopted conformations in which all of the nucleotide portions remained tightly bound to the enzyme and interactions with key catalytic residues were maintained. These observations indicate that, for GpA, a significant proportion of the bound nucleotide adopts non-productive conformations and that adding the terminal phosphate as in GpAp shifts the equilibrium of the bound conformations towards structures capable of undergoing catalysis. Incorporating this property into the kinetic equations yields an increase in both the apparent rate constant (kcat) and the apparent dissociation constant (K(M)) for GpAp versus GpA. The increase in K(M), caused by the presence of additional non-productive binding modes for GpA, should however be counterbalanced by the propensity of free GpA to adopt folded conformations in solution, which are unable to bind the enzyme and by the tighter binding of GpAp (Giraldo J, Wodak SJ, Van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998; 283:863-882). Addition of the terminal phosphate is shown to significantly influence the collective motion of the enzyme in a manner that fosters interactions with key catalytic residues, representing a further likely contribution to the catalytic rate enhancement.
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Affiliation(s)
- Jesús Giraldo
- Grup de Modelització Estructural i Funcional de Sistemes Biològics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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Kuusela S, Lönnberg H. Metal ion-promoted hydrolysis of uridine 2′, 3′ - cyclic monophosphate: Effect of metal chelates and uncomplexed aquo ions. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.610051205] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Peeters A, Swerts B, Van Alsenoy C. Ab Initio and Molecular Dynamics Study of the Active Site of the Reaction between Ribonuclease A and Cytidyl-3‘,5‘-Adenosine. J Phys Chem B 2003. [DOI: 10.1021/jp027648d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anik Peeters
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Ben Swerts
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Christian Van Alsenoy
- Department of Chemistry, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Wilrijk, Belgium
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36
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Synthesis, structural and biological evaluation of GlyAla based lanthanide macrocyclic conjugates as supramolecular ribonuclease mimics. Polyhedron 2003. [DOI: 10.1016/s0277-5387(02)01402-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Ichikawa K, Tarnai M, Uddin MK, Nakata K, Sato S. Hydrolysis of natural and artificial phosphoesters using zinc model compound with a histidine-containing pseudopeptide. J Inorg Biochem 2002; 91:437-50. [PMID: 12175936 DOI: 10.1016/s0162-0134(02)00452-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Zinc(II) complex with histidine-containing pseudopeptide derived from N,N'-bis(benzylhistidyl) diethylenetriamine L was examined as catalyst for the hydrolysis of bis(p-nitrophenyl) phosphate (BNPP), p-nitrophenyl phosphate (NPP), adenylyl-(3'-5')adenosine (ApA), thymidylyl-(3'-5') thymidine (TpT) and PBR 322 supercoiled DNA. The stepwise protonation constants of the ligand, stability constants for its zinc(II) complex LZn have been determined potentiometrically in aqueous solution. LZn efficiently hydrolyzed BNPP and NPP and their pseudo-first-order rate constants k(obs) are 1.1 x 10(-5) s(-1) and 2.1 x 10(-5) s(-1), respectively. Bell-shaped pH-k(obs) profile was seen in BNPP hydrolysis around pH 7. Kinetic parameters were obtained from temperature dependence of hydrolysis rate constants where entropy of activation showed considerably high negative value. ApA and TpT as RNA-type and DNA-type dinucleotides were slowly hydrolyzed by LZn. On the basis of the kinetic evidence of bell-shaped pH-k(obs) profile and species distribution curve, we propose a mechanism for LZn-promoted hydrolysis of BNPP as well as ApA where cooperative achieve of zinc-hydroxo and zinc-aqua complex species may be responsible for enzymatic activity. The agarose gel electrophoresis and AFM demonstrated that LZn performed good activity on the selective cleavage of pBR322 supercoiled DNA at pH 7.0 providing evidence for its probable applicability.
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Affiliation(s)
- Kazuhiko Ichikawa
- Division of Material Science, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan.
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Affiliation(s)
- Bodo Baumeister
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
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Shinozuka K, Nakashima Y, Shimizu K, Sawai H. Synthesis and characterization of polyamine-based biomimetic catalysts as artificial ribonuclease. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:117-30. [PMID: 11303558 DOI: 10.1081/ncn-100001441] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Several polyamine derivatives (I-V) conjugated with or without an intercalative moiety were prepared as ribonuclease mimics. Although no DNA-cleaving activity was observed for all compounds tested, mimics I, III, and V bearing an intercalative moiety along with the primary amine and/or imidazole moieties exhibited potent RNA-cleaving activity at near physiological pH. The RNA-cleaving reactions of the compounds show characteristic bell-shaped pH dependency, and the optimal pH values for III and V were well correlated to the pKa values of their active sites, primary amine, and imidazole moieties.
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Affiliation(s)
- K Shinozuka
- Department of Chemistry, Faculty of Engineering, Gunma University, Kiryu City, Japan.
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40
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Acceleration of acid-catalyzed transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate by organic solvents. Org Lett 2000; 2:377-80. [PMID: 10814327 DOI: 10.1021/ol991321m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] Transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate in the presence of 0.092 M HClO4 is 50-5000 times faster in acetonitrile, 1,4-dioxane, methanol, ethanol, N,N-dimethylformamide, or dimethyl sulfoxide than in water. This demonstrates the importance of tuning the microenvironments in designing synthetic nucleases.
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41
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Suh J, Hong SH. Catalytic Activity of Ni(II)−Terpyridine Complex in Phosphodiester Transesterification Remarkably Enhanced by Self-Assembly of Terpyridines on Poly(ethylenimine). J Am Chem Soc 1998. [DOI: 10.1021/ja982705v] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junghun Suh
- Contribution from the Department of Chemistry and Center for Molecular Catalysis, Seoul National University, Seoul 151-742, Korea
| | - Sang Hyun Hong
- Contribution from the Department of Chemistry and Center for Molecular Catalysis, Seoul National University, Seoul 151-742, Korea
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42
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Fletcher MC, Kuderova A, Cygler M, Lee JS. Creation of a ribonuclease abzyme through site-directed mutagenesis. Nat Biotechnol 1998; 16:1065-7. [PMID: 9831037 DOI: 10.1038/3519] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The development of abzymes (antibody/enzymes) is one method of creating reagents with novel catalytic activity. To date, most abzymes have been obtained by immunization with transition state analogs. We have chosen to start with an existing antibody and convert it into an enzyme by the addition of catalytic residues to the binding site. We have introduced a histidine residue into antibody Jel 103 and converted it into an abzyme that cleaves poly(rI) with a kinetic efficiency of about 100 M(-1) sec(-1).
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Affiliation(s)
- M C Fletcher
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
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43
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Toward the development of metal-based synthetic nucleases and peptidases: a rationale and progress report in applying the principles of coordination chemistry. Coord Chem Rev 1998. [DOI: 10.1016/s0010-8545(98)00157-x] [Citation(s) in RCA: 487] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Trawick BN, Daniher AT, Bashkin JK. Inorganic Mimics of Ribonucleases and Ribozymes: From Random Cleavage to Sequence-Specific Chemistry to Catalytic Antisense Drugs. Chem Rev 1998; 98:939-960. [PMID: 11848920 DOI: 10.1021/cr960422k] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bobby N. Trawick
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
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45
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46
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Hegg EL, Deal KA, Kiessling LL, Burstyn JN. Hydrolysis of Double-Stranded and Single-Stranded RNA in Hairpin Structures by the Copper(II) Macrocycle Cu([9]aneN(3))Cl(2). Inorg Chem 1997; 36:1715-1718. [PMID: 11669765 DOI: 10.1021/ic960955b] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Eric L. Hegg
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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47
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Perreault DM, Anslyn EV. Der Mechanismus der RNA-Spaltung durch Umesterung – eine vereinheitlichende Analyse des aktuellen Diskussionsstandes. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971090505] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Bruice TC, Tsubouchi A, Dempcy RO, Olson LP. One- and Two-Metal Ion Catalysis of the Hydrolysis of Adenosine 3‘-Alkyl Phosphate Esters. Models for One- and Two-Metal Ion Catalysis of RNA Hydrolysis. J Am Chem Soc 1996. [DOI: 10.1021/ja9607300] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Akira Tsubouchi
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Robert O. Dempcy
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Leif P. Olson
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
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49
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Kuusela S, Lönnberg H. Zn2+-Promoted Hydrolysis of 3′,5′-Dinucleoside Monophosphates and Polyribonucleotides. The Effect of Nearest Neighbours on the Cleavage of Phosphodiester Bonds. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002466] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Breslow R, Dong SD, Webb Y, Xu R. Further Studies on the Buffer-Catalyzed Cleavage and Isomerization of Uridyluridine. Medium and Ionic Strength Effects on Catalysis by Morpholine, Imidazole, and Acetate Buffers Help Clarify the Mechanisms Involved and Their Relationship to the Mechanism Used by the Enzyme Ribonuclease and by a Ribonuclease Mimic. J Am Chem Soc 1996. [DOI: 10.1021/ja9526933] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ronald Breslow
- Contribution from the Department of Chemistry, Columbia University, New York, New York 10027
| | - Steven D. Dong
- Contribution from the Department of Chemistry, Columbia University, New York, New York 10027
| | - Yael Webb
- Contribution from the Department of Chemistry, Columbia University, New York, New York 10027
| | - Ruo Xu
- Contribution from the Department of Chemistry, Columbia University, New York, New York 10027
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