1
|
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.
Collapse
Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
| |
Collapse
|
2
|
Danneberg F, Westemeier H, Horx P, Zellmann F, Dörr K, Kalden E, Zeiger M, Akpinar A, Berger R, Göbel MW. RNA Hydrolysis by Heterocyclic Amidines and Guanidines: Parameters Affecting Reactivity. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Friederike Danneberg
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Hauke Westemeier
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Philip Horx
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Felix Zellmann
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Kathrin Dörr
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Elisabeth Kalden
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Mirco Zeiger
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Abdullah Akpinar
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| | - Robert Berger
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Straße 35032 Marburg Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie Goethe-Universität Frankfurt Max-von-Laue-Str. 7 D-60438 Frankfurt am Main Germany
| |
Collapse
|
3
|
Yepremyan A, Mekhail MA, Niebuhr BP, Pota K, Sadagopan N, Schwartz TM, Green KN. Synthesis of 12-Membered Tetra-aza Macrocyclic Pyridinophanes Bearing Electron-Withdrawing Groups. J Org Chem 2020; 85:4988-4998. [PMID: 32208700 DOI: 10.1021/acs.joc.0c00188] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The number of substituted pyridine pyridinophanes found in the literature is limited due to challenges associated with 12-membered macrocycle and modified pyridine synthesis. Most notably, the electrophilic character at the 4-position of pyridine in pyridinophanes presents a unique challenge for introducing electrophilic chemical groups. Likewise, of the few reported, most substituted pyridine pyridinophanes in the literature are limited to electron-donating functionalities. Herein, new synthetic strategies for four new macrocycles bearing the electron-withdrawing groups CN, Cl, NO2, and CF3 are introduced. Potentiometric titrations were used to determine the protonation constants of the new pyridinophanes. Further, the influence of such modifications on the chemical behavior is predicted by comparing the potentiometric results to previously reported systems. X-ray diffraction analysis of the 4-Cl substituted species and its Cu(II) complex are also described to demonstrate the metal binding nature of these ligands. DFT analysis is used to support the experimental findings through energy calculations and ESP maps. These new molecules serve as a foundation to access a range of new pyridinophane small molecules and applications in future work.
Collapse
Affiliation(s)
- Akop Yepremyan
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Magy A Mekhail
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Brian P Niebuhr
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Kristof Pota
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Nishanth Sadagopan
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Timothy M Schwartz
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| | - Kayla N Green
- Department of Chemistry and Biochemistry, Texas Christian University, 2950 W. Bowie, Fort Worth, Texas 76129, United States
| |
Collapse
|
4
|
Gair JJ, Haines BE, Filatov AS, Musaev DG, Lewis JC. Di-Palladium Complexes are Active Catalysts for Mono-N-Protected Amino Acid-Accelerated Enantioselective C–H Functionalization. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph J. Gair
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Brandon E. Haines
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Alexander S. Filatov
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Djamaladdin G. Musaev
- Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
5
|
Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
Collapse
Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| |
Collapse
|
6
|
Gonzalez P, Pota K, Turan LS, da Costa VCP, Akkaraju G, Green KN. Synthesis, Characterization, and Activity of a Triazine Bridged Antioxidant Small Molecule. ACS Chem Neurosci 2017; 8:2414-2423. [PMID: 28768410 DOI: 10.1021/acschemneuro.7b00184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metal-ion misregulation and oxidative stress continue to be components of the continually evolving hypothesis describing the molecular origins of Alzheimer's disease. Therefore, these features are viable targets for synthetic chemists to explore through hybridizations of metal-binding ligands and antioxidant units. To date, the metal-binding unit in potential therapeutic small molecules has largely been inspired by clioquinol with the exception of a handful of heterocyclic small molecules and open-chain systems. Heterocyclic small molecules such as cyclen (1,4,7,10-tetraazacyclododecane) have the advantage of straightforward N-based modifications, allowing the addition of functional groups. In this work, we report the synthesis of a triazine bridged system containing two cyclen metal-binding units and an antioxidant coumarin appendage inspired by nature. This new potential therapeutic molecule shows the ability to bind copper in a unique manner compared to other chelates proposed to treat Alzheimer's disease. DPPH and TEAC assays exploring the activity of N-(2-((4,6-di(1,4,7,10-tetraazacyclododecan-1-yl)-1,3,5-triazin-2-yl)amino)ethyl)-2-oxo-2H-chromene-3-carboxamide (molecule 1) show that the molecule is antioxidant. Cellular studies of molecule 1 indicate a low toxicity (EC50 = 80 μM) and the ability to protect HT-22 neuronal cells from cell death induced by Aβ + copper(II), thus demonstrating the potential for molecule 1 to serve as a multimodal therapeutic for Alzheimer's disease.
Collapse
Affiliation(s)
- Paulina Gonzalez
- Department of Chemistry
and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Kristof Pota
- Department of Chemistry
and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Lara Su Turan
- Department of Chemistry
and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Viviana C. P. da Costa
- Department of Chemistry
and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Giridhar Akkaraju
- Department of Biology, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Kayla N. Green
- Department of Chemistry
and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| |
Collapse
|
7
|
Laine M, Lönnberg T, Helkearo M, Lönnberg H. Cleavage of short oligoribonucleotides by a Zn2+ binding multi-nucleating azacrown conjugate. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
8
|
Salvio R, Volpi S, Cacciapaglia R, Sansone F, Mandolini L, Casnati A. Upper Rim Bifunctional cone-Calix[4]arenes Based on a Ligated Metal Ion and a Guanidinium Unit as DNAase and RNAase Mimics. J Org Chem 2016; 81:4728-35. [DOI: 10.1021/acs.joc.6b00644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Stefano Volpi
- Dipartimento
di Chimica, Università degli Studi di Parma, Parco Area
delle Scienze 17/a, 43124 Parma, Italy
| | - Roberta Cacciapaglia
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Francesco Sansone
- Dipartimento
di Chimica, Università degli Studi di Parma, Parco Area
delle Scienze 17/a, 43124 Parma, Italy
| | - Luigi Mandolini
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Alessandro Casnati
- Dipartimento
di Chimica, Università degli Studi di Parma, Parco Area
delle Scienze 17/a, 43124 Parma, Italy
| |
Collapse
|
9
|
2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine and Its Benzene Analog as Nonmetallic Cleaving Agents of RNA Phosphodiester Linkages. Int J Mol Sci 2015; 16:17798-811. [PMID: 26247935 PMCID: PMC4581222 DOI: 10.3390/ijms160817798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 07/13/2015] [Accepted: 07/28/2015] [Indexed: 01/10/2023] Open
Abstract
2,6-Bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)pyridine (11a) and 1,3-bis(1,4,7,10-tetraazacyclododecan-1-ylmethyl)benzene (11b) have been shown to accelerate at 50 mmol·L−1 concentration both the cleavage and mutual isomerization of uridylyl-3′,5′-uridine and uridylyl-2′,5′-uridine by up to two orders of magnitude. The catalytically active ionic forms are the tri- (in the case of 11b) tetra- and pentacations. The pyridine nitrogen is not critical for efficient catalysis, since the activity of 11b is even slightly higher than that of 11a. On the other hand, protonation of the pyridine nitrogen still makes 11a approximately four times more efficient as a catalyst, but only for the cleavage reaction. Interestingly, the respective reactions of adenylyl-3′,5′-adenosine were not accelerated, suggesting that the catalysis is base moiety selective.
Collapse
|
10
|
Lain L, Lönnberg H, Lönnberg T. Participation of an additional 4'-hydroxymethyl group in the cleavage and isomerization of ribonucleoside 3'-phosphodiesters. Org Biomol Chem 2015; 13:4737-42. [PMID: 25805021 DOI: 10.1039/c5ob00400d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
4'-(Hydroxymethyl)uridylyl-3',5'-thymidine, an RNA model bearing an extra hydroxymethyl group at the 4'-position of the 3'-linked nucleoside, has been prepared and its cleavage and isomerization reactions studied over a wide pH range (from 0 to 12). Overall, the pH-rate profiles of these reactions were very similar to those of uridylyl-3',5'-uridine (UpU) - only a very modest acceleration was observed under acidic and neutral conditions. Evidently, hydrogen bond assistance by the additional hydroxymethyl function does not play a significant role.
Collapse
Affiliation(s)
- Luigi Lain
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
| | | | | |
Collapse
|
11
|
Lönnberg T, Hutchinson M, Rokita S. Selective Alkylation of C-Rich Bulge Motifs in Nucleic Acids by Quinone Methide Derivatives. Chemistry 2015. [PMID: 26220692 DOI: 10.1002/chem.201502014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A quinone methide precursor featuring a bis-cyclen anchoring moiety has been synthesized and its capacity to alkylate oligonucleotide targets quantified in the presence and absence of divalent metal ions (Zn(2+) , Ni(2+) and Cd(2+) ). The oligonucleotides were designed for testing the sequence and secondary structure specificity of the reaction. Gel electrophoretic analysis revealed predominant alkylation of C-rich bulges, regardless of the presence of divalent metal ions or even the bis-cyclen anchor. This C-selectivity appears to be an intrinsic property of the quinone methide electrophile as reflected by its reaction with an equimolar mixture of the 2'-deoxynucleosides. Only dA-N1 and dC-N3 alkylation products were detected initially and only the dC adduct persisted for detection under conditions of the gel electrophoretic analysis.
Collapse
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA). .,Department of Chemistry, University of Turku, 20014 Turku (Finland).
| | - Mark Hutchinson
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA)
| | - Steven Rokita
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA)
| |
Collapse
|
12
|
Renny JS, Tomasevich LL, Tallmadge EH, Collum DB. Method of continuous variations: applications of job plots to the study of molecular associations in organometallic chemistry. Angew Chem Int Ed Engl 2013; 52:11998-2013. [PMID: 24166797 PMCID: PMC4028694 DOI: 10.1002/anie.201304157] [Citation(s) in RCA: 429] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 11/10/2022]
Abstract
Applications of the method of continuous variations (MCV or the Method of Job) to problems of interest to organometallic chemists are described. MCV provides qualitative and quantitative insights into the stoichiometries underlying association of m molecules of A and n molecules of B to form A(m)B(n) . Applications to complex ensembles probe associations that form metal clusters and aggregates. Job plots in which reaction rates are monitored provide relative stoichiometries in rate-limiting transition structures. In a specialized variant, ligand- or solvent-dependent reaction rates are dissected into contributions in both the ground states and transition states, which affords insights into the full reaction coordinate from a single Job plot. Gaps in the literature are identified and critiqued.
Collapse
Affiliation(s)
- Joseph S. Renny
- Contribution from the Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - Laura L. Tomasevich
- Contribution from the Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - Evan H. Tallmadge
- Contribution from the Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| | - David B. Collum
- Contribution from the Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University, Ithaca, New York 14853-1301
| |
Collapse
|
13
|
Renny JS, Tomasevich LL, Tallmadge EH, Collum DB. Methode der kontinuierlichen Variation: Verwendung von Job-Plots zur Untersuchung molekularer Assoziationen in der metallorganischen Chemie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304157] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
14
|
Lönnberg T, Luomala M. Intracomplex general acid/base catalyzed cleavage of RNA phosphodiester bonds: the leaving group effect. Org Biomol Chem 2012; 10:6785-91. [PMID: 22825538 DOI: 10.1039/c2ob25958c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The general acid/base catalyzed cleavage of a number of alkyl esters of uridine-3'- (and -5'-)phosphate has been studied by utilizing a cleaving agent, in which the catalytic moiety (a substituted 1,3,5-triazine) is tethered to an anchoring Zn(II):cyclen moiety. Around pH 7, formation of a strong ternary complex between uracil, Zn(II) and cyclen brings the general acid/base catalyst close to the scissile phosphodiester linkage, resulting in rate acceleration of 1-2 orders of magnitude with the uridine-3'-phosphodiesters. Curiously, no acceleration was observed with their 5'-counterparts. A β(lg) value of -0.7 has been determined for the general acid/base catalyzed cleavage, consistent with a proton transfer to the leaving group in the rate-limiting step.
Collapse
|