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Pastwińska J, Karwaciak I, Karaś K, Bachorz RA, Ratajewski M. RORγT agonists as immune modulators in anticancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:189021. [PMID: 37951483 DOI: 10.1016/j.bbcan.2023.189021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023]
Abstract
RORγT is a transcription factor that directs the development of Th17 lymphocytes and other IL-17-expressing cells (e.g., Tc17 and ILC3 cells). These cells are involved in the body's defense against pathogenic bacteria and fungi, but they also participate in maintaining the proinflammatory environment in some autoimmune diseases and play a role in the immune system's response to cancer. Similar to other members of the nuclear receptor superfamily, the activity of RORγT is regulated by low-molecular-weight ligands. Therefore, extensive efforts have been dedicated to identifying inverse agonists that diminish the activity of this receptor and subsequently inhibit the development of autoimmune diseases. Unfortunately, in the pursuit of an ideal inverse agonist, the development of agonists has been overlooked. It is important to remember that these types of compounds, by stimulating lymphocytes expressing RORγT (Th17 and Tc17), can enhance the immune system's response to tumors. In this review, we present recent advancements in the biology of RORγT agonists and their potential application in anticancer therapy.
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Affiliation(s)
- Joanna Pastwińska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Iwona Karwaciak
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Rafał A Bachorz
- Laboratory of Molecular Modeling, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland.
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Bachorz RA, Pastwińska J, Nowak D, Karaś K, Karwaciak I, Ratajewski M. The application of machine learning methods to the prediction of novel ligands for ROR γ/ROR γT receptors. Comput Struct Biotechnol J 2023; 21:5491-5505. [PMID: 38022699 PMCID: PMC10663739 DOI: 10.1016/j.csbj.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
In this work, we developed and applied a computational procedure for creating and validating predictive models capable of estimating the biological activity of ligands. The combination of modern machine learning methods, experimental data, and the appropriate setup of molecular descriptors led to a set of well-performing models. We thoroughly inspected both the methodological space and various possibilities for creating a chemical feature space. The resulting models were applied to the virtual screening of the ZINC20 database to identify new, biologically active ligands of RORγ receptors, which are a subfamily of nuclear receptors. Based on the known ligands of RORγ, we selected candidates and calculate their predicted activities with the best-performing models. We chose two candidates that were experimentally verified. One of these candidates was confirmed to induce the biological activity of the RORγ receptors, which we consider proof of the efficacy of the proposed methodology.
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Affiliation(s)
- Rafał A. Bachorz
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
| | - Joanna Pastwińska
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
| | - Damian Nowak
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
| | - Kaja Karaś
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
| | - Iwona Karwaciak
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
| | - Marcin Ratajewski
- Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź, 93-232, Poland
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Karaś K, Karwaciak I, Chałaśkiewicz K, Sałkowska A, Pastwińska J, Bachorz RA, Ratajewski M. Anti-hepatocellular carcinoma activity of the cyclin-dependent kinase inhibitor AT7519. Biomed Pharmacother 2023; 164:115002. [PMID: 37311277 DOI: 10.1016/j.biopha.2023.115002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancerous tumors and one of the leading causes of death among cancer-related disorders. Chemotherapy is ineffective in HCC patients, and the number of drugs that are in use is limited. Thus, new molecules are needed that could increase the effectiveness of anti-HCC regimens. Here, we show that AT7519, a CDK inhibitor, exerts positive effects on HCC cells: it inhibits proliferation, migration and clonogenicity. Detailed analysis of the transcriptomes of cells treated with this compound indicated that AT7519 affects a substantial portion of genes that are associated with HCC development and progression. Moreover, we showed that the concomitant use of AT7519 with gefitinib or cabozantinib sensitized HCC cells to these drugs. Thus, our research indicates that AT7519 is worth considering in monotherapy for hepatocellular carcinoma patients or in combination with other drugs, e.g., gefitinib or cabozantinib.
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Affiliation(s)
- Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Iwona Karwaciak
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Katarzyna Chałaśkiewicz
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Anna Sałkowska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Joanna Pastwińska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland
| | - Rafał A Bachorz
- Laboratory of Molecular Modeling, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232, Lodz, Poland
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland.
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Pastwińska J, Karaś K, Sałkowska A, Karwaciak I, Chałaśkiewicz K, Wojtczak BA, Bachorz RA, Ratajewski M. Identification of Corosolic and Oleanolic Acids as Molecules Antagonizing the Human RORγT Nuclear Receptor Using the Calculated Fingerprints of the Molecular Similarity. Int J Mol Sci 2022; 23:ijms23031906. [PMID: 35163824 PMCID: PMC8837092 DOI: 10.3390/ijms23031906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
RORγT is a protein product of the RORC gene belonging to the nuclear receptor subfamily of retinoic-acid-receptor-related orphan receptors (RORs). RORγT is preferentially expressed in Th17 lymphocytes and drives their differentiation from naive CD4+ cells and is involved in the regulation of the expression of numerous Th17-specific cytokines, such as IL-17. Because Th17 cells are implicated in the pathology of autoimmune diseases (e.g., psoriasis, inflammatory bowel disease, multiple sclerosis), RORγT, whose activity is regulated by ligands, has been recognized as a drug target in potential therapies against these diseases. The identification of such ligands is time-consuming and usually requires the screening of chemical libraries. Herein, using a Tanimoto similarity search, we found corosolic acid and other pentacyclic tritepenes in the library we previously screened as compounds highly similar to the RORγT inverse agonist ursolic acid. Furthermore, using gene reporter assays and Th17 lymphocytes, we distinguished compounds that exert stronger biological effects (ursolic, corosolic, and oleanolic acid) from those that are ineffective (asiatic and maslinic acids), providing evidence that such combinatorial methodology (in silico and experimental) might help wet screenings to achieve more accurate results, eliminating false negatives.
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Affiliation(s)
- Joanna Pastwińska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Anna Sałkowska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Iwona Karwaciak
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Katarzyna Chałaśkiewicz
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Błażej A. Wojtczak
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland;
| | - Rafał A. Bachorz
- Laboratory of Molecular Modeling, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland;
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
- Correspondence: ; Tel.: +48-42-209-33-89
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Karaś K, Sałkowska A, Sobalska-Kwapis M, Walczak-Drzewiecka A, Strapagiel D, Dastych J, Bachorz RA, Ratajewski M. Digoxin, an Overlooked Agonist of RORγ/RORγT. Front Pharmacol 2019; 9:1460. [PMID: 30666196 PMCID: PMC6330298 DOI: 10.3389/fphar.2018.01460] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/29/2018] [Indexed: 11/30/2022] Open
Abstract
Digoxin was one of the first identified RORγT receptor inverse agonists inhibiting the differentiation of Th17 cells. However, this compound exhibits inhibitory activity at relatively high concentrations that mediate cytotoxic effects. We previously identified several cardenolides that are structurally similar to digoxin that were able to induce RORγ/RORγT-dependent transcription. These observations encouraged us to reanalyze the effects of digoxin on RORγ/RORγT-dependent transcription at low, noncytotoxic concentrations. Digoxin induced RORγ/RORγT-dependent transcription in HepG2 and Th17 cells. Furthermore, analysis of the transcriptomes of Th17 cells cultured in the presence of digoxin revealed the induction of the expression of numerous Th17-specific genes, including IL17A/F, IL21, IL22, IL23R, CCR4, and CCR6. Thus, our study, which includes data obtained from intact cells, indicates that digoxin, similar to other cardenolides, is a potent RORγ/RORγT receptor activator and that its structure may serve as a starting point for the design of dedicated molecules that can be used in the development of adoptive cell therapy (ACT).
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Affiliation(s)
- Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Anna Sałkowska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Aurelia Walczak-Drzewiecka
- Laboratory of Cellular Immunology, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Rafał A Bachorz
- Laboratory of Molecular Modeling, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Karaś K, Sałkowska A, Walczak-Drzewiecka A, Ryba K, Dastych J, Bachorz RA, Ratajewski M. The cardenolides strophanthidin, digoxigenin and dihydroouabain act as activators of the human RORγ/RORγT receptors. Toxicol Lett 2018; 295:314-324. [DOI: 10.1016/j.toxlet.2018.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/22/2018] [Accepted: 07/04/2018] [Indexed: 12/21/2022]
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Bachorz RA, Bischoff FA, Glöss A, Hättig C, Höfener S, Klopper W, Tew DP. The MP2-F12 method in the Turbomole program package. J Comput Chem 2011; 32:2492-513. [PMID: 21590779 DOI: 10.1002/jcc.21825] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 03/25/2011] [Accepted: 03/27/2011] [Indexed: 01/21/2023]
Abstract
A detailed description of the explicitly correlated second-order Møller-Plesset perturbation theory (MP2-F12) method, as implemented in the TURBOMOLE program package, is presented. The TURBOMOLE implementation makes use of density fitting, which greatly reduces the prefactor for integral evaluation. Methods are available for the treatment of ground states of open- and closed-shell species, using unrestricted as well as restricted (open-shell) Hartree-Fock reference determinants. Various methodological choices and approximations are discussed. The performance of the TURBOMOLE implementation is illustrated by example calculations of the molecules leflunomide, prednisone, methotrexate, ethylenedioxytetrafulvalene, and a cluster model for the adsorption of methanol on the zeolite H-ZSM-5. Various basis sets are used, including the correlation-consistent basis sets specially optimized for explicitly correlated calculations (cc-pVXZ-F12).
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Affiliation(s)
- Rafał A Bachorz
- Center for Functional Nanostructures (CFN, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Pfaffen C, Frey HM, Ottiger P, Leutwyler S, Bachorz RA, Klopper W. Large-amplitude vibrations of an N–H⋯π hydrogen bonded cis-amide–benzene complex. Phys Chem Chem Phys 2010; 12:8208-18. [DOI: 10.1039/c002056g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Tew DP, Hättig C, Bachorz RA, Klopper W. Explicitly Correlated Coupled-Cluster Theory. Challenges and Advances in Computational Chemistry and Physics 2010. [DOI: 10.1007/978-90-481-2885-3_20] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Abstract
We characterized valence-type and dipole-bound anionic states of uracil using various electronic structure methods. We found that the most stable anion is related to neither the canonical 2,4-dioxo nor a rare imino-hydroxy tautomer. Instead, it is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion is characterized by an electron vertical detachment energy (VDE) of 1267 meV and it is adiabatically stable with respect to the canonical neutral by 3.93 kcal mol(-1). It is also more stable by 2.32 and 5.10 kcal mol(-1) than the dipole-bound and valence anion, respectively, of the canonical tautomer. The VDE values for the former and the latter are 73 and 506 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2499 meV has a proton transferred from N3H to C5. It is less stable than the neutral canonical tautomer by 1.38 kcal mol(-1). The mechanism of formation of anionic tautomers with the carbon C5 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of anionic tautomers with carbon atoms protonated might be unstable upon an excess electron detachment. Indeed, the neutral systems resulting from electron detachment from anionic tautomers with carbon atoms protonated evolve along barrier-free decomposition pathways to a linear or a bicyclo structure, which might be viewed as lesions to RNA. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral and the two most stable tautomers have carbon atoms protonated.
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Affiliation(s)
- Rafał A Bachorz
- Department of Chemistry, University of Gdańsk, 80-952 Gdańsk, Poland
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Abstract
The H(3)(+) potential energy surface is sampled at 5900 geometries with the emphasis on the nonequilibrium and asymptotic points. Apart from the Born-Oppenheimer energy converged to the accuracy better than 0.02 cm(-1), the adiabatic and the leading relativistic corrections are computed at each geometry. To represent analytically the potential energy surface, the parameters of a power series are determined by fitting to the computed energy points. Possible choice of nuclear masses simulating the nonadiabatic effects in solving the nuclear Schrodinger equation is analyzed. A set of theoretically predicted rovibrational transitions is confronted with the experimental data in the 10,700-13,700 cm(-1) window of the spectra.
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Affiliation(s)
- Rafał A Bachorz
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland.
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Klopper W, Bachorz RA, Tew DP, Aguilera-Iparraguirre J, Carissan Y, Hättig C. Accurate Coupled Cluster Calculations of the Reaction Barrier Heights of Two CH3• + CH4 Reactions. J Phys Chem A 2009; 113:11679-84. [DOI: 10.1021/jp902753s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wim Klopper
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Rafał A. Bachorz
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - David P. Tew
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Jorge Aguilera-Iparraguirre
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Yannick Carissan
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Christof Hättig
- Institut für Physikalische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany, Universités dʼAix-Marseille I, II & III—CNRS, UMR 6263: Institut des Sciences Moléculaires de Marseille (iSm2), F-13397 Marseille Cedex 20, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Ottiger P, Pfaffen C, Leist R, Leutwyler S, Bachorz RA, Klopper W. Strong N−H···π Hydrogen Bonding in Amide−Benzene Interactions. J Phys Chem B 2009; 113:2937-43. [DOI: 10.1021/jp8110474] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp Ottiger
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Roman Leist
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Rafał A. Bachorz
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
| | - Wim Klopper
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
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Bachorz RA, Lupica G, Gutowski M, Haranczyk M. Electrostatic potential maps of damaged DNA studied by image analysis tools. 8-Oxoguanine and abasic site lesions. J Mol Model 2009; 15:817-27. [PMID: 19130099 DOI: 10.1007/s00894-008-0434-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 12/05/2008] [Indexed: 11/28/2022]
Abstract
Changes of electrostatic potential around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. The electrostatic potential around the DNA fragments containing either the intact guanine-cytosine pair or 8-oxoguanine-cytosine or the guanine-abasic site was projected on a cylindrical surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were compared using image analysis methods. Occurrence of abasic site and 8-oxoguanine lesions were found to be reflected in the EP maps. In the case of the 8-oxoguanine lesion, the two phosphate groups and countercations of the damaged strand are moved away from the lesion in opposite directions, whereas they are moved in the same direction in the case of the abasic site lesion. The characteristic features of 8-oxoguanine lesion might be identified in the major groove, whereas the features of abasic site lesion the minor groove.
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Affiliation(s)
- Rafał A Bachorz
- Chemical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Bachorz RA, Klopper W, Gutowski M, Li X, Bowen KH. Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies. J Chem Phys 2008; 129:054309. [PMID: 18698902 DOI: 10.1063/1.2965128] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.
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Affiliation(s)
- Rafał A Bachorz
- Center for Functional Nanostructures (CFN) and Lehrstuhl für Theoretische Chemie, Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany
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Eustis SN, Radisic D, Bowen KH, Bachorz RA, Haranczyk M, Schenter GK, Gutowski M. Electron-Driven Acid-Base Chemistry: Proton Transfer from Hydrogen Chloride to Ammonia. Science 2008; 319:936-9. [DOI: 10.1126/science.1151614] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Bachorz RA, Bischoff FA, Höfener S, Klopper W, Ottiger P, Leist R, Frey JA, Leutwyler S. Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions. Phys Chem Chem Phys 2008; 10:2758-66. [DOI: 10.1039/b718494h] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Li X, Bowen KH, Haranczyk M, Bachorz RA, Mazurkiewicz K, Rak J, Gutowski M. Photoelectron spectroscopy of adiabatically bound valence anions of rare tautomers of the nucleic acid bases. J Chem Phys 2007; 127:174309. [DOI: 10.1063/1.2795719] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Leist R, Frey JA, Ottiger P, Frey HM, Leutwyler S, Bachorz RA, Klopper W. Nucleobase–Fluorobenzene Interactions: Hydrogen Bonding Wins over π Stacking. Angew Chem Int Ed Engl 2007; 46:7449-52. [PMID: 17722215 DOI: 10.1002/anie.200701171] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Roman Leist
- Department of Chemistry and Biochemistry, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Abstract
A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.
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Affiliation(s)
- Rafał A Bachorz
- Center for Functional Nanostructures (CFN), Universität Karlsruhe (TH), D-76128 Karlsruhe, Germany
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Mazurkiewicz K, Bachorz RA, Gutowski M, Rak J. On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study. J Phys Chem B 2006; 110:24696-707. [PMID: 17134233 DOI: 10.1021/jp065666f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).
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Affiliation(s)
- Kamil Mazurkiewicz
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Bachorz RA, Harańczyk M, Dabkowska I, Rak J, Gutowski M. Anion of the formic acid dimer as a model for intermolecular proton transfer induced by a π* excess electron. J Chem Phys 2005; 122:204304. [PMID: 15945721 DOI: 10.1063/1.1899144] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The neutral and anionic formic acid dimers have been studied at the second-order Moller-Plesset and coupled-cluster level of theory with single, double, and perturbative triple excitations with augmented, correlation-consistent basis sets of double- and triple-zeta quality. Scans of the potential-energy surface for the anion were performed at the density-functional level of theory with a hybrid B3LYP functional and a high-quality basis set. Our main finding is that the formic acid dimer is susceptible to intermolecular proton transfer upon an excess electron attachment. The unpaired electron occupies a pi(*) orbital, the molecular moiety that accommodates an excess electron "buckles," and a proton is transferred to the unit where the excess electron is localized. As a consequence of these geometrical transformations, the electron vertical detachment energy becomes substantial, 2.35 eV. The anion is barely adiabatically unstable with respect to the neutral at 0 K. However, at standard conditions and in terms of Gibbs free energy, the anion is more stable than the neutral by +37 meV. The neutral and anionic dimers display different IR characteristics. In summary, the formic acid dimer can exist in two quasidegenerate states (neutral and anionic), which can be viewed as "zero" and "one" in the binary system. These two states are switchable and distinguishable.
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Affiliation(s)
- Rafał A Bachorz
- Department of Chemistry, Quantum Chemistry Group, Adam Mickiewicz University, Poznań 60-780, Poland
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