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Ichijo R, Kamimura T, Kawai G. Interaction between a fluoroquinolone derivative KG022 and RNAs: Effect of base pairs 3′ adjacent to the bulged residues. Front Mol Biosci 2023; 10:1145528. [PMID: 36999159 PMCID: PMC10043337 DOI: 10.3389/fmolb.2023.1145528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
RNA-targeted small molecules are a promising modality in drug discovery. Recently, we found that a fluoroquinolone derivative, KG022, can bind to RNAs with bulged C or G. To clarify the RNA specificity of KG022, we analyzed the effect of the base pair located at the 3′side of the bulged residue. It was found that KG022 prefers G-C and A-U base pairs at the 3′side. Solution structures of the complexes of KG022 with the four RNA molecules with bulged C or G and G-C or A-U base pairs at the 3′side of the bulged residue were determined to find that the fluoroquinolone moiety is located between two purine bases, and this may be the mechanism of the specificity. This work provides an important example of the specificity of RNA-targeted small molecules.
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Affiliation(s)
- Rika Ichijo
- Graduate School of Engineering, Chiba Institute of Technology, Chiba, Japan
| | | | - Gota Kawai
- Graduate School of Engineering, Chiba Institute of Technology, Chiba, Japan
- *Correspondence: Gota Kawai,
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2
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Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota SS, Zhao J, Douglas JT, Gao P, Holmstrom ED, Miao Y, Wang J. Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Res 2021; 49:7870-7883. [PMID: 34283224 PMCID: PMC8373063 DOI: 10.1093/nar/gkab602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5'-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues. In this report, we unambiguously determined that a known risdiplam analogue, SMN-C2, binds to single-stranded GA-rich RNA in a sequence-specific manner. The minimum required binding sequence for SMN-C2 was identified as GAAGGAAGG. We performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which captured spontaneous binding of a risdiplam analogue to the target nucleic acids. We uncovered, for the first time, a ligand-binding pocket formed by two sequential GAAG loop-like structures. The simulation findings were highly consistent with experimental data obtained from saturation transfer difference (STD) NMR and structure-affinity-relationship studies of the risdiplam analogues. Together, these studies illuminate us to understand the molecular basis of single-stranded purine-rich RNA recognition by small-molecule splicing modulators with an unprecedented binding mode.
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Affiliation(s)
- Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Ankita Ramprasad
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Xiao Wang
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Sadikshya Aryal
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Srinivas S Thota
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Justin T Douglas
- Nuclear Magnetic Resonance Lab, University of Kansas, Lawrence, KS 66045, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, KS 66047, USA
| | - Erik D Holmstrom
- Department of Molecular Biosciences and Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
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Jastrzab R, Nowak M, Zabiszak M, Odani A, Kaczmarek MT. Significance and properties of the complex formation of phosphate and polyphosphate groups in particles present in living cells. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
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5
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Blindauer CA, Holý A, Operschall BP, Sigel A, Song B, Sigel H. Metal Ion‐Coordinating Properties in Aqueous Solutions of the Antivirally Active Nucleotide Analogue (
S
)‐9‐[3‐Hydroxy‐2‐(phosphonomethoxy)propyl]adenine (HPMPA) – Quantification of Complex Isomeric Equilibria. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Claudia A. Blindauer
- Department of Chemistry Inorganic Chemistry University of Basel Spitalstrasse 51 4056 Basel Switzerland
- Department of Chemistry Inorganic Chemistry University of Warwick Coventry CV4 7AL UK
| | - Antonín Holý
- Institute of Organic Chemistry and Biochemistry Centre of Novel Antivirals and Antineoplastics Academy of Sciences 16610 Prague Czech Republic
| | - Bert P. Operschall
- Department of Chemistry Inorganic Chemistry University of Basel Spitalstrasse 51 4056 Basel Switzerland
| | - Astrid Sigel
- Department of Chemistry Inorganic Chemistry University of Basel Spitalstrasse 51 4056 Basel Switzerland
| | - Bin Song
- Department of Chemistry Inorganic Chemistry University of Basel Spitalstrasse 51 4056 Basel Switzerland
- Centre of Novel Antivirals and Antineoplastics Vertex Pharmaceuticals Inc. 02210 Boston MA USA
| | - Helmut Sigel
- Department of Chemistry Inorganic Chemistry University of Basel Spitalstrasse 51 4056 Basel Switzerland
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Blindauer CA, Griesser R, Holý A, Operschall BP, Sigel A, Song B, Sigel H. Intramolecular π-stacks in mixed-ligand copper(II) complexes formed by heteroaromatic amines and antivirally active acyclic nucleotide analogs carrying a hydroxy-2-(phosphonomethoxy)propyl residue ‡. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1490019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Claudia A. Blindauer
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Rolf Griesser
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
| | - Antonín Holý
- Institute of Organic Chemistry and Biochemistry, Centre of Novel Antivirals and Antineoplastics, Academy of Sciences, Prague, Czech Republic
| | - Bert P. Operschall
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
| | - Astrid Sigel
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
| | - Bin Song
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
- Vertex Pharmaceuticals Inc., Boston, MA, USA
| | - Helmut Sigel
- Department of Chemistry, Inorganic Chemistry, University of Basel, Basel, Switzerland
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Blindauer CA, Sigel A, Operschall BP, Holý A, Sigel H. Metal-ion binding properties of (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (HPMPC, Cidofovir). A nucleotide analogue with activity against DNA viruses. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Characterization of the one-electron oxidized Cu(II)-salen complexes with a side chain aromatic ring: the effect of the indole ring on the Cu(II)-phenoxyl radical species. J Biol Inorg Chem 2017; 23:51-59. [PMID: 29218633 DOI: 10.1007/s00775-017-1508-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022]
Abstract
To gain insights into the role of the proximal indole ring in the redox-active metal center as seen in galactose oxidase, we prepared the Cu(II)-salen-type complexes having a pendent indol-3-ylmethyl (1), methyl (2) or benzyl (3) group substituted on the ethylenediamine moiety and investigated the structures and redox properties by various physicochemical methods and theoretical calculations. Neutral complexes 1, 2, and 3 showed no significant difference in the UV-Vis-NIR and EPR spectra. One-electron oxidation of 1, 2, and 3 by addition of 1 equiv. of thianthrenyl radical gave [1]SbCl 6 , [2]SbCl 6 , and [3]SbCl 6 , respectively, which could be assigned to relatively localized phenoxyl radical species. The cyclic and differential pulse voltammograms of [1]SbCl 6 showed two redox waves with a large separation between the first and second redox potentials compared with the separations observed for [2]SbCl 6 and [3]SbCl 6 . This suggests that [1]SbCl 6 is more stabilized than [2]SbCl 6 and [3]SbCl 6 . The NIR band of [1]SbCl 6 showed a larger blue shift than that of [2]SbCl 6 and [3]SbCl 6 . The EPR spectrum of [2]SbCl 6 exhibited an intense signal at the g value of 2 due to partial disproportionation to form the EPR active two-electron oxidized complex [2] 2+ , while the EPR intensity of [1]SbCl 6 was much weaker than that of [2]SbCl 6 . These results indicate that the pendent indole moiety stabilizes the Cu(II)-phenoxyl radical in [1]SbCl 6 most probably by stacking with the phenoxyl moiety, which is further supported by DFT calculations.
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9
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance. mBio 2017; 8:mBio.02296-16. [PMID: 28351923 PMCID: PMC5371416 DOI: 10.1128/mbio.02296-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons ensure a rapid and "on demand" response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.IMPORTANCE The integron system confers upon bacteria a rapid adaptation capability in changing environments. Specifically, integrons are involved in the continuous emergence of bacteria resistant to almost all antibiotic treatments. The international situation is critical, and in 2050, the annual number of deaths caused by multiresistant bacteria could reach 10 million, exceeding the incidence of deaths related to cancer. It is crucial to increase our understanding of antibiotic resistance dissemination and therefore integron recombination dynamics to find new approaches to cope with the worldwide problem of multiresistance. Here, we studied the dynamics of recombination and dissemination of gene encoding cassettes carried on integrons. By combining in silico and in vivo analyses, we show that cassette excision is highly regulated by replication and by the intrinsic properties of cassette recombination sites. We also demonstrated differences in the dynamics of cassette recombination between mobile and sedentary chromosomal integrons (MIs and SCIs). For MIs, a high cassette recombination rate is favored and timed to conditions when generating diversity (upon which selection can act) allows for a rapid response to environmental conditions and stresses. In contrast, for SCIs, cassette excisions are less frequent, limiting cassette loss and ensuring a large pool of cassettes. We therefore confirm a role of SCIs as reservoirs of adaptive functions and demonstrate that the remarkable adaptive success of integron recombination system is due to its intricate regulation.
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Lozinova TA, Lobanov AV, Lander AV. Photoinduced formation of hydrogen peroxide in aqueous solutions of adenine derivatives at 77 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416110157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Nivina A, Escudero JA, Vit C, Mazel D, Loot C. Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites. Nucleic Acids Res 2016; 44:7792-803. [PMID: 27496283 PMCID: PMC5027507 DOI: 10.1093/nar/gkw646] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/05/2016] [Accepted: 07/10/2016] [Indexed: 01/29/2023] Open
Abstract
The integron is a bacterial recombination system that allows acquisition, stockpiling and expression of cassettes carrying protein-coding sequences, and is responsible for the emergence and rise of multiresistance in Gram-negative bacteria. The functionality of this system depends on the insertion of promoterless cassettes in correct orientation, allowing their expression from the promoter located upstream of the cassette array. Correct orientation is ensured by strand selectivity of integron integrases for the bottom strand of cassette recombination sites (attC), recombined in form of folded single-stranded hairpins. Here, we investigated the basis of such strand selectivity by comparing recombination of wild-type and mutated attC sites with different lengths, sequences and structures. We show that all three unpaired structural features that distinguish the bottom and top strands contribute to strand selectivity. The localization of Extra-Helical Bases (EHBs) directly favors integrase binding to the bottom strand. The Unpaired Central Spacer (UCS) and the Variable Terminal Structure (VTS) influence strand selectivity indirectly, probably through the stabilization of the bottom strand and the resulting synapse due to the nucleotide skew between the two strands. These results underscore the importance of the single-stranded nature of the attC site that allows such tight control over integron cassette orientation.
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Affiliation(s)
- Aleksandra Nivina
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - José Antonio Escudero
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Claire Vit
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Didier Mazel
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Céline Loot
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
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Kataev EA, Shumilova TA, Fiedler B, Anacker T, Friedrich J. Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study. J Org Chem 2016; 81:6505-14. [PMID: 27314892 DOI: 10.1021/acs.joc.6b01130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations.
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Affiliation(s)
- Evgeny A Kataev
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tatiana A Shumilova
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Benjamin Fiedler
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Tony Anacker
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Joachim Friedrich
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz , 09107 Chemnitz, Germany
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Blindauer CA, Sigel A, Operschall BP, Griesser R, Holý A, Sigel H. Extent of intramolecular π stacks in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and the anticancer and antivirally active 9-[2-(phosphonomethoxy)ethyl]guanine (PMEG). A comparison with related acyclic nucleotide analogues. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gómez-Coca RB, Sigel A, Operschall BP, Holý A, Sigel H. Solution properties of metal ion complexes formed with the antiviral and cytostatic nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]-2-amino-6-dimethylaminopurine (PME2A6DMAP). CAN J CHEM 2014. [DOI: 10.1139/cjc-2014-0041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The acidity constants of protonated 9-[2-(phosphonomethoxy)ethyl]-2-amino-6-dimethylaminopurine (H3(PME2A6DMAP)+) are considered, and the stability constants of the M(H;PME2A6DMAP)+ and M(PME2A6DMAP) complexes (M2+ = Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, or Cd2+) were measured by potentiometric pH titrations in aqueous solution (25 °C; I = 0.1 mol/L, NaNO3). In the M(H;PME2A6DMAP)+ species, H+ and M2+ (mainly outersphere) are at the phosphonate group; this is relevant for phosphoryl-diester bridges in nucleic acids because, in the present system, there is no indication for a M2+–purine binding. This contrasts, for example, with the complexes formed by 9-[2-(phosphonomethoxy)ethyl]adenine, M(H;PMEA)+, where M2+ is mainly situated at the adenine residue. Application of log [Formula: see text] vs. [Formula: see text] plots for simple phosph(on)ate ligands, R–PO32− (R being a residue that does not affect M2+ binding), proves that all M(PME2A6DMAP) complexes have larger stabilities than what would be expected for a M2+–phosphonate coordination. Comparisons with M(PME–R) complexes, where R is a noncoordinating residue of the (phosphonomethoxy)ethane chain, allow one to conclude that the increased stability is due to the formation of five-membered chelates involving the ether–oxygen of the –CH2–O–CH2–PO32− residue: the percentages of formation of these M(PME2A6DMAP)cl/O chelates, which occur in intramolecular equilibria, vary between 20% (Sr2+, Ba2+) and 50% (Zn2+, Cd2+), up to a maximum of 67% (Cu2+). Any M2+ interaction with N3 or N7 of the purine moiety, as in the parent M(PMEA) complexes, is suppressed by the (C2)NH2 and (C6)N(CH3)2 substituents. This observation, together with the previously determined stacking properties, offers an explanation why PME2A6DMAP2– has remarkable therapeutic effects.
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Affiliation(s)
- Raquel B. Gómez-Coca
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
- Department of Food Characterization and Analysis, Instituto de la Grasa, Spanish National Research Council (CSIC), Avda. Padre García Tejero 4, E-41012 Seville, Spain
| | - Astrid Sigel
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Bert P. Operschall
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Antonín Holý
- Institute of Organic Chemistry and Biochemistry, Centre of Novel Antivirals and Antineoplastics, Academy of Sciences, CZ-16610 Prague, Czech Republic
| | - Helmut Sigel
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
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