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Verteramo ML, Ignjatović MM, Kumar R, Wernersson S, Ekberg V, Wallerstein J, Carlström G, Chadimová V, Leffler H, Zetterberg F, Logan DT, Ryde U, Akke M, Nilsson UJ. Interplay of halogen bonding and solvation in protein-ligand binding. iScience 2024; 27:109636. [PMID: 38633000 PMCID: PMC11021960 DOI: 10.1016/j.isci.2024.109636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein-ligand complexes involving single halogen substitutions - F, Cl, Br, and I - and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.
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Affiliation(s)
| | | | - Rohit Kumar
- Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, Lund, Sweden
| | | | | | - Ulf Ryde
- Department of Chemistry, Lund University, Lund, Sweden
| | - Mikael Akke
- Department of Chemistry, Lund University, Lund, Sweden
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2
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Gunaga SS, Bryce DL. Modulation of Rotational Dynamics in Halogen-Bonded Cocrystalline Solids. J Am Chem Soc 2023; 145:19005-19017. [PMID: 37586107 DOI: 10.1021/jacs.3c06343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Dynamic processes are responsible for the functionality of a range of materials, biomolecules, and catalysts. We report a detailed systematic study of the modulation of methyl rotational dynamics via the direct and the indirect influence of noncovalent halogen bonds. For this purpose, a novel series of cocrystalline architectures featuring halogen bonds (XB) to tetramethylpyrazine (TMP) is designed and prepared using gas-phase, solution, and solid-state mechanochemical methods. Single-crystal X-ray diffraction reveals the capacity of molecular bromine as well as weak chloro-XB donors to act as robust directional structure-directing elements. Methyl rotational barriers (Ea) measured using variable-temperature deuterium solid-state NMR range from 3.75 ± 0.04 kJ mol-1 in 1,3,5-trichloro-2,4,6-trifluorobenzene·TMP to 7.08 ± 0.15 kJ mol-1 in 1,4-dichlorotetrafluorobenzene·TMP. Ea data for a larger series of TMP cocrystals featuring chloro-, bromo-, and iodo-XB donors are shown to be governed by a combination of steric and electronic factors. The average number of carbon-carbon close contacts to the methyl group is found to be a key steric metric capable of rationalizing the observed trends within each of the Cl, Br, and I series. Differences between each series are accounted for by considering the strength of the σ-hole on the XB donor. One possible route to modulating dynamics is therefore via designer cocrystals of variable stoichiometry, maintaining the core chemical features of interest between a given donor and acceptor while simultaneously modifying the number of carbon close contacts affecting dynamics. These principles may provide design opportunities to modulate more complex geared or cascade dynamics involving larger functional groups.
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Affiliation(s)
- Shubha S Gunaga
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
| | - David L Bryce
- Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, and Nexus for Quantum Technologies, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario K1N 6N5 Canada
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3
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Piña MDLN, Bauzá A. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Int J Mol Sci 2023; 24:13035. [PMID: 37685843 PMCID: PMC10488009 DOI: 10.3390/ijms241713035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.
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Affiliation(s)
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Baleares, Spain;
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4
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A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies. Int J Mol Sci 2023; 24:ijms24065530. [PMID: 36982603 PMCID: PMC10056977 DOI: 10.3390/ijms24065530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
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5
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Gao Y, Zhang L, Wang Z, Lu L. Aggregation-Induced Electrochemiluminescence and Nitric Oxide Recognition by Halogen Bonding with a Ruthenium(II) Complex. Chempluschem 2023; 88:e202200421. [PMID: 36808260 DOI: 10.1002/cplu.202200421] [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: 11/22/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/21/2023]
Abstract
In this study, a new strategy for NO detection based on the aggregation-induced electrochemical luminescence (AIECL) of a ruthenium-based complex and the halogen bonding effect was developed. First, [Ru(phen)2 (phen-Br2 )]2+ (phen : 1,10-phenanthroline, phen-Br2 : 3,8-dibromo-1,10-phenanthroline) was synthesized and exhibited aggregation-induced emission (AIE) and AIECL properties in a poor solvent (H2 O). [Ru(phen)2 (phen-Br2 )]2+ exhibited greatly enhanced AIECL properties compared to its AIE intensity. When the volume fraction of water (fw , v %) in the H2 O-acetonitrile (MeCN) system was increased from 30 to 90 %, the photoluminescence and electrochemiluminescence (ECL) intensities were three- and 800-fold that of the pure MeCN system, respectively. Dynamic light scattering and scanning electron microscopy results indicated that [Ru(phen)2 (phen-Br2 )]2+ aggregated into nanoparticles. AIECL is sensitive to NO because of its halogen bonding effect. The C-Br⋅⋅⋅N bond between [Ru(phen)2 (phen-Br2 )]2+ and NO increased the distance of complex molecules, resulting in ECL quenching. A detection limit of 2 nM was obtained with 5 orders of magnitude linear range. The combination of the AIECL system and the halogen bond effect expands the theoretical research and applications in biomolecular detection, molecular sensors, and stages of medical diagnosis.
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Affiliation(s)
- Yafang Gao
- Key Laboratory of Beijing on Regional Air Pollution Control Department of Environmental Science, Beijing University of Technology, No.100 pingleyuan, Beijing, China
| | - Linlin Zhang
- Key Laboratory of Beijing on Regional Air Pollution Control Department of Environmental Science, Beijing University of Technology, No.100 pingleyuan, Beijing, China
| | - Ziqi Wang
- Key Laboratory of Beijing on Regional Air Pollution Control Department of Environmental Science, Beijing University of Technology, No.100 pingleyuan, Beijing, China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control Department of Environmental Science, Beijing University of Technology, No.100 pingleyuan, Beijing, China
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6
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Forni A, Russo R, Rapeti G, Pieraccini S, Sironi M. Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene. Molecules 2021; 26:7126. [PMID: 34885707 PMCID: PMC8659280 DOI: 10.3390/molecules26237126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists' community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H2O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group.
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Affiliation(s)
- Alessandra Forni
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
| | - Rosario Russo
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Giacomo Rapeti
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Stefano Pieraccini
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Maurizio Sironi
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
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7
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Donald KJ, Prasad S, Wilson K. Group 14 Central Atoms and Halogen Bonding in Different Dielectric Environments: How Germanium Outperforms Silicon. Chempluschem 2021; 86:1387-1396. [PMID: 34464519 DOI: 10.1002/cplu.202100294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/01/2021] [Indexed: 11/10/2022]
Abstract
The nature of halogen bonding under different dielectric conditions remains underexplored, especially for inorganic systems. The structural and energetic properties of model halogen bonded complexes (R3 M-I-NH3 for R=H and F, and M=C, Si, and Ge) are examined computationally for relative permittivities between 1 and 109 using an implicit solvent model. We confirm and assess the exceptionally high maximum potentials at the sigma hole on I (Vs,max ) in F3 Ge-I relative to cases where M=C or Si. In particular, Ge far outperforms Si in mediating inductive effects. Linear relationships, typically with R2 >0.97, are identified between Vs,max , the full point charge on I in R3 M-I, and the interaction energy, and optimized I-N distance in the complexes. An anomalous trend is identified in which, for each M, F3 M-I-NH3 becomes less stable as the optimized I-N distance gets shorter in different dielectric environments; it is explained using the F-I-NH3 complex as a reference.
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Affiliation(s)
- Kelling J Donald
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA
| | - Supreeth Prasad
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA
| | - Kaitlin Wilson
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA 23173, USA
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8
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Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. J Chem Theory Comput 2021; 17:5369-5378. [PMID: 34232642 DOI: 10.1021/acs.jctc.1c00362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The halogen bond (or X-bond) is a noncovalent interaction that is increasingly recognized as an important design tool for engineering protein-ligand interactions and controlling the structures of proteins and nucleic acids. In the past decade, there have been significant efforts to characterize the structure-energy relationships of this interaction in macromolecules. Progress in the computational modeling of X-bonds in biological molecules, however, has lagged behind these experimental studies, with most molecular mechanics/dynamics-based simulation methods not properly treating the properties of the X-bond. We had previously derived a force field for biological X-bonds (ffBXB) based on a set of potential energy functions that describe the anisotropic electrostatic and shape properties of halogens participating in X-bonds. Although fairly accurate for reproducing the energies within biomolecular systems, including X-bonds engineered into a DNA junction, the ffBXB with its seven variable parameters was considered to be too unwieldy for general applications. In the current study, we have generalized the ffBXB by reducing the number of variables to just one for each halogen type and show that this remaining electrostatic variable can be estimated for any new halogenated molecule through a standard restricted electrostatic potential calculation of atomic charges. In addition, we have generalized the ffBXB for both nucleic acids and proteins. As a proof of principle, we have parameterized this reduced and more general ffBXB against the AMBER force field. The resulting parameter set was shown to accurately recapitulate the quantum mechanical landscape and experimental interaction energies of X-bonds incorporated into DNA junction and T4 lysozyme model systems. Thus, this reduced and generalized ffBXB is more readily adaptable for incorporation into classical molecular mechanics/dynamics algorithms, including those commonly used to design inhibitors against therapeutic targets in medicinal chemistry and materials in biomolecular engineering.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anthony K Rappé
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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9
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Peccati F, Jiménez-Osés G. Enthalpy-Entropy Compensation in Biomolecular Recognition: A Computational Perspective. ACS OMEGA 2021; 6:11122-11130. [PMID: 34056267 PMCID: PMC8153931 DOI: 10.1021/acsomega.1c00485] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/07/2021] [Indexed: 05/08/2023]
Abstract
This mini-review provides an overview of the enthalpy-entropy compensation phenomenon in the simulation of biomacromolecular recognition, with particular emphasis on ligand binding. We approach this complex phenomenon from the point of view of practical computational chemistry. Without providing a detailed description of the plethora of existing methodologies already reviewed in depth elsewhere, we present a series of examples to illustrate different approaches to interpret and predict compensation phenomena at an atomistic level, which is far from trivial to predict using canonical, classic textbook assumptions.
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Affiliation(s)
- Francesca Peccati
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), Bizkaia
Technology Park, Building
801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), Bizkaia
Technology Park, Building
801A, 48160 Derio, Spain
- Ikerbasque, Basque
Foundation for Science, 48013 Bilbao, Spain
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10
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Czarny RS, Ho AN, Shing Ho P. A Biological Take on Halogen Bonding and Other Non-Classical Non-Covalent Interactions. CHEM REC 2021; 21:1240-1251. [PMID: 33886153 DOI: 10.1002/tcr.202100076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/07/2021] [Indexed: 01/23/2023]
Abstract
Classical hydrogen bonds have, for many decades, been the dominant non-covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non-classical non-covalent (NC-NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure-function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC-NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research.
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Affiliation(s)
- Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Alexander N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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11
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Nunes RS, Vila-Viçosa D, Costa PJ. Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions. J Am Chem Soc 2021; 143:4253-4267. [DOI: 10.1021/jacs.0c12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rafael Santana Nunes
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Paulo J. Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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12
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Piña MDLN, Frontera A, Bauzá A. Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study. ACS Chem Biol 2020; 15:1942-1948. [PMID: 32469201 DOI: 10.1021/acschembio.0c00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
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Abstract
Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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Abstract
Obtaining high-quality models for nucleic acid structures by automated model building programs (AMB) is still a challenge. The main reasons are the rather low resolution of the diffraction data and the large number of rotatable bonds in the main chains. The application of the most popular and documented AMB programs (e.g., PHENIX.AUTOBUILD, NAUTILUS and ARP/wARP) may provide a good assessment of the state of the art. Quite recently, a cyclic automated model building (CAB) package was described; it is a new AMB approach that makes the use of BUCCANEER for protein model building cyclic without modifying its basic algorithms. The applications showed that CAB improves the efficiency of BUCCANEER. The success suggested an extension of CAB to nucleic acids—in particular, to check if cyclically including NAUTILUS in CAB may improve its effectiveness. To accomplish this task, CAB algorithms designed for protein model building were modified to adapt them to the nucleic acid crystallochemistry. CAB was tested using 29 nucleic acids (DNA and RNA fragments). The phase estimates obtained via molecular replacement (MR) techniques were automatically submitted to phase refinement and then used as input for CAB. The experimental results from CAB were compared with those obtained by NAUTILUS, ARP/wARP and PHENIX.AUTOBUILD.
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15
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Riel AMS, Rowe RK, Ho EN, Rappé AK, Berryman OB, Ho PS. Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry. Acc Chem Res 2019; 52:2870-2880. [PMID: 31318520 PMCID: PMC7328900 DOI: 10.1021/acs.accounts.9b00189] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The halogen bond (XB) has become an important tool for molecular design in all areas of chemistry, including crystal and materials engineering and medicinal chemistry. Its similarity to the hydrogen bond (HB) makes the relationship between these interactions complex, at times competing against and other times orthogonal to each other. Recently, our two laboratories have independently reported and characterized a synergistic relationship, in which the XB is enhanced through direct intramolecular HBing to the electron-rich belt of the halogen. In one study, intramolecular HBing from an amine polarizes the iodopyridinium XB donors of a bidentate anion receptor. The resulting HB enhanced XB (or HBeXB) preorganizes and further augments the XB donors. Consequently, the affinity of the receptor for halogen anions was significantly increased. In a parallel study, a meta-chlorotyrosine was engineered into T4 lysozyme, resulting in a HBeXB that increased the thermal stability and activity of the enzyme at elevated temperatures. The crystal structure showed that the chlorine of the noncanonical amino acid formed a XB to the protein backbone, which augmented the HB of the wild-type enzyme. Calorimetric analysis resulted in an enthalpic contribution of this Cl-XB to the stability of the protein that was an order of magnitude greater than previously determined in biomolecules. Quantum mechanical (QM) calculations showed that rotating the hydroxyl group of the tyrosine to point toward rather than away from the halogen greatly increased its potential to serve as a XB donor, equivalent to what was observed experimentally. In sum, the two systems described here show that the HBeXB concept extends the range of interaction energies and geometries to be significantly greater than that of the XB alone. Additionally, surveys of structural databases indicate that the components for this interaction are already present in many existing molecular systems. The confluence of the independent studies from our two laboratories demonstrates the reach of the HBeXB across both chemistry and biochemistry and that intentional engineering of this enhanced interaction will extend the applications of XBs beyond these two initial examples.
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Affiliation(s)
- Asia Marie S. Riel
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT
| | - Rhianon K. Rowe
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
| | - Ethan N. Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
| | - A. K. Rappé
- Department of Chemistry, Colorado State University, Fort Collins, CO
| | - Orion B. Berryman
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
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16
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Chen Y, Zhang H, Guo F, Zhou W, Deng C, Zhang J, Liao J. The O1/H3-preferred 1:1 H-bonding and the electron-cloud migration induced by H-bonding or non-specific interactions: A systematic study on the interactions between dimethyl phthalate and 1-, 2- or 3-alkanol (C2-C6). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Jimmy Huang PJ, Moon WJ, Liu J. Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA. Biochemistry 2018; 58:422-429. [PMID: 30272443 DOI: 10.1021/acs.biochem.8b00900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I2) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the Rp and Sp stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I2 also required Na+, consistent with the property of Ce13d and confirming the similar role of I2 as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I2 detection. With EDTA for masking metal ions, I2 was selectively detected down to 4.7 nM. Oxidation of I- with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I2/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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18
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Nunes R, Vila-Viçosa D, Machuqueiro M, Costa PJ. Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field. J Chem Theory Comput 2018; 14:5383-5392. [PMID: 30215528 DOI: 10.1021/acs.jctc.8b00278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to Rmin provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.
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Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal.,Centro de Química Estrutural, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
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19
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Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
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Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
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20
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Fox JM, Zhao M, Fink MJ, Kang K, Whitesides GM. The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition. Annu Rev Biophys 2018; 47:223-250. [DOI: 10.1146/annurev-biophys-070816-033743] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.
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Affiliation(s)
- Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, Republic of Korea
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
- The Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
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21
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Sheet SK, Sen B, Patra SK, Rabha M, Aguan K, Khatua S. Aggregation-Induced Emission-Active Ruthenium(II) Complex of 4,7-Dichloro Phenanthroline for Selective Luminescent Detection and Ribosomal RNA Imaging. ACS APPLIED MATERIALS & INTERFACES 2018; 10:14356-14366. [PMID: 29683310 DOI: 10.1021/acsami.7b19290] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The development of red emissive aggregation-induced emission (AIE) active probes for organelle-specific imaging is of great importance. Construction of metal complex-based AIE-active materials with metal-to-ligand charge transfer (MLCT), ligand-to-metal charge transfer (LMCT) emission together with the ligand-centered and intraligand (LC/ILCT) emission is a challenging task. We developed a red emissive ruthenium(II) complex, 1[PF6]2, and its perchlorate analogues of the 4,7-dichloro phenanthroline ligand. 1[PF6]2 has been characterized by spectroscopic and single-crystal X-ray diffraction. Complex 1 showed AIE enhancement in water, highly dense polyethylene glycol media, and also in the solid state. The possible reason behind the AIE property may be the weak supramolecular π···π, C-H···π, and C-Cl···H interactions between neighboring phen ligands as well as C-Cl···O halogen bonding (XB). The crystal structures of the two perchlorate analogues revealed C-Cl···O distances shorter than the sum of the van der Waals radii, which confirmed the XB interaction. The AIE property was supported by scanning electron microscopy, transmission electron microscopy, dynamic light scattering, and atomic force microscopy studies. Most importantly, the probe was found to be low cytotoxicity and to efficiently permeate the cell membrane. The cell-imaging experiments revealed rapid staining of the nucleolus in HeLa cells via the interaction with nucleolar ribosomal ribonucleic acid (rRNA). It is expected that the supramolecular interactions as well as C-Cl···O XB interaction with rRNA is the origin of aggregation and possible photoluminescence enhancement. To the best of our knowledge, this is the first report of red emissive ruthenium(II) complex-based probes with AIE characteristics for selective rRNA detection and nucleolar imaging.
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22
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Structural Examination of Halogen-Bonded Co-Crystals of Tritopic Acceptors. Molecules 2018; 23:molecules23010163. [PMID: 29342853 PMCID: PMC6017714 DOI: 10.3390/molecules23010163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 11/16/2022] Open
Abstract
A series of tritopic N-heterocyclic compounds containing electrostatically and geometrically equivalent binding sites were synthesized and subjected to systematic co-crystallizations with selected perfluoroiodoarenes in order to map out their structural landscapes. More than 70% of the attempted reactions produced a co-crystal as indicated by IR spectroscopy. Four new crystal structures are reported and in all of them, at least one potential binding site on the acceptor is left vacant. The absence of halogen bonds to all sites can be ascribed primarily due to deactivation of the σ-hole on the iodo-arene donors and partially due to steric hindrance. The tritopic acceptors containing 5,6-dimethylbenzimidazole derivatives yield discrete tetrameric aggregates in the solid state, whereas the pyrazole and imidazole analogues assemble into halogen-bonded 1-D chains.
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23
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Oliva C, Sánchez-Murcia PA, Rico E, Bravo A, Menéndez M, Gago F, Jiménez-Ruiz A. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res 2017; 45:9030-9045. [PMID: 28911117 PMCID: PMC5587815 DOI: 10.1093/nar/gkx629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022] Open
Abstract
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145–180 is indeed far more active than its wild-type counterpart at pH values >7.0. In addition, we discovered that (i) LiEndoG exists as a homodimer, (ii) replacement of Ser211 in the active-site SRGH motif with the canonical aspartate from the DRGH motif of other nucleases leads to a catalytically deficient enzyme, (iii) the activity of the S211D variant can be restored upon the concomitant replacement of Ala247 with Arg and (iv) a C-terminal extension is responsible for the observed preferential cleavage of single-stranded DNA (ssDNA) and ssDNA–dsDNA junctions. Taken together, our results support the view that LiEndoG is a multidomain molecular machine whose nuclease activity can be subtly modulated or even abrogated through architectural changes brought about by environmental conditions and interaction with other binding partners.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Catalytic Domain
- Cloning, Molecular
- DNA Cleavage
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Hydrogen-Ion Concentration
- Kinetics
- Leishmania infantum/chemistry
- Leishmania infantum/enzymology
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Deletion
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Cristina Oliva
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Pedro A. Sánchez-Murcia
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Eva Rico
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Ana Bravo
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
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24
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Abstract
The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br···S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single-crystal structure of the junction shows the geometry of the Br···S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to or slightly more stable than the analogous O acceptor, with a -3.5 kcal/mol difference in ΔΔH25°C and -0.4 kcal/mol ΔΔG25°C (including an entropic penalty ΔΔS25°C of -10 cal/(mol K)). Thus sulfur is shown to be a favorable acceptor for bromine X-bonds, extending the application of this interaction for the design of inhibitors and biological materials.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - Matthew Saxton
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
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26
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Structure of the Holliday junction: applications beyond recombination. Biochem Soc Trans 2017; 45:1149-1158. [PMID: 28842529 DOI: 10.1042/bst20170048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/24/2022]
Abstract
The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.
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27
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Abstract
Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.
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Affiliation(s)
- Michal H Kolář
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, I-06123 Perugia, Italy
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28
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Shah MB, Liu J, Zhang Q, Stout CD, Halpert JR. Halogen-π Interactions in the Cytochrome P450 Active Site: Structural Insights into Human CYP2B6 Substrate Selectivity. ACS Chem Biol 2017; 12:1204-1210. [PMID: 28368100 DOI: 10.1021/acschembio.7b00056] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Numerous cytochrome P450 (CYP) 2B6 substrates including drugs and environmental chemicals are halogenated. To assess the role of halogen-π bonds in substrate selectivity and orientation in the active site, structures of four CYP2B6 monoterpenoid complexes were solved by X-ray crystallography. Bornyl bromide exhibited dual orientations in the active site with the predominant orientation revealing a bromine-π bond with the Phe108 side chain. Bornane demonstrated two orientations with equal occupancy; in both, the C2 atom that bears the bromine in bornyl bromide was displaced by more than 2.5 Å compared with the latter complex. The bromine in myrtenyl bromide π-bonded with Phe297 in CYP2B6, whereas the two major orientations in the active site mutant I114V exhibited bromine-π interactions with two additional residues, Phe108 and Phe115. Analysis of existing structures suggests that halogen-π interactions may be unique to the CYP2B enzymes within CYP family 2 but are also important for CYP3A enzymes.
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Affiliation(s)
- Manish B. Shah
- School
of Pharmacy, University of Connecticut, Storrs, Connecticut, United States
| | - Jingbao Liu
- School
of Pharmacy, University of Connecticut, Storrs, Connecticut, United States
| | - Qinghai Zhang
- The
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States
| | - C. David Stout
- The
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States
| | - James R. Halpert
- School
of Pharmacy, University of Connecticut, Storrs, Connecticut, United States
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29
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Scholfield MR, Ford MC, Carlsson ACC, Butta H, Mehl RA, Ho PS. Structure–Energy Relationships of Halogen Bonds in Proteins. Biochemistry 2017; 56:2794-2802. [DOI: 10.1021/acs.biochem.7b00022] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew R. Scholfield
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anna-Carin C. Carlsson
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Hawera Butta
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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30
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Rowe RK, Ho PS. Relationships between hydrogen bonds and halogen bonds in biological systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:255-264. [PMID: 28362290 DOI: 10.1107/s2052520617003109] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.
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Affiliation(s)
- Rhianon K Rowe
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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31
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Santos LA, da Cunha EFF, Ramalho TC. Toward the Classical Description of Halogen Bonds: A Quantum Based Generalized Empirical Potential for Fluorine, Chlorine, and Bromine. J Phys Chem A 2017; 121:2442-2451. [DOI: 10.1021/acs.jpca.6b13112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucas A. Santos
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Elaine F. F. da Cunha
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
- Center for Basic
and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
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32
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Wang JW, Chen C, Li YJ, Luo YH, Sun BW. Halogen-bonding contacts determining the crystal structure and fluorescence properties of organic salts. NEW J CHEM 2017. [DOI: 10.1039/c7nj02034a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different inorganic anions tuning halogen-bonding contacts to form different 3D networks with various absorption and emission properties.
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Affiliation(s)
- Jing-Wen Wang
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing 211189
- P. R. China
| | - Chen Chen
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing 211189
- P. R. China
| | - Yao-Ja Li
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing 211189
- P. R. China
| | - Yang-Hui Luo
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing 211189
- P. R. China
| | - Bai-Wang Sun
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing 211189
- P. R. China
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33
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Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Biochemistry 2016; 55:5781-5789. [PMID: 27653243 PMCID: PMC5258817 DOI: 10.1021/acs.biochem.6b00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5-Hydroxymethylcytosine (5hmC) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hmC on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GxCC trinucleotide core sequence (where xC is C, 5hmC, or the methylated 5mC), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hmC junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in 5hmC or from a bridging water in the 5mC structure provide approximately 1.5-2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G5hmCC and G5mCC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hmC and 5mC are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating 5hmC into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.
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Affiliation(s)
- Crystal M. Vander Zanden
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Rhianon K. Rowe
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Amanda J. Broad
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Adam B. Robertson
- Department of Molecular Microbiology, Sognsvannsveien 20, NO-0027, Oslo University Hospital, Oslo, Norway
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
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34
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Zimmermann MO, Lange A, Zahn S, Exner TE, Boeckler FM. Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine. J Chem Inf Model 2016; 56:1373-83. [DOI: 10.1021/acs.jcim.6b00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markus O. Zimmermann
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Andreas Lange
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Stefan Zahn
- Physikalisch-Chemisches
Institut, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring
17, 35392 Gießen, Germany
| | - Thomas E. Exner
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls Universität Tübingen, Sand 1, 72076 Tübingen, Germany
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35
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Insights into halogen bond-driven enantioseparations. J Chromatogr A 2016; 1467:228-238. [PMID: 27328882 DOI: 10.1016/j.chroma.2016.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/19/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
Abstract
Although the halogen bond (XB) has been so far mainly studied in silico and in the solid state, its potential impact in solution is yet to be fully understood. In this study, we describe the first systematic investigation on the halogen bond in solvated environment by high-performance liquid chromatography (HPLC). Thirty three atropisomeric polyhalogenated-4,4'-bipyridines (HBipys), containing Cl, Br and I as substituents, were selected and used as potential XB donors (XBDs) on two cellulose-based chiral stationary phases (CSPs) containing potential XB acceptors (XBAs). The impact of the halogens on the enantiodiscrimination mechanism was investigated and iodine showed a pivotal role on the enantioseparation in non-polar medium. Electrostatic potentials (EPs) were computed to understand the electrostatic component of CSP-analyte interaction. Moreover, van't Hoff studies for ten HBipys were performed and the thermodynamic parameters governing the halogen-dependent enantioseparations are discussed. Finally, a molecular dynamic (MD) simulation is proposed to model halogen bond in polysaccharide-analyte complexes by inclusion of a charged extra point to represent the positive 'σ-hole' on the halogen atom. On the basis of both experimental results and theoretical data, we have profiled the halogen bond as a chemo-, regio-, site- and stereoselective interaction which can work in HPLC environment besides other known interactions based on the complementarity between selector and selectand.
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36
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Abstract
The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
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Affiliation(s)
- Gabriella Cavallo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Pierangelo Metrangolo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Roberto Milani
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Tullio Pilati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Arri Priimagi
- Department
of Chemistry and Bioengineering, Tampere
University of Technology, Korkeakoulunkatu 8, FI-33101 Tampere, Finland
| | - Giuseppe Resnati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Giancarlo Terraneo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
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37
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Affiliation(s)
- Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Federal Republic of Germany
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacky University, 771 46 Olomouc, Czech Republic
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38
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Li B, Zang SQ, Wang LY, Mak TC. Halogen bonding: A powerful, emerging tool for constructing high-dimensional metal-containing supramolecular networks. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.09.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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39
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Ciancaleoni G, Macchioni A, Rocchigiani L, Zuccaccia C. A PGSE NMR approach to the characterization of single and multi-site halogen-bonded adducts in solution. RSC Adv 2016. [DOI: 10.1039/c6ra17455h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The diffusional PGSE NMR technique allows a detailed characterization of single- and multi-site halogen-bonded systems.
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Affiliation(s)
- Gianluca Ciancaleoni
- Departamento de Química
- Universidade Federal de Santa Catarina
- 88040-900 Florianópolis
- Brazil
| | - Alceo Macchioni
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Universitá degli Studi di Perugia
- Perugia
- Italy
| | - Luca Rocchigiani
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Universitá degli Studi di Perugia
- Perugia
- Italy
| | - Cristiano Zuccaccia
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Universitá degli Studi di Perugia
- Perugia
- Italy
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40
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
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41
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Gilday LC, Robinson SW, Barendt TA, Langton MJ, Mullaney BR, Beer PD. Halogen Bonding in Supramolecular Chemistry. Chem Rev 2015; 115:7118-95. [DOI: 10.1021/cr500674c] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia C. Gilday
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sean W. Robinson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy A. Barendt
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthew J. Langton
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin R. Mullaney
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul D. Beer
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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42
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Zimmermann MO, Lange A, Boeckler FM. Evaluating the potential of halogen bonding in molecular design: automated scaffold decoration using the new scoring function XBScore. J Chem Inf Model 2015; 55:687-99. [PMID: 25654403 DOI: 10.1021/ci5007118] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a QM-derived empirical scoring function for the interaction between aromatic halogenated ligands and the carbonyl oxygen atom of the protein backbone. Applying this scoring function, we developed an algorithm that evaluates the potential of protein-bound ligands to form favorable halogen-bonding contacts upon scaffold decoration with chlorine, bromine, or iodine. Full recovery of all existing halogen bonds in the PDB involving the protein backbone was achieved with our protocol. Interestingly, the potential for introducing halogen bonds through scaffold decoration of unsubstituted aromatic carbon atoms appears to easily match the number of previously known halogen bonds. Our approach can thus be used as a blueprint for integration of halogen bonding into general empirical scoring functions, which at present ignore this interaction. Most importantly, we were able to identify a substantial number of protein-ligand complexes where the benefits and challenges of introducing a halogen bond by molecular design can be studied experimentally.
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Affiliation(s)
- Markus O Zimmermann
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Lange
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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43
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Kratzer P, Ramming B, Römisch S, Maas G. The iodine–oxygen halogen bond: solid-state structures of 3-iodopropiolamides. CrystEngComm 2015. [DOI: 10.1039/c5ce00365b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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44
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Scholfield MR, Ford MC, Vander Zanden CM, Billman MM, Ho PS, Rappé AK. Force Field Model of Periodic Trends in Biomolecular Halogen Bonds. J Phys Chem B 2014; 119:9140-9. [PMID: 25338128 DOI: 10.1021/jp509003r] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry--its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as an accurate computational tool that can be applied, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular-based materials.
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Affiliation(s)
| | | | | | - M Marie Billman
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | | | - Anthony K Rappé
- ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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45
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Celis-Barros C, Saavedra-Rivas L, Salgado JC, Cassels BK, Zapata-Torres G. Molecular dynamics simulation of halogen bonding mimics experimental data for cathepsin L inhibition. J Comput Aided Mol Des 2014; 29:37-46. [DOI: 10.1007/s10822-014-9802-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022]
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46
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Takemura A, McAllister LJ, Hart S, Pridmore NE, Karadakov PB, Whitwood AC, Bruce DW. Halogen- and hydrogen-bonded salts and co-crystals formed from 4-halo-2,3,5,6-tetrafluorophenol and cyclic secondary and tertiary amines: orthogonal and non-orthogonal halogen and hydrogen bonding, and synthetic analogues of halogen-bonded biological systems. Chemistry 2014; 20:6721-32. [PMID: 24796890 PMCID: PMC4324131 DOI: 10.1002/chem.201402128] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 12/15/2022]
Abstract
Co-crystallisation of, in particular, 4-iodotetrafluorophenol with a series of secondary and tertiary cyclic amines results in deprotonation of the phenol and formation of the corresponding ammonium phenate. Careful examination of the X-ray single-crystal structures shows that the phenate anion develops a C=O double bond and that the C-C bond lengths in the ring suggest a Meissenheimer-like delocalisation. This delocalisation is supported by the geometry of the phenate anion optimised at the MP2(Full) level of theory within the aug-cc-pVDZ basis (aug-cc-pVDZ-PP on I) and by natural bond orbital (NBO) analyses. With sp(2) hybridisation at the phenate oxygen atom, there is strong preference for the formation of two non-covalent interactions with the oxygen sp(2) lone pairs and, in the case of secondary amines, this occurs through hydrogen bonding to the ammonium hydrogen atoms. However, where tertiary amines are concerned, there are insufficient hydrogen atoms available and so an electrophilic iodine atom from a neighbouring 4-iodotetrafluorophenate group forms an I⋅⋅⋅O halogen bond to give the second interaction. However, in some co-crystals with secondary amines, it is also found that in addition to the two hydrogen bonds forming with the phenate oxygen sp(2) lone pairs, there is an additional intermolecular I⋅⋅⋅O halogen bond in which the electrophilic iodine atom interacts with the C=O π-system. All attempts to reproduce this behaviour with 4-bromotetrafluorophenol were unsuccessful. These structural motifs are significant as they reproduce extremely well, in low-molar-mass synthetic systems, motifs found by Ho and co-workers when examining halogen-bonding interactions in biological systems. The analogy is cemented through the structures of co-crystals of 1,4-diiodotetrafluorobenzene with acetamide and with N-methylbenzamide, which, as designed models, demonstrate the orthogonality of hydrogen and halogen bonding proposed in Ho's biological study.
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Affiliation(s)
- Akihiro Takemura
- Department of Chemistry, University of York, Heslington, York YO10 5DD (UK)
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47
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Viger-Gravel J, Leclerc S, Korobkov I, Bryce DL. Direct Investigation of Halogen Bonds by Solid-State Multinuclear Magnetic Resonance Spectroscopy and Molecular Orbital Analysis. J Am Chem Soc 2014; 136:6929-42. [DOI: 10.1021/ja5013239] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jasmine Viger-Gravel
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Sophie Leclerc
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Ilia Korobkov
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - David L. Bryce
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
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48
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Ren J, He Y, Chen W, Chen T, Wang G, Wang Z, Xu Z, Luo X, Zhu W, Jiang H, Shen J, Xu Y. Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors. J Med Chem 2014; 57:3588-93. [PMID: 24702184 DOI: 10.1021/jm5002315] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.
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Affiliation(s)
- Jing Ren
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS) , 555 Zuchongzhi Road, Shanghai 201203, China
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49
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Tranchant I, Vera L, Czarny B, Amoura M, Cassar E, Beau F, Stura EA, Dive V. Halogen bonding controls selectivity of FRET substrate probes for MMP-9. ACTA ACUST UNITED AC 2014; 21:408-13. [PMID: 24583051 DOI: 10.1016/j.chembiol.2014.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 11/18/2022]
Abstract
Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases that catalyze cleavage of extracellular matrix and nonmatrix proteins. MMPs play a role in tissue remodeling, and their uncontrolled activity is associated with number of diseases, including tumor metastasis. Thus, there is a need to develop methods to monitor MMP activity, and number of probes has been previously described. The key problem many probes encounter is the issue of selectivity, since 23 human MMPs, despite playing different physiological roles, have structurally similar active sites. Here, we introduce the halogen bonding concept into the probe design and show that the probe containing iodine exhibits an unprecedented selectivity for MMP-9. We provide structure-based explanation for the selectivity, confirming that it is due to formation of the halogen bond that supports catalysis, and we highlight the value of exploring halogen bonding in the context of selective probe design.
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Affiliation(s)
- Isabelle Tranchant
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Laura Vera
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Bertrand Czarny
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Mehdi Amoura
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Evelyne Cassar
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Fabrice Beau
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Enrico A Stura
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Vincent Dive
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France.
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50
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Viger-Gravel J, Meyer JE, Korobkov I, Bryce DL. Probing halogen bonds with solid-state NMR spectroscopy: observation and interpretation of J(77Se,31P) coupling in halogen-bonded PSe⋯I motifs. CrystEngComm 2014. [DOI: 10.1039/c4ce00345d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Intra-halogen bond J couplings measured via NMR spectroscopy and interpreted using natural localized molecular orbitals offer novel insights into this class of non-covalent interaction.
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Affiliation(s)
- Jasmine Viger-Gravel
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - Julia E. Meyer
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - Ilia Korobkov
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - David L. Bryce
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| |
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