1
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Fortuna A, Costa PJ. Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations. J Chem Inf Model 2023; 63:7464-7475. [PMID: 38010191 DOI: 10.1021/acs.jcim.3c01561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Compounds containing halogens can form halogen bonds (XBs) with biological targets such as proteins and membranes due to their anisotropic electrostatic potential. To accurately describe this anisotropy, off-center point-charge (EP) models are commonly used in force field methods, allowing the description of XBs at the molecular mechanics and molecular dynamics level. Various EP implementations have been documented in the literature, and despite being efficient in reproducing protein-ligand geometries and sampling of XBs, it is unclear how well these EP models predict experimental properties such as hydration free energies (ΔGhyd), which are often used to validate force field performance. In this work, we report the first assessment of three EP models using alchemical free energy calculations to predict ΔGhyd values. We show that describing the halogen anisotropy using some EP models can lead to a slight improvement in the prediction of the ΔGhyd when compared with the models without EP, especially for the chlorinated compounds; however, this improvement is not related to the establishment of XBs but is most likely due to the improvement of the sampling of hydrogen bonds. We also highlight the importance of the choice of the EP model, especially for the iodinated molecules, since a slight tendency to improve the prediction is observed for compounds with a larger σ-hole but significantly worse results were obtained for compounds that are weaker XB donors.
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Affiliation(s)
- Andreia Fortuna
- BioISI─Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, Lisbon 1649-003, Portugal
| | - Paulo J Costa
- BioISI─Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
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2
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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3
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Dallocchio R, Dessì A, Sechi B, Chankvetadze B, Jibuti G, Cossu S, Mamane V, Peluso P. Enantioseparation of planar chiral ferrocenes on cellulose-based chiral stationary phases: Benzoate versus carbamate pendant groups. Electrophoresis 2023; 44:203-216. [PMID: 36177685 DOI: 10.1002/elps.202200205] [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: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 02/01/2023]
Abstract
In this study, the enantioseparation of 14 planar chiral ferrocenes containing halogen atoms, and methyl, iodoethynyl, phenyl, and 2-naphthyl groups, as substituents, was explored with a cellulose tris(4-methylbenzoate) (CMB)-based chiral column under multimodal elution conditions. n-Hexane/2-propanol (2-PrOH) 95:5 v/v, pure methanol (MeOH), and MeOH/water 90:10 v/v were used as mobile phases (MPs). With CMB, baseline enantioseparations were achieved for nine analytes with separation factors (α) ranging from 1.24 to 1.77, whereas only three analytes could be enantioseparated with 1.14 ≤ α ≤ 1.51 on a cellulose tris(3,5-dimethylphenylcarbamate) (CDMPC)-based column, used as a reference for comparison, under the same elution conditions. Pendant group-dependent reversal of the enantiomer elution order was observed in several cases by changing CMB to CDMPC. The impact of analyte and chiral stationary phase (CSP) structure, and MP polarity on the enantioseparation, was evaluated. The two cellulose-based CSPs featured by different pendant groups were also compared in terms of thermodynamics. For this purpose, enthalpy (ΔΔH°), entropy (ΔΔS°) and free energy (ΔΔG°) differences, isoenantioselective temperatures (Tiso ), and enthalpy/entropy ratios (Q), associated with the enantioseparations, were derived from van 't Hoff plots by using n-hexane/2-PrOH 95:5 v/v and methanol/water 90:10 v/v as MPs. With the aim to disclose the functions of the different substituents in mechanisms and noncovalent interactions underlying analyte-selector complex formation at molecular level, electrostatic potential (V) analysis and molecular dynamics simulations were used as computational techniques. On this basis, enantioseparations and related mechanisms were investigated by integrating theoretical and experimental data.
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Affiliation(s)
- Roberto Dallocchio
- Enantioselective Chromatography and Molecular Recognition Unit, Istituto di Chimica Biomolecolare (ICB) CNR, Sassari, Italy
| | - Alessandro Dessì
- Enantioselective Chromatography and Molecular Recognition Unit, Istituto di Chimica Biomolecolare (ICB) CNR, Sassari, Italy
| | - Barbara Sechi
- Enantioselective Chromatography and Molecular Recognition Unit, Istituto di Chimica Biomolecolare (ICB) CNR, Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Tbilisi, Georgia
| | - Giorgi Jibuti
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Tbilisi, Georgia
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Mestre Venezia, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR 7177, CNRS-Université de Strasbourg, Strasbourg, France
| | - Paola Peluso
- Enantioselective Chromatography and Molecular Recognition Unit, Istituto di Chimica Biomolecolare (ICB) CNR, Sassari, Italy
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Bogado ML, Villafañe RN, Gómez Chavez JL, Angelina EL, Sosa GL, Peruchena NM. Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. J Chem Inf Model 2022; 62:6494-6507. [PMID: 36044012 DOI: 10.1021/acs.jcim.2c00475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein pockets that form a halogen bond (X-bond) with a halogenated ligand molecule simultaneously form other (mainly hydrophobic) interactions with the halogen atom that can be considered as its "X-bond environment" (XBenv). Most studies in the field have focused on the X-bond, with the properties of the XBenv usually overlooked. In this work, we derived a protocol that evaluates the XBenv strength as a measure of the propensity of a protein pocket to host an X-bond. The charge density-based topological descriptors in combination with machine learning tools were employed to predict formation and strength of the interactions that conform the XBenv as a function of their geometrical parameters. On the basis of these results, we propose that the XBenv can be used as a footprint to judge the chance of a protein pocket to form an X-bond.
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Affiliation(s)
- María Lucrecia Bogado
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Roxana Noelia Villafañe
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - José Leonardo Gómez Chavez
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Emilio Luis Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Gladis Laura Sosa
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Nélida María Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA, Universidad Nacional del Nordeste, CONICET, FaCENA, Av. Libertad 5470, Corrientes 3400, Argentina
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5
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Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022; 40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fares Fenanir
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| | - Abderrahmane Semmeq
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS, Sétif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France.,IUT de Moselle-Est, Université de Lorraine, Saint-Avold, France
| | | | - Smain Amira
- Laboratory of Phytotherapy Applied to Chroniques Diseases, University Ferhat Abbas, Sétif, Algeria
| | - Hocine Laouer
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
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6
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An in vitro study of the 5-methyl- and 5-bromo/chloro substituted 2-hydroxy-3-nitrochalcones as α-glucosidase and/or α-amylase inhibitors with potential anti-inflammatory activity. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02980-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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1,5-Dichloroethanoanthracene Derivatives As Antidepressant Maprotiline Analogs: Synthesis, DFT Computational Calculations, and Molecular Docking. J CHEM-NY 2022. [DOI: 10.1155/2022/1196244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The chlorinated tetracyclic 1,5-dichloro-9,10-dihydro-9,10-ethanoanthracen-12-yl)-N-methylmethanamine 1, a maprotiline analog, has been synthesized via reduction and the Diels–Alder reaction followed by reductive amination of aldehyde 2.1D-NMR (DEPT) and 2D-NMR (HSQC, DQF-COSY) techniques were recruited for structural elucidation in addition to HRMS. Density functional theory calculations were performed to identify the possible isomers of the intermediate compound aldehyde 2; these calculations were in good agreement with experimental results where aldehyde 2 could exist in three isomers with comparable energies. In addition, the side chain of this aldehyde 2 was extended via the Wittig reaction to obtain the unsaturated ester 5 that was subjected to selective olefinic catalytic hydrogenation to obtain the corresponding saturated ester 6. Molecular docking simulation showed that all the compounds (1, 2, 5, and 6) have high antidepressant activities and form stable complexes with LeuT by inhibiting the neurotransmitter reuptake at the synapse and hence are good candidates as antidepressant drugs.
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8
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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9
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Computational modeling of potential milciclib derivatives inhibitor-CDK2 binding through global docking and accelerated molecular dynamics simulations. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Peluso P, Mamane V. Stereoselective Processes Based on σ-Hole Interactions. Molecules 2022; 27:molecules27144625. [PMID: 35889497 PMCID: PMC9323542 DOI: 10.3390/molecules27144625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
The σ-hole interaction represents a noncovalent interaction between atoms with σ-hole(s) on their surface (such as halogens and chalcogens) and negative sites. Over the last decade, significant developments have emerged in applications where the σ-hole interaction was demonstrated to play a key role in the control over chirality. The aim of this review is to give a comprehensive overview of the current advancements in the use of σ-hole interactions in stereoselective processes, such as formation of chiral supramolecular assemblies, separation of enantiomers, enantioselective complexation and asymmetric catalysis.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede Secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy
- Correspondence: (P.P.); (V.M.)
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR CNRS 7177, Equipe LASYROC, 1 Rue Blaise Pascal, 67008 Strasbourg, France
- Correspondence: (P.P.); (V.M.)
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11
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Leskourová A, Kolář MH. The effect of off-center σ -hole on the atom-centered partial charges in halogenated molecules. J Comput Chem 2022; 43:864-869. [PMID: 35298034 DOI: 10.1002/jcc.26841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/07/2022]
Abstract
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ -hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ -hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the restricted electrostatic potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The σ -hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.
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Affiliation(s)
- Aneta Leskourová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michal H Kolář
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
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12
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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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13
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Frontera A, Bauzá A. Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases. Org Biomol Chem 2021; 19:6858-6864. [PMID: 34319314 DOI: 10.1039/d1ob01212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.
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Affiliation(s)
- Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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14
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Fortuna A, Costa PJ. Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges. J Chem Inf Model 2021; 61:3361-3375. [PMID: 34185532 DOI: 10.1021/acs.jcim.1c00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In force-field methods, the usage of off-center point charges, also called extra points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics/molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X-EP distances. Poisson-Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (ΔGsolv) of small molecules, often to compute binding free energies (ΔGbind) at the MM-PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charge models and the lack of specific PB radii for halogens compatible with such implementations, in this work, we assessed the performance of PBSA calculations for the estimation of ΔGsolv values in water (ΔGhyd), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the general AMBER force field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM general force field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.
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Affiliation(s)
- Andreia Fortuna
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Paulo J Costa
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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15
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Dallocchio R, Sechi B, Dessì A, Chankvetadze B, Cossu S, Mamane V, Weiss R, Pale P, Peluso P. Enantioseparations of polyhalogenated 4,4'-bipyridines on polysaccharide-based chiral stationary phases and molecular dynamics simulations of selector-selectand interactions. Electrophoresis 2021; 42:1853-1863. [PMID: 33742705 DOI: 10.1002/elps.202100049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/12/2022]
Abstract
2'-(4-Pyridyl)- and 2'-(4-hydroxyphenyl)-TCIBPs (TCIBP = 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridyl) are chiral compounds that showed interesting inhibition activity against transthyretin fibrillation in vitro. We became interested in their enantioseparation since we noticed that the M-stereoisomer is more effective than the P-enantiomer. Based thereon, we recently reported the enantioseparation of 2'-substituted TCIBP derivatives with amylose-based chiral columns. Following this study, herein we describe the comparative enantioseparation of both 2'-(4-pyridyl)- and 2'-(4-hydroxyphenyl)-TCIBPs on four cellulose phenylcarbamate-based chiral columns aiming to explore the effect of the polymer backbone, as well as the nature and position of substituents on the side groups on the enantioseparability of these compounds. In the frame of this project, the impact of subtle variations of analyte and polysaccharide structures, and mobile phase (MP) polarity on retention and selectivity was evaluated. The effect of temperature on retention and selectivity was also considered, and overall thermodynamic parameters associated with the analyte adsorption onto the CSP surface were derived from van 't Hoff plots. Interesting cases of enantiomer elution order (EEO) reversal were observed. In particular, the EEO was shown to be dependent on polysaccharide backbone, the elution sequence of the two analytes being P-M and M-P on cellulose and amylose tris(3,5-dimethylphenylcarbamate), respectively. In this regard, a theoretical investigation based on molecular dynamics (MD) simulations was performed by using amylose and cellulose tris(3,5-dimethylphenylcarbamate) nonamers as virtual models of the polysaccharide-based selectors. This exploration at the molecular level shed light on the origin of the enantiodiscrimination processes.
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Affiliation(s)
- Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB CNR, Sede secondaria di Sassari, Sassari, Italy
| | - Barbara Sechi
- Istituto di Chimica Biomolecolare ICB CNR, Sede secondaria di Sassari, Sassari, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB CNR, Sede secondaria di Sassari, Sassari, Italy
| | - Bezhan Chankvetadze
- School of Exact and Natural Sciences, Institute of Physical and Analytical Chemistry, Tbilisi State University, Tbilisi, Georgia
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Mestre, Venezia, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR 7177, CNRS-Université de Strasbourg, Strasbourg, France
| | - Robin Weiss
- Institut de Chimie de Strasbourg, UMR 7177, CNRS-Université de Strasbourg, Strasbourg, France
| | - Patrick Pale
- Institut de Chimie de Strasbourg, UMR 7177, CNRS-Université de Strasbourg, Strasbourg, France
| | - Paola Peluso
- Istituto di Chimica Biomolecolare ICB CNR, Sede secondaria di Sassari, Sassari, Italy
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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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17
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Mathew B, Carradori S, Guglielmi P, Uddin MS, Kim H. New Aspects of Monoamine Oxidase B Inhibitors: The Key Role of Halogens to Open the Golden Door. Curr Med Chem 2021; 28:266-283. [PMID: 31965939 DOI: 10.2174/0929867327666200121165931] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/07/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
A large plethora of drugs and promising lead compounds contain halogens in their structures. The introduction of such moieties strongly modulates their physical-chemical features as well as pharmacokinetic and pharmacodynamic profile. The most important outcome was shown to be the ability of these halogens to favourably influence the drug-target interaction and energetic stability within the active site by the establishment of halogen bonds. This review attempted to demonstrate the key role exerted by these versatile moieties when correctly located in an organic scaffold to display Monoamine Oxidase (MAO) inhibition and selectivity towards the B isoform of this important enzyme. Human MAOs are well-recognized as therapeutic targets for mood disorders and neurodegenerative diseases and medicinal chemists were prompted to discover the structural requirements crucial to discriminate the slight differences between the active sits of the two isoforms (MAO-A and MAOB). The analysis of the structure-activity relationships of the most important scaffolds (hydrazothiazoles, coumarins, chromones, chalcones, pyrazolines) and the impact of halogen (F, Cl, Br and I) insertion on this biological activity and isozyme selectivity have been reported being a source of inspiration for the medicinal chemists.
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Affiliation(s)
- Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti 66100, Italy
| | - Paolo Guglielmi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
| | - Hoon Kim
- Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Korea
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18
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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19
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Tschakert J, Zhong Q, Martin-Jimenez D, Carracedo-Cosme J, Romero-Muñiz C, Henkel P, Schlöder T, Ahles S, Mollenhauer D, Wegner HA, Pou P, Pérez R, Schirmeisen A, Ebeling D. Surface-controlled reversal of the selectivity of halogen bonds. Nat Commun 2020; 11:5630. [PMID: 33159060 PMCID: PMC7648107 DOI: 10.1038/s41467-020-19379-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/01/2020] [Indexed: 11/08/2022] Open
Abstract
Intermolecular halogen bonds are ideally suited for designing new molecular assemblies because of their strong directionality and the possibility of tuning the interactions by using different types of halogens or molecular moieties. Due to these unique properties of the halogen bonds, numerous areas of application have recently been identified and are still emerging. Here, we present an approach for controlling the 2D self-assembly process of organic molecules by adsorption to reactive vs. inert metal surfaces. Therewith, the order of halogen bond strengths that is known from gas phase or liquids can be reversed. Our approach relies on adjusting the molecular charge distribution, i.e., the σ-hole, by molecule-substrate interactions. The polarizability of the halogen and the reactiveness of the metal substrate are serving as control parameters. Our results establish the surface as a control knob for tuning molecular assemblies by reversing the selectivity of bonding sites, which is interesting for future applications.
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Affiliation(s)
- Jalmar Tschakert
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Qigang Zhong
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Daniel Martin-Jimenez
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Jaime Carracedo-Cosme
- Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232, Las Rozas de Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, E-41013, Seville, Spain
| | - Pascal Henkel
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Tobias Schlöder
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian Ahles
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Doreen Mollenhauer
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Physical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Hermann A Wegner
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Pablo Pou
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - André Schirmeisen
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Daniel Ebeling
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany.
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20
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Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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21
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de Oliveira BG, Zabardasti A, do Rego DG, Pour MM. The formation of H···X hydrogen bond, C···X carbon-halide or Si···X tetrel bonds on the silylene-halogen dimers (X = F or Cl): intermolecular strength, molecular orbital interactions and prediction of covalency. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02644-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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22
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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23
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Rational Design, Synthesis, Characterization and Evaluation of Iodinated 4,4'-Bipyridines as New Transthyretin Fibrillogenesis Inhibitors. Molecules 2020; 25:molecules25092213. [PMID: 32397334 PMCID: PMC7248964 DOI: 10.3390/molecules25092213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine structure is proposed as a novel chemical scaffold for the design of new transthyretin (TTR) fibrillogenesis inhibitors. In the frame of a proof-of-principle exploration, four chiral 3,3',5,5'-tetrachloro-2-iodo-2'-substituted-4,4'- bipyridines were rationally designed and prepared from a simple trihalopyridine in three steps, including a Cu-catalysed Finkelstein reaction to introduce iodine atoms on the heteroaromatic scaffold, and a Pd-catalysed coupling reaction to install the 2'-substituent. The corresponding racemates, along with other five chiral 4,4'-bipyridines containing halogens as substituents, were enantioseparated by high-performance liquid chromatography in order to obtain pure enantiomer pairs. All stereoisomers were tested against the amyloid fibril formation (FF) of wild type (WT)-TTR and two mutant variants, V30M and Y78F, in acid mediated aggregation experiments. Among the 4,4'-bipyridine derivatives, interesting inhibition activity was obtained for both enantiomers of the 3,3',5,5'-tetrachloro-2'-(4-hydroxyphenyl)-2-iodo-4,4'-bipyridine. In silico docking studies were carried out in order to explore possible binding modes of the 4,4'-bipyridine derivatives into the TTR. The gained results point out the importance of the right combination of H-bond sites and the presence of iodine as halogen-bond donor. Both experimental and theoretical evidences pave the way for the utilization of the iodinated 4,4'-bipyridine core as template to design new promising inhibitors of TTR amyloidogenesis.
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A Halogen Bonding Perspective on Iodothyronine Deiodinase Activity. Molecules 2020; 25:molecules25061328. [PMID: 32183289 PMCID: PMC7144113 DOI: 10.3390/molecules25061328] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022] Open
Abstract
Iodothyronine deiodinases (Dios) are involved in the regioselective removal of iodine from thyroid hormones (THs). Deiodination is essential to maintain TH homeostasis, and disruption can have detrimental effects. Halogen bonding (XB) to the selenium of the selenocysteine (Sec) residue in the Dio active site has been proposed to contribute to the mechanism for iodine removal. Polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are known disruptors of various pathways of the endocrine system. Experimental evidence shows PBDEs and their hydroxylated metabolites (OH-BDEs) can inhibit Dio, while data regarding PCB inhibition are limited. These xenobiotics could inhibit Dio activity by competitively binding to the active site Sec through XB to prevent deiodination. XB interactions calculated using density functional theory (DFT) of THs, PBDEs, and PCBs to a methyl selenolate (MeSe−) arrange XB strengths in the order THs > PBDEs > PCBs in agreement with known XB trends. THs have the lowest energy C–X*-type unoccupied orbitals and overlap with the Se lp donor leads to high donor-acceptor energies and the greatest activation of the C–X bond. The higher energy C–Br* and C–Cl* orbitals similarly result in weaker donor-acceptor complexes and less activation of the C–X bond. Comparison of the I···Se interactions for the TH group suggest that a threshold XB strength may be required for dehalogenation. Only highly brominated PBDEs have binding energies in the same range as THs, suggesting that these compounds may inhibit Dio and undergo debromination. While these small models provide insight on the I···Se XB interaction itself, interactions with other active site residues are governed by regioselective preferences observed in Dios.
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Kurczab R, Kucwaj-Brysz K, Śliwa P. The Significance of Halogen Bonding in Ligand-Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D 4 Receptor. Molecules 2019; 25:E91. [PMID: 31881785 PMCID: PMC6983170 DOI: 10.3390/molecules25010091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 11/21/2022] Open
Abstract
Recently, a computational approach combining a structure-activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand-receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand-receptor complex by halogen bonding.
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Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland;
| | - Katarzyna Kucwaj-Brysz
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Cracow, Poland;
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
| | - Paweł Śliwa
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155 Cracow, Poland;
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Santos LDA, Prandi IG, Ramalho TC. Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest. Front Chem 2019; 7:848. [PMID: 31921771 PMCID: PMC6923750 DOI: 10.3389/fchem.2019.00848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
Essential to understanding life, the biomolecular phenomena have been an important subject in science, therefore a necessary path to be covered to make progress in human knowledge. To fully comprehend these processes, the non-covalent interactions are the key. In this review, we discuss how specific protein-ligand interactions can be efficiently described by low computational cost methods, such as Molecular Mechanics (MM). We have taken as example the case of the halogen bonds (XB). Albeit generally weaker than the hydrogen bonds (HB), the XBs play a key role to drug design, enhancing the affinity and selectivity toward the biological target. Along with the attraction between two electronegative atoms in XBs explained by the σ-hole model, important orbital interactions, as well as relief of Pauli repulsion take place. Nonetheless, such electronic effects can be only well-described by accurate quantum chemical methods that have strong limitations dealing with supramolecular systems due to their high computational cost. To go beyond the poor description of XBs by MM methods, reparametrizing the force-fields equations can be a way to keep the balance between accuracy and computational cost. Thus, we have shown the steps to be considered when parametrizing force-fields to achieve reliable results of complex non-covalent interactions at MM level for In Silico drug design methods.
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Affiliation(s)
| | - Ingrid G. Prandi
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czechia
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27
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Nunes R, Vila-Viçosa D, Costa PJ. Tackling Halogenated Species with PBSA: Effect of Emulating the σ-Hole. J Chem Theory Comput 2019; 15:4241-4251. [PMID: 31142112 DOI: 10.1021/acs.jctc.9b00106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To model halogen-bond phenomena using classical force fields, an extra point (EP) of charge is frequently introduced at a given distance from the halogen (X) to emulate the σ-hole. The resulting molecular dynamics (MD) trajectories can be used in subsequent molecular mechanics (MM) combined with Poisson-Boltzmann and surface area calculations (PBSA) to estimate protein-ligand binding free energies (Δ Gbind). While EP addition improves the MM/MD description of halogen-containing systems, its effect on the calculation of solvation free energies (Δ Gsolv) using the PBSA approach is yet to be assessed. As the PBSA calculations depend, among other parameters, on the empirical assignment of radii (PB radii), a problematic issue arises, since standard halogen radii are smaller than the typical X···EP distances, thus placing the EP within the solvent dielectric. Herein, we took a common literature EP parametrization scheme, which uses X···EP = Rmin and RESP charges in the context of GAFF, and performed a comprehensive study on the performance of PBSA (using three different setups) in the calculation of Δ Gsolv values for 142 halogenated compounds (bearing Cl, Br, or I) for which the experimental values are known. By conducting an optimization (minimizing the error against experimental values), we provide a new optimized set of halogen PB radii, for each PBSA setup, that should be used in the context of the aforementioned scenario. A simultaneous optimization of PB radii and X···EP distances shows that a wide range of distance/radius pairs can be used without significant loss of accuracy, therefore laying the basis for expanding this halogen radii optimization strategy to other force fields and EP implementations. As ligand Δ Gsolv estimation is an important term in the determination of protein-ligand Δ Gbind, this work is particularly relevant in the framework of structure-based virtual screening and related computer-aided drug design routines.
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28
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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Uddin N, Ahmed S, Khan AM, Mazharol Hoque M, Halim MA. Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy. J Biomol Struct Dyn 2019; 38:901-917. [PMID: 30938661 DOI: 10.1080/07391102.2019.1591302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methotrexate is a widely used anti-metabolite in cancer chemotherapy. A series of halogenated drugs is designed from Methotrexate to assess their interactions with human dihydrofolate reductase. The aim of this study is to evaluate the performance of the modified drugs compared to the parent Methotrexate. Density Functional Theory is employed to optimize these drugs. Molecular docking calculation of these optimized drugs against dihydrofolate reductase is performed to find out binding affinity. In addition, molecular dynamics simulation is considered for the complexes of best two modified drugs with their receptors. Modifications by the halogens show significant changes in the charge distribution, dipole moment, thermodynamic stability, enthalpy and free energy. The highest binding affinity value (-36.401 KJ/mol) was obtained for M14. Hybrid quantum mechanics/molecular mechanics calculation shows a binding energy of -255.140 KJ/mol. Modified drugs have significant hydrogen and non-covalent bonding interactions with amino acids of the receptor. Molecular dynamics simulation disclosed that the root-mean-square-deviation of the alpha carbon associated with M6-1KMV and M14-1KMV complexes is 2.367 Å and 2.622 Å, respectively. Moreover, the interactions between modified drugs and receptor are mostly persevered in 25 nanosecond molecular dynamics simulation. Ensemble-based docking also confirmed that modified drugs show strong non-bonding interactions with different crystallographic and molecular dynamics based conformers. The best scored drugs show considerable pharmacokinetic properties. Modified derivatives M5, M6, M8, M10, M13 and M14 show the better binding affinity and a good number of hydrogen and other non-bonding interactions with the target protein which are similar to other anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nizam Uddin
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh.,Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
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Peluso P, Dessì A, Dallocchio R, Mamane V, Cossu S. Recent studies of docking and molecular dynamics simulation for liquid-phase enantioseparations. Electrophoresis 2019; 40:1881-1896. [PMID: 30710444 DOI: 10.1002/elps.201800493] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/16/2022]
Abstract
Liquid-phase enantioseparations have been fruitfully applied in several fields of science. Various applications along with technical and theoretical advancements contributed to increase significantly the knowledge in this area. Nowadays, chromatographic techniques, in particular HPLC on chiral stationary phase, are considered as mature technologies. In the last thirty years, CE has been also recognized as one of the most versatile technique for analytical scale separation of enantiomers. Despite the huge number of papers published in these fields, understanding mechanistic details of the stereoselective interaction between selector and selectand is still an open issue, in particular for high-molecular weight chiral selectors like polysaccharide derivatives. With the ever growing improvement of computer facilities, hardware and software, computational techniques have become a basic tool in enantioseparation science. In this field, molecular docking and dynamics simulations proved to be extremely adaptable to model and visualize at molecular level the spatial proximity of interacting molecules in order to predict retention, selectivity, enantiomer elution order, and profile noncovalent interaction patterns underlying the recognition process. On this basis, topics and trends in using docking and molecular dynamics as theoretical complement of experimental LC and CE chiral separations are described herein. The basic concepts of these computational strategies and seminal studies performed over time are presented, with a specific focus on literature published between 2015 and November 2018. A systematic compilation of all published literature has not been attempted.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, Strasbourg, Alsace, France
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi DSMN, Università Ca' Foscari Venezia, Mestre Venezia, Veneto, Italy
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31
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Mphahlele MJ, Agbo EN, Gildenhuys S. Synthesis and Evaluation of the 4-Substituted 2-Hydroxy-5-Iodochalcones and Their 7-Substituted 6-Iodoflavonol Derivatives for Inhibitory Effect on Cholinesterases and β-Secretase. Int J Mol Sci 2018; 19:ijms19124112. [PMID: 30567381 PMCID: PMC6321475 DOI: 10.3390/ijms19124112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 11/24/2022] Open
Abstract
A series of 2-aryl-3-hydroxy-6-iodo-4H-chromen-4-ones substituted at the 7-position with a halogen atom (X = F, Cl and Br) or methoxy group and their corresponding 4-substituted 2-hydroxy-5-iodochalcone precursors were evaluated in vitro for inhibitory effect against acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and β-secretase (BACE1) activities. Although moderate inhibitory effect was observed for the chalcones against AChE, derivatives 2h, 2j and 2n exhibited significant inhibitory effect against BChE and BACE-1. The 2-aryl-7-fluoro-8-iodoflavonols 3b and 3c, on the other hand, exhibited increased activity and selectivity against AChE and reduced effect on BACE-1. The flavonols 3h, 3i, 3k, 3l and 3p exhibited moderate inhibitory effect against AChE, but significant inhibition against BChE. Compounds 2j and 3l exhibited non-competitive mode of inhibition against BACE-1. Molecular docking predicted strong interactions with the protein residues in the active site of BACE-1 implying these compounds bind with the substrate. Similarly docking studies predicted interaction of the most active compounds with both CAS and PAS of either AChE or BChE with mixed type of enzyme inhibition confirmed by kinetic studies.
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Affiliation(s)
- Malose J Mphahlele
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Emmanuel N Agbo
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Private Bag X06, Florida 1710, South Africa.
| | - Samantha Gildenhuys
- Department of Life & Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Private Bag X06, Florida 1710, South Africa.
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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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33
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Dallocchio R, Dessì A, Solinas M, Arras A, Cossu S, Aubert E, Mamane V, Peluso P. Halogen bond in high-performance liquid chromatography enantioseparations: Description, features and modelling. J Chromatogr A 2018; 1563:71-81. [PMID: 29871805 DOI: 10.1016/j.chroma.2018.05.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 02/08/2023]
Abstract
Halogen bond (XB)-driven enantioseparations involve halogen-centred regions of electronic charge depletion (σ-hole) as electrophilic recognition sites. The knowledge in this field is still in its infancy. Indeed, although the influence of halogens on enantioseparation have been often considered, only recently the function of electrophilic halogens (Cl, Br, I) as enantioseparations 'drivers' has been demonstrated by our groups. Further to these studies, in this paper we focus on some unexplored issues. First, as XB-driven chiral recognition mechanisms are at an early stage of comprehension, a theoretical investigation based on a series of 32 molecular dynamic (MD) simulations was performed by using polyhalogenated 4,4'-bipyridines and polysaccharide-based polymers as ligands and receptors, respectively. Enantiomer elution orders (EEOs) were derived from calculations and the theoretical model accounted for some analyte- and chiral stationary phase (CSP)-dependent experimental EEO inversions. Then, the function of halogen-centred σ-holes in competitive systems, presenting also hydrogen bond (HB) centres as recognition sites, was considered. In this regard, Pirkle's enantioseparations of halogenated compounds performed on Whelk-O1 were theoretically re-examined and electrostatic potentials (EPs) associated with both σ-holes on halogens and HB centres were computed and compared. Then, the enantioseparation of halogenated 2-nitro-1-arylethanols was performed on cellulose tris(3,5-dimethylphenylcarbamate) (CDMPC) and the influence of halogen substituents on the chromatographic results was evaluated by correlating theoretical and experimental data.
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Affiliation(s)
- Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, I-07100 Li Punti, Sassari, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, I-07100 Li Punti, Sassari, Italy
| | - Maurizio Solinas
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, I-07100 Li Punti, Sassari, Italy
| | - Antonio Arras
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, I-07100 Li Punti, Sassari, Italy
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi DSMN, Università Ca' Foscari di Venezia, Via Torino 155, I-30172 Mestre Venezia, Italy
| | - Emmanuel Aubert
- Cristallographie, Résonance Magnétique et Modélisations (CRM2), UMR CNRS 7036, Université de Lorraine, Bd des Aiguillettes, 54506 Vandoeuvre-les-Nancy, France
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR CNRS 7177, Equipe LASYROC, 1 rue Blaise Pascal, 67008 Strasbourg Cedex, France.
| | - Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, I-07100 Li Punti, Sassari, Italy.
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34
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Saleem L, Altaf AA, Badshah A, Rauf MK, Waseem A, Danish M, Azam SS, Arshad MN, Asiri AM, Ahmad S, Gul R. Structural investigations, anti-leishmanial, antibacterial and docking studies of new pentavalent antimony carboxylates. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.01.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Peluso P, Mamane V, Dallocchio R, Dessì A, Villano R, Sanna D, Aubert E, Pale P, Cossu S. Polysaccharide-based chiral stationary phases as halogen bond acceptors: A novel strategy for detection of stereoselective σ-hole bonds in solution. J Sep Sci 2018; 41:1247-1256. [PMID: 29239526 DOI: 10.1002/jssc.201701206] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/15/2022]
Abstract
In the last few years, halogen bonds have been exploited in a variety of research areas both in the solid state and in solution. Nevertheless, several factors make formation and detection of halogen bonds in solution challenging. Moreover, to date, few chiral molecules containing electrophilic halogens as recognition sites have been reported. Recently, we described the first series of halogen-bond-driven enantioseparations performed on cellulose tris(3,5-dimethylphenylcarbamate) by high-performance liquid chromatography. Herein the performances of amylose tris(3,5-dimethylphenylcarbamate) as halogen bond acceptor were also investigated and compared with respect to cellulose tris(3,5-dimethylphenylcarbamate). With the aim to explore the effect of polysaccharide backbone on the enantioseparations, the thermodynamic parameters governing the halogen-dependent enantioseparations on both cellulose and amylose polymers were determined by a study at variable temperature and compared. Molecular dynamics were performed to model the halogen bond in polysaccharide-analyte complexes. Chiral halogenated 4,4'-bipyridines were used as test compounds (halogen bond donors). On this basis, a practical method for detection of stereoselective halogen bonds in solution was developed, which is based on the unprecedented use of high-performance liquid chromatography as technical tool with polysaccharide polymers as molecular probes (halogen bond acceptors). The analytical strategy showed higher sensitivity for the detection of weak halogen bonds.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB CNR - Sede secondaria di Sassari, Sassari, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, UMR 7177, Equipe LASYROC, Strasbourg, France
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB CNR - Sede secondaria di Sassari, Sassari, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB CNR - Sede secondaria di Sassari, Sassari, Italy
| | - Rosaria Villano
- Istituto di Chimica Biomolecolare ICB CNR - Sede secondaria di Sassari, Sassari, Italy
| | - Daniele Sanna
- Istituto di Chimica Biomolecolare ICB CNR - Sede secondaria di Sassari, Sassari, Italy
| | - Emmanuel Aubert
- CRM2, UMR CNRS 7036, Université de Lorraine, Vandoeuvre-les-Nancy, France
| | - Patrick Pale
- Institut de Chimie de Strasbourg, UMR 7177, Equipe LASYROC, Strasbourg, France
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Mestre Venezia, Italy
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36
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Zhang Q, Xu Z, Shi J, Zhu W. Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank. J Chem Inf Model 2017. [DOI: 10.1021/acs.jcim.7b00235] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Qian Zhang
- Department
of Computer Science and Technology, East China Normal University, Shanghai 200241, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin du Foriest, B-1420 Braine-l′Alleud, Belgium
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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37
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Halogen bonding in medicinal chemistry: from observation to prediction. Future Med Chem 2017; 9:637-640. [DOI: 10.4155/fmc-2017-0052] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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38
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Titov OI, Shulga DA, Palyulin VA, Zefirov NS. Quadrupole correction for halogen bonding description in virtual screening and molecular docking. DOKLADY CHEMISTRY 2016. [DOI: 10.1134/s0012500816110100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Rahman A, Ali MT, Shawan MMAK, Sarwar MG, Khan MAK, Halim MA. Halogen-directed drug design for Alzheimer's disease: a combined density functional and molecular docking study. SPRINGERPLUS 2016; 5:1346. [PMID: 27588239 PMCID: PMC4987752 DOI: 10.1186/s40064-016-2996-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/03/2016] [Indexed: 11/10/2022]
Abstract
A series of halogen-directed donepezil drugs has been designed to inhibit acetyl cholinesterase (AChE). Density Functional theory (DFT) has been employed to optimize the chair as well as boat conformers of the parent drug and modified ligands at B3LYP/MidiX and B3LYP/6-311G + (d,p) level of theories. Charge distribution, dipole moment, enthalpy, free energy and molecular orbitals of these ligands are also investigated to understand how the halogen-directed modifications impact the ligand structure and govern the non-bonding interactions with the receptors. Molecular docking calculation has been performed to understand the similarities and differences between the binding modes of unmodified and halogenated chair-formed ligands. Molecular docking indicated donepezil and modified ligands had non-covalent interactions with hydrophobic gorges and anionic subsites of AChE. The -CF3-directed ligand possessed the most negative binding affinity. Non-covalent interactions within the ligand-receptor systems were found to be mostly hydrophobic and π- stacking type. F, Cl and -CF3 containing ligands emerge as effective and selective AChE inhibitors, which can strongly interact with the two active sites of AChE. In addition, we have also investigated selected pharmacokinetic parameters of the parent and modified ligands.
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Affiliation(s)
- Adhip Rahman
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
| | - Mohammad Tuhin Ali
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Mohammad Mahfuz Ali Khan Shawan
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Dhaka, 1342 Bangladesh
| | - Mohammed Golam Sarwar
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Mohammad A. K. Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961 The Kingdom of Saudi Arabia
| | - Mohammad A. Halim
- Division of Computer Aided Drug Design, Green Research Centre, BICCB, 38 Green Road West, Dhaka, 1205 Bangladesh
- Institut Lumière Matière, Université Lyon 1 – CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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40
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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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Luchi AM, Angelina EL, Andujar SA, Enriz RD, Peruchena NM. Halogen bonding in biological context: a computational study of D2 dopamine receptor. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3586] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Adriano M. Luchi
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA; Universidad Nacional del Nordeste, CONICET, FACENA; Av. Libertad 5470 Corrientes 3400 Argentina
| | - Emilio L. Angelina
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA; Universidad Nacional del Nordeste, CONICET, FACENA; Av. Libertad 5470 Corrientes 3400 Argentina
| | - Sebastián A. Andujar
- Instituto Multidisciplinario de Investigaciones Biológicas San Luis; Universidad Nacional de San Luis, CONICET, FQBF; Chacabuco 917 San Luis 5700 Argentina
| | - Ricardo D. Enriz
- Instituto Multidisciplinario de Investigaciones Biológicas San Luis; Universidad Nacional de San Luis, CONICET, FQBF; Chacabuco 917 San Luis 5700 Argentina
| | - Nélida M. Peruchena
- Lab. Estructura Molecular y Propiedades, IQUIBA-NEA; Universidad Nacional del Nordeste, CONICET, FACENA; Av. Libertad 5470 Corrientes 3400 Argentina
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42
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Koebel MR, Schmadeke G, Posner RG, Sirimulla S. AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina. J Cheminform 2016; 8:27. [PMID: 27195023 PMCID: PMC4870740 DOI: 10.1186/s13321-016-0139-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don’t account for halogen bonding in their scoring functions and are not able to utilize this new approach. In this study a new and improved halogen bonding scoring function (XBSF) is presented along with its implementation in the AutoDock Vina molecular docking software. This new improved program is termed as AutoDock VinaXB, where XB stands for the halogen bonding parameters that were added. Results XBSF scoring function is derived based on the X···A distance and C–X···A angle of interacting atoms. The distance term was further corrected to account for the polar flattening effect of halogens. A total of 106 protein-halogenated ligand complexes were tested and compared in terms of binding affinity and docking poses using Vina and VinaXB. VinaXB performed superior to Vina in the majority of instances. VinaXB was closer to native pose both above and below 2 Å deviation categories almost twice as frequently as Vina. Conclusions Implementation of XBSF into AutoDock Vina has been shown to improve the accuracy of the docking result with regards to halogenated ligands. AutoDock VinaXB addresses the issues of halogen bonds that were previously being scored unfavorably due to repulsion factors, thus effectively lowering the output RMSD values. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0139-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mathew R Koebel
- Department of Basic Sciences, St. Louis College of Pharmacy, 4588 Parkview Place, Saint Louis, MO 63110 USA
| | - Grant Schmadeke
- Department of Basic Sciences, St. Louis College of Pharmacy, 4588 Parkview Place, Saint Louis, MO 63110 USA
| | - Richard G Posner
- Department of Biological Sciences, Northern Arizona University, S San Francisco St, Flagstaff, AZ 86001 USA
| | - Suman Sirimulla
- Department of Basic Sciences, St. Louis College of Pharmacy, 4588 Parkview Place, Saint Louis, MO 63110 USA
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43
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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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44
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Abstract
Halogen bonding (XB) is being extensively explored for its potential use in advanced materials and drug design. Despite significant progress in describing this interaction by theoretical and experimental methods, the chemical nature remains somewhat elusive, and it seems to vary with the selected system. In this work we present a detailed DFT analysis of three-center asymmetric halogen bond (XB) formed between dihalogen molecules and variously 4-substituted 1,2-dimethoxybenzene. The energy decomposition, orbital, and electron density analyses suggest that the contribution of electrostatic stabilization is comparable with that of non-electrostatic factors. Both terms increase parallel with increasing negative charge of the electron donor molecule in our model systems. Depending on the orientation of the dihalogen molecules, this bifurcated interaction may be classified as 'σ-hole - lone pair' or 'σ-hole - π' halogen bonds. Arrangement of the XB investigated here deviates significantly from a recent IUPAC definition of XB and, in analogy to the hydrogen bonding, the term bifurcated halogen bond (BXB) seems to be appropriate for this type of interaction.
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Affiliation(s)
- Martin Novák
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-625 00 Brno, Czech Republic.
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45
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Synthesis of Chlorinated Tetracyclic Compounds and Testing for Their Potential Antidepressant Effect in Mice. Molecules 2016; 21:61. [PMID: 26742028 PMCID: PMC6273077 DOI: 10.3390/molecules21010061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 11/17/2022] Open
Abstract
The synthesis of the tetracyclic compounds 1-(4,5-dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)-N-methylmethanamine (5) and 1-(1,8-dichloro-9,10-dihydro-9,10-ethanoanthracen-11-yl)-N-methylmethanamine (6) as a homologue of the anxiolytic and antidepressant drugs benzoctamine and maprotiline were described. The key intermediate aldehydes (3) and (4) were successfully synthesized via a [4 + 2] cycloaddition between acrolein and 1,8-dichloroanthracene. The synthesized compounds were investigated for antidepressant activity using the forced swimming test. Compounds (5), (6) and (3) showed significant reduction in the mice immobility indicating significant antidepressant effects. These compounds significantly reduced the immobility times at a dose 80 mg/kg by 84.0%, 86.7% and 71.1% respectively.
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46
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Rauf MK, Shaheen U, Asghar F, Badshah A, Nadhman A, Azam S, Ali MI, Shahnaz G, Yasinzai M. Antileishmanial, DNA Interaction, and Docking Studies of Some Ferrocene-Based Heteroleptic Pentavalent Antimonials. Arch Pharm (Weinheim) 2015; 349:50-62. [PMID: 26627058 DOI: 10.1002/ardp.201500312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/31/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022]
Abstract
A series of ferrocenyl pentavalent antimonials (1-8) were synthesized and characterized by elemental analysis, FT-IR, and multinuclear ((1) H and (13) C) NMR spectroscopy. These antimonials were evaluated for their antileishmanial potential against Leishmania tropica KWH23, and by biocompatibility and membrane permeability assays. Moreover, mechanistic studies were carried out, mediated by DNA targeting followed by computational docking of ferrocenyl antimonials against the leishmanial trypanothione reductase enzyme. It was observed that the antimonials 1-8 were 390-fold more efficacious (IC50 ) as compared with the standard antimonial drug used. Cytotoxicity results showed that these antimonials are highly active even at low concentrations and are biocompatible with human macrophages. Antimonials 1-8 exhibited extensive intercalation with DNA and, furthermore, docking interactions highlighted the potential interactive binding of the anitimonials within the trypanothione reductase active site, with van der Waals interactions contributing significantly to the process. Hence, it is suggested that the reported antimonials demonstrate high efficacy, less toxicity, and target multiple sites of the Leishmania parasite.
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Affiliation(s)
| | - Ummara Shaheen
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Faiza Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amin Badshah
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Akhtar Nadhman
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sikander Azam
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Gul Shahnaz
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Masoom Yasinzai
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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47
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Metal–ion binding by cyclic halogen-bonded structures: A theoretical study using M–(BrZ)4 clusters (Z = F or NH2; M = Li+, Na+, or Mg2+). Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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48
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Dureckova H, Woo TK, Alavi S, Ripmeester JA. Molecular dynamics simulation of halogen bonding in Cl2, BrCl, and mixed Cl2/Br2 clathrate hydrates. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Clathrate hydrate phases of dihalogen molecules have properties that differ from those of other guest molecules of similar size. The water oxygen–chlorine distances in the structure I (sI) Cl2 hydrate are smaller than the sum of the van der Waals radii of oxygen and chlorine. Bromine hydrate forms a unique clathrate hydrate structure that is not seen in other guest substances. In mixed Cl2/Br2 structure I hydrate, the water oxygen–bromine distances are also smaller than the sum of the oxygen and bromine van der Waals radii. We previously studied the structure of three dihalogen clathrate hydrates using single crystal X-ray diffraction and described these structural features in terms of halogen bonding between the dihalogen and water molecules. In this work, we perform molecular dynamics simulations of cubic sI Cl2, mixed Cl2/Br2, and BrCl clathrate hydrate phases. We perform quantum chemical computations on the dihalogen molecules to determine the nature of σ-hole near the halogen atoms. We fit the electrostatic potential of the molecules to point charge models including dummy atoms that represent σ-holes adjacent to the halogen molecules. Molecular dynamics simulations are used to determine the lattice constants, radial distribution functions, and guest dynamics in these phases. We determine the effect of guest size and difference in halogen bonding on the properties of the clathrate hydrate phase. Simulations for the Cl2, BrCl, and mixed Cl2/Br2 hydrates are performed with small cages of the sI clathrate hydrate phases completely full or filled with experimental occupancies with Cl2 guests.
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Affiliation(s)
- Hana Dureckova
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tom K. Woo
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Saman Alavi
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - John A. Ripmeester
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
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49
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Fanfrlík J, Ruiz FX, Kadlčíková A, Řezáč J, Cousido-Siah A, Mitschler A, Haldar S, Lepšík M, Kolář MH, Majer P, Podjarny AD, Hobza P. The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition. ACS Chem Biol 2015; 10:1637-42. [PMID: 25919404 DOI: 10.1021/acschembio.5b00151] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effect of halogen-to-hydrogen bond substitution on the binding energetics and biological activity of a human aldose reductase inhibitor has been studied using X-ray crystallography, IC50 measurements, advanced binding free energy calculations, and simulations. The replacement of Br or I atoms by an amine (NH2) group has not induced changes in the original geometry of the complex, which made it possible to study the isolated features of selected noncovalent interactions in a biomolecular complex.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Francesc X. Ruiz
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Aneta Kadlčíková
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Alexandra Cousido-Siah
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - André Mitschler
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Pavel Majer
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Alberto D. Podjarny
- Department
of Integrative Biology, IGBMC, CNRS, INSERM, UdS, 1 rue Laurent Fries 67404, Illkirch CEDEX, France
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and
IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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50
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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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