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Milesi P, Baldelli Bombelli F, Lanfrancone L, Gomila RM, Frontera A, Metrangolo P, Terraneo G. Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes. Chem Asian J 2024; 19:e202301033. [PMID: 38501888 DOI: 10.1002/asia.202301033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.
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Affiliation(s)
- Pietro Milesi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Luisa Lanfrancone
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
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Meier E, Seichter W, Mazik M. Combination of Hydrogen and Halogen Bonds in the Crystal Structures of 5-Halogeno-1 H-isatin-3-oximes: Involvement of the Oxime Functionality in Halogen Bonding. Molecules 2024; 29:1174. [PMID: 38474688 DOI: 10.3390/molecules29051174] [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: 12/14/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Various functional groups have been considered as acceptors for halogen bonds, but the oxime functionality has received very little attention in this context. In this study, we focus on the analysis of the hydrogen and halogen bond preferences observed in the crystal structures of 5-halogeno-1H-isatin-3-oximes. These molecules can be involved in various non-covalent interactions, and the competition between these interactions has a decisive influence on their self-organization. In particular, we were interested to see whether the crystal structures of 5-halogeno-1H-isatin-3-oximes, especially bromine- and iodine-substituted ones, are characterized by the presence of halogen bonds formed with the oxime functionality. The oxime group proved its ability to compete with the other strong donor and acceptor sites by participating in the formation of cyclic hydrogen-bonded heterosynthons oxime∙∙∙amide and Ooxime∙∙∙Br/I halogen bonds.
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Affiliation(s)
- Eric Meier
- Institut Für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
| | - Wilhelm Seichter
- Institut Für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
| | - Monika Mazik
- Institut Für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
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Sun J, Decato DA, Bryantsev VS, John EA, Berryman OB. The interplay between hydrogen and halogen bonding: substituent effects and their role in the hydrogen bond enhanced halogen bond. Chem Sci 2023; 14:8924-8935. [PMID: 37621436 PMCID: PMC10445465 DOI: 10.1039/d3sc02348f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.
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Affiliation(s)
- Jiyu Sun
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | | | - Eric A John
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
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Wang Z, Ma J, Wang T, Qin C, Hu X, Mosa A, Ling W. Environmental health risks induced by interaction between phthalic acid esters (PAEs) and biological macromolecules: A review. CHEMOSPHERE 2023; 328:138578. [PMID: 37023900 DOI: 10.1016/j.chemosphere.2023.138578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
As a kind of compounds abused in industry productions, phthalic acid esters (PAEs) cause serious problems in natural environment. PAEs pollution has penetrated into environmental media and human food chain. This review consolidates the updated information to assess the occurrence and distribution of PAEs in each transmission section. It is found that micrograms per kilogram of PAEs are exposed to humans through daily diets. After entering the human body, PAEs often undergo the metabolic process of hydrolysis to monoesters phthalates and conjugation process. Unfortunately, in the process of systemic circulation, PAEs will interact with biological macromolecules in vivo under the action of non-covalent binding, which is also the essence of biological toxicity. The interactions usually operate in the following pathways: (a) competitive binding; (b) functional interference; and (c) abnormal signal transduction. While the non-covalent binding forces mainly contain hydrophobic interaction, hydrogen bond, electrostatic interaction, and π interaction. As a typical endocrine disruptor, the health risks of PAEs often start with endocrine disorder, further leading to metabolic disruption, reproductive disorders, and nerve injury. Besides, genotoxicity and carcinogenicity are also attributed to the interaction between PAEs and genetic materials. This review also pointed out that the molecular mechanism study on biological toxicity of PAEs are deficient. Future toxicological research should pay more attention to the intermolecular interactions. This will be beneficial for evaluating and predicting the biological toxicity of pollutants at molecular scale.
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Affiliation(s)
- Zeming Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Junchao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Tingting Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516, Mansoura, Egypt
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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6
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Zheng J, Suwardi A, Wong CJE, Loh XJ, Li Z. Halogen bonding regulated functional nanomaterials. NANOSCALE ADVANCES 2021; 3:6342-6357. [PMID: 36133496 PMCID: PMC9419782 DOI: 10.1039/d1na00485a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/22/2021] [Indexed: 06/16/2023]
Abstract
Non-covalent interactions have gained increasing attention for use as a driving force to fabricate various supramolecular architectures, exhibiting great potential in crystal and materials engineering and supramolecular chemistry. As one of the most powerful non-covalent bonds, the halogen bond has recently received increasing attention in functional nanomaterial design. The present review describes the latest studies based on halogen bonding induced self-assembly and its applications. Due to the high directionality and controllable interaction strength, halogen bonding can provide a facile platform for the design and synthesis of a myriad of nanomaterials. In addition, both the fundamental aspects and the real engineering applications are discussed, which encompass molecular recognition and sensing, organocatalysis, and controllable multifunctional materials and surfaces.
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Affiliation(s)
- Jie Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research) Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Ady Suwardi
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research) Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Claris Jie Ee Wong
- Department of Material Science and Engineering, National University of Singapore S117576 Singapore
| | - Xian Jun Loh
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research) Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
| | - Zibiao Li
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research) Fusionopolis Way, Innovis, #08-03 Singapore 138634 Singapore
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7
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Khairat R, Elhossini R, Sobreira N, Wohler E, Otaify G, Mohamed AM, Abdel Raouf ER, Sayed I, Aglan M, Ismail S, Temtamy SA. Expansion of the phenotypic and mutational spectrum of Carpenter syndrome. Eur J Med Genet 2021; 65:104377. [PMID: 34748996 DOI: 10.1016/j.ejmg.2021.104377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 10/14/2021] [Accepted: 11/02/2021] [Indexed: 11/29/2022]
Abstract
Carpenter syndrome 1 (CRPT1) is an acrocephalopolysyndactyly (ACPS) disorder characterized by craniosynostosis, polysyndactyly, obesity, and other malformations. It is caused by mutations in the gene RAB23. We are reporting on two patients from two unrelated consanguineous Egyptian families. Patient 1 presented with an atypical clinical presentation of Carpenter syndrome including overgrowth with advanced bone age, epileptogenic changes on electroencephalogram and autistic features. Patient 2 presented with typical clinical features suggestive of Carpenter syndrome. Therefore, Patient 1 was subjected to whole exome sequencing (WES) to find an explanation for his unusual features and Patient 2 was subjected to Sanger sequencing of the coding exons of theRAB23 gene to confirm the diagnosis. We identified a novel homozygous missense RAB23 variant (NM_001278668:c.T416C:p.Leu139Pro) in Patient 1 and a novel homozygous splicing variant (NM_016277.5:c.398+1G > A) in Patient 2. We suggest that the overgrowth with advanced bone age, electroencephalogram epileptogenic changes, and autistic features seen in Patient 1 are an expansion of the Carpenter phenotype and could be due to the novel missense RAB23 variant. Additionally, the novel identified RAB23 variants in Patient 1 and 2 broaden the spectrum of variants associated with Carpenter syndrome.
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Affiliation(s)
- Rabab Khairat
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
| | - Rasha Elhossini
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth Wohler
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ghada Otaify
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Amal M Mohamed
- Department of Human Cytogenetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Ehab R Abdel Raouf
- Department of Children of Special Needs, Medicine and Clinical Studies Research Institute, National Research Centre, Cairo, Egypt
| | - Inas Sayed
- Department of Oro-dental Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mona Aglan
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Samira Ismail
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Samia A Temtamy
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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8
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Benito M, Roselló Y, Barceló-Oliver M, Frontera A, Molins E. Uracil Derivatives for Halogen-Bonded Cocrystals. Int J Mol Sci 2021; 22:ijms221910663. [PMID: 34639004 PMCID: PMC8508742 DOI: 10.3390/ijms221910663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Among non-covalent interactions, halogen bonding is emerging as a new powerful tool for supramolecular self-assembly. Here, along with a green and effective method, we report three new halogen-bonded cocrystals containing uracil derivatives and 1,2,4,5-tetrafluoro-3,6-diiodobenzene as X-bond donor coformer. These multicomponent solids were prepared both by solvent-drop grinding and solution methods and further characterized by powder and single-crystal X-ray diffraction, Fourier-transformed infrared spectroscopy, and thermal methods (TGA-DSC). In order to study the relative importance of hydrogen versus halogen bonds in the crystal packing, computational methods were applied.
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Affiliation(s)
- Mónica Benito
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (M.B.); (A.F.); (E.M.)
| | - Yannick Roselló
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
| | - Miquel Barceló-Oliver
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
- Correspondence: (M.B.); (A.F.); (E.M.)
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (M.B.); (A.F.); (E.M.)
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Aschi M, Toto Brocchi G, Portalone G. A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine. Molecules 2021; 26:molecules26113111. [PMID: 34070959 PMCID: PMC8196974 DOI: 10.3390/molecules26113111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C-Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).
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Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi di L’Aquila, Via Vetoio 10, 67100 Coppito, Italy;
| | - Giorgia Toto Brocchi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Gustavo Portalone
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Roma, Italy;
- Correspondence:
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10
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Staroń J, Pietruś W, Bugno R, Kurczab R, Satała G, Warszycki D, Lenda T, Wantuch A, Hogendorf AS, Hogendorf A, Duszyńska B, Bojarski AJ. Tuning the activity of known drugs via the introduction of halogen atoms, a case study of SERT ligands - Fluoxetine and fluvoxamine. Eur J Med Chem 2021; 220:113533. [PMID: 34049262 DOI: 10.1016/j.ejmech.2021.113533] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022]
Abstract
The selective serotonin reuptake inhibitors (SSRIs), acting at the serotonin transporter (SERT), are one of the most widely prescribed antidepressant medications. All five approved SSRIs possess either fluorine or chlorine atoms, and there is a limited number of reports describing their analogs with heavier halogens, i.e., bromine and iodine. To elucidate the role of halogen atoms in the binding of SSRIs to SERT, we designed a series of 22 fluoxetine and fluvoxamine analogs substituted with fluorine, chlorine, bromine, and iodine atoms, differently arranged on the phenyl ring. The obtained biological activity data, supported by a thorough in silico binding mode analysis, allowed the identification of two partners for halogen bond interactions: the backbone carbonyl oxygen atoms of E493 and T497. Additionally, compounds with heavier halogen atoms were found to bind with the SERT via a distinctly different binding mode, a result not presented elsewhere. The subsequent analysis of the prepared XSAR sets showed that E493 and T497 participated in the largest number of formed halogen bonds. The XSAR library analysis led to the synthesis of two of the most active compounds (3,4-diCl-fluoxetine 42, SERT Ki = 5 nM and 3,4-diCl-fluvoxamine 46, SERT Ki = 9 nM, fluoxetine SERT Ki = 31 nM, fluvoxamine SERT Ki = 458 nM). We present an example of the successful use of a rational methodology to analyze binding and design more active compounds by halogen atom introduction. 'XSAR library analysis', a new tool in medicinal chemistry, was instrumental in identifying optimal halogen atom substitution.
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Affiliation(s)
- Jakub Staroń
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland.
| | - Wojciech Pietruś
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Ryszard Bugno
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Grzegorz Satała
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Dawid Warszycki
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Tomasz Lenda
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Anna Wantuch
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Adam S Hogendorf
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Agata Hogendorf
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Beata Duszyńska
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343, Kraków, Poland
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11
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Czarny RS, Ho AN, Shing Ho P. A Biological Take on Halogen Bonding and Other Non-Classical Non-Covalent Interactions. CHEM REC 2021; 21:1240-1251. [PMID: 33886153 DOI: 10.1002/tcr.202100076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/07/2021] [Indexed: 01/23/2023]
Abstract
Classical hydrogen bonds have, for many decades, been the dominant non-covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non-classical non-covalent (NC-NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure-function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC-NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research.
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Affiliation(s)
- Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Alexander N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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12
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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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13
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Orthogonal hydrogen and halogen bonding facilitate intermolecular charge transfer between barbaturic acid and molecular halogens over g-C3N4 nanosheet: A comparative experimental and DFT calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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14
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Van der Maelen JF, Ceroni M, Ruiz J. The X-ray constrained wavefunction of the [Mn(CO) 4{(C 6H 5) 2P-S-C(Br 2)-P(C 6H 5) 2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:802-814. [PMID: 33017314 DOI: 10.1107/s2052520620009889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.
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Affiliation(s)
- Juan F Van der Maelen
- Dept. Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
| | - Mario Ceroni
- Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Javier Ruiz
- Dept. Química Orgánica e Inorgánica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
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15
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Mehrparvar S, Wölper C, Gleiter R, Haberhauer G. The Carbonyl⋅⋅⋅Tellurazole Chalcogen Bond as a Molecular Recognition Unit: From Model Studies to Supramolecular Organic Frameworks. Angew Chem Int Ed Engl 2020; 59:17154-17161. [PMID: 32533583 PMCID: PMC7540342 DOI: 10.1002/anie.202005374] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 02/06/2023]
Abstract
In the last years, chalcogen bonding, the noncovalent interaction involving chalcogen centers, has emerged as interesting alternative to the ubiquitous hydrogen bonding in many research areas. Here, we could show by means of high-level quantum chemical calculations that the carbonyl⋅⋅⋅tellurazole chalcogen bond is at least as strong as conventional hydrogen bonds. Using the carbonyl⋅⋅⋅tellurazole binding motif, we were able to design complex supramolecular networks in solid phase starting from tellurazole-substituted cyclic peptides. X-ray analyses reveal that the rigid structure of the cyclic peptides is caused by hydrogen bonds, whereas the supramolecular network is held together by chalcogen bonding. The type of the supramolecular network depends on peptide used; both linear wires and a honeycomb-like supramolecular organic framework (SOF) were observed. The unique structure of the SOF shows two channels filled with different types of solvent mixtures that are either locked or freely movable.
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Affiliation(s)
- Saber Mehrparvar
- Institut für Organische ChemieUniversität Duisburg-EssenUniversitätsstraße 745117EssenGermany
| | - Christoph Wölper
- Institut für Organische ChemieUniversität Duisburg-EssenUniversitätsstraße 745117EssenGermany
| | - Rolf Gleiter
- Organisch-Chemisches InstitutUniversität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Gebhard Haberhauer
- Institut für Organische ChemieUniversität Duisburg-EssenUniversitätsstraße 745117EssenGermany
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16
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Mehrparvar S, Wölper C, Gleiter R, Haberhauer G. Die Carbonyl⋅⋅⋅Tellurazol‐Chalkogenbindung als molekulare Erkennungseinheit: Von Modellstudien zu supramolekularen organischen Gerüstverbindungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Saber Mehrparvar
- Institut für Organische Chemie Universität Duisburg-Essen Universitätsstraße 7 D-45117 Essen Deutschland
| | - Christoph Wölper
- Institut für Organische Chemie Universität Duisburg-Essen Universitätsstraße 7 D-45117 Essen Deutschland
| | - Rolf Gleiter
- Organisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 270 D-69120 Heidelberg Deutschland
| | - Gebhard Haberhauer
- Institut für Organische Chemie Universität Duisburg-Essen Universitätsstraße 7 D-45117 Essen Deutschland
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17
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Pizzi A, Pigliacelli C, Bergamaschi G, Gori A, Metrangolo P. Biomimetic engineering of the molecular recognition and self-assembly of peptides and proteins via halogenation. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213242] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Critical comparison of R X⋯Y and R H⋯Y directionality in halogen and hydrogen bonds using modern computational chemistry methods. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Abstract
Sulfur is a widely used halogen bond (XB) acceptor, but only a limited number of neutral XB acceptors with bifurcated sp3-S sites have been reported. In this work a new bidentate XB acceptor, 1-(4-pyridyl)-4-thiopyridine (PTP), which combines sp3-S and sp2-N acceptor sites, is introduced. Three halogen bonded cocrystals were obtained by using 1,4-diiodobenzene (DIB), 1,4-diiodotetrafluorobenzene (DIFB), and iodopentafluorobenzene (IPFB) as XB donors and PTP as acceptor. The structures of the cocrystals showed some XB selectivity between the S and N donors in PTP. However, the limited contribution of XB to the overall molecular packing in these three cocrystals and the results from DSC measurements clearly point out the synergetic influence and interplay of all noncovalent interactions in crystal packing of these compounds.
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20
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Riel AMS, Rowe RK, Ho EN, Rappé AK, Berryman OB, Ho PS. Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry. Acc Chem Res 2019; 52:2870-2880. [PMID: 31318520 PMCID: PMC7328900 DOI: 10.1021/acs.accounts.9b00189] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The halogen bond (XB) has become an important tool for molecular design in all areas of chemistry, including crystal and materials engineering and medicinal chemistry. Its similarity to the hydrogen bond (HB) makes the relationship between these interactions complex, at times competing against and other times orthogonal to each other. Recently, our two laboratories have independently reported and characterized a synergistic relationship, in which the XB is enhanced through direct intramolecular HBing to the electron-rich belt of the halogen. In one study, intramolecular HBing from an amine polarizes the iodopyridinium XB donors of a bidentate anion receptor. The resulting HB enhanced XB (or HBeXB) preorganizes and further augments the XB donors. Consequently, the affinity of the receptor for halogen anions was significantly increased. In a parallel study, a meta-chlorotyrosine was engineered into T4 lysozyme, resulting in a HBeXB that increased the thermal stability and activity of the enzyme at elevated temperatures. The crystal structure showed that the chlorine of the noncanonical amino acid formed a XB to the protein backbone, which augmented the HB of the wild-type enzyme. Calorimetric analysis resulted in an enthalpic contribution of this Cl-XB to the stability of the protein that was an order of magnitude greater than previously determined in biomolecules. Quantum mechanical (QM) calculations showed that rotating the hydroxyl group of the tyrosine to point toward rather than away from the halogen greatly increased its potential to serve as a XB donor, equivalent to what was observed experimentally. In sum, the two systems described here show that the HBeXB concept extends the range of interaction energies and geometries to be significantly greater than that of the XB alone. Additionally, surveys of structural databases indicate that the components for this interaction are already present in many existing molecular systems. The confluence of the independent studies from our two laboratories demonstrates the reach of the HBeXB across both chemistry and biochemistry and that intentional engineering of this enhanced interaction will extend the applications of XBs beyond these two initial examples.
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Affiliation(s)
- Asia Marie S. Riel
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT
| | - Rhianon K. Rowe
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
| | - Ethan N. Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
| | - A. K. Rappé
- Department of Chemistry, Colorado State University, Fort Collins, CO
| | - Orion B. Berryman
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO
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21
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Decato DA, Riel AMS, Berryman OB. Anion Influence on the Packing of 1,3-Bis(4-Ethynyl-3-Iodopyridinium)-Benzene Halogen Bond Receptors. CRYSTALS 2019; 9:522. [PMID: 32219003 PMCID: PMC7098683 DOI: 10.3390/cryst9100522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rigid and directional arylethynyl scaffolds have been widely successful across diverse areas of chemistry. Utilizing this platform, we present three new structures of a dicationic 1,3-bis(4-ethynyl-3-iodopyridinium)-benzene halogen bonding receptor with tetrafluoroborate, nitrate, and hydrogen sulfate. Structural analysis focuses on receptor conformation, anion shape, solvation, and long range packing of these systems. Coupled with our previously reported structures, we conclude that anions can be classified as building units within this family of halogen bonding receptors. Two kinds of antiparallel dimers are observed for these dicationic receptors. An off-centered species is most frequent, present among geometrically diverse anions, and assorted receptor conformations. In contrast, the centered antiparallel dimers are observed with receptors adopting a bidentate conformation in the solid-state. While anions support the solid-state formation of dimers, the molecular geometry and characteristics (planarity, rigidity, and directionality) of arylethynyl systems increases the likelihood of dimer formation by limiting efficient packing arrangements. The significantly larger cation may have considerable influence on the solid-state packing, as similar cationic arylethynyl systems also display these dimers, suggesting.
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Affiliation(s)
- Daniel A. Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Dr, Missoula, MT 59812, USA
| | - Asia Marie S. Riel
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Dr, Missoula, MT 59812, USA
| | - Orion B. Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Dr, Missoula, MT 59812, USA
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22
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Carreño A, Páez-Hernández D, Zúñiga C, Ramírez-Osorio A, Nevermann J, Rivera-Zaldívar MM, Otero C, Fuentes JA. Prototypical cis-ruthenium(II) complexes present differential fluorescent staining in walled-cell models (yeasts). CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00714-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Hou M, Li Q, Scheiner S. Comparison between Hydrogen and Halogen Bonds in Complexes of 6‐OX‐Fulvene with Pnicogen and Chalcogen Electron Donors. Chemphyschem 2019; 20:1978-1984. [DOI: 10.1002/cphc.201900340] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Mingchang Hou
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan UT 84322–0300 USA
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24
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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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25
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Brammer L. Halogen bonding, chalcogen bonding, pnictogen bonding, tetrel bonding: origins, current status and discussion. Faraday Discuss 2019; 203:485-507. [PMID: 28980683 DOI: 10.1039/c7fd00199a] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen. This article is based upon my Closing Remarks Lecture at the 203rd Faraday Discussion meeting on Halogen Bonding in Supramolecular and Solid State Chemistry, held in Ottawa, Canada, on 10-12th July, 2017. The Discussion included papers on fundamentals and applications of halogen bonding in the solid state and solution phase. Analogous interactions involving main group elements outside group 17 were also examined. In the closing lecture and in this article these contributions have been grouped into the four themes: (a) fundamentals, (b) beyond the halogen bond, (c) characterisation, and (d) applications. The lecture and paper also include a short reflection on past work that has a bearing on the Discussion.
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Affiliation(s)
- Lee Brammer
- Department of Chemistry, University of Sheffield, Brook Hill S3 7HF, UK.
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26
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Perera MD, Aakeröy CB. Organocatalysis by a multidentate halogen-bond donor: an alternative to hydrogen-bond based catalysis. NEW J CHEM 2019. [DOI: 10.1039/c9nj01404g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Stoichiometric organocatalysis using a charge-neutral bis-iodoethynyl halogen-bond decorated scaffold.
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27
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Franchini D, Dapiaggi F, Pieraccini S, Forni A, Sironi M. Halogen bonding in the framework of classical force fields: The case of chlorine. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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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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29
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Riel AMS, Decato DA, Sun J, Massena CJ, Jessop MJ, Berryman OB. The intramolecular hydrogen bonded-halogen bond: a new strategy for preorganization and enhanced binding. Chem Sci 2018; 9:5828-5836. [PMID: 30079195 PMCID: PMC6050591 DOI: 10.1039/c8sc01973h] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/13/2018] [Indexed: 01/02/2023] Open
Abstract
Natural and synthetic molecules use weak noncovalent forces to preorganize structure and enable remarkable function. Herein, we introduce the intramolecular hydrogen bonded-halogen bond (HB-XB) as a novel method to preorganize halogen bonding (XBing) molecules, while generating a polarization-enhanced XB. Positioning a fluoroaniline between two iodopyridinium XB donors engendered intramolecular hydrogen bonding (HBing) to the electron-rich belt of both XB donors. NMR solution studies established the efficacy of the HB-XB. The receptor with HB-XBs (G2XB) displayed a nearly 9-fold increase in halide binding over control receptors. Gas-phase density functional theory conformational analysis indicated that the amine stabilizes the bidentate conformation. Furthermore, gas-phase interaction energies showed that the bidentate HB-XBs of G2XBme2+ are more than 3.2 kcal mol-1 stronger than the XBs in a control without the intramolecular HB. Additionally, crystal structures confirm that HB-XBs form tighter contacts with I- and Br- and produce receptors that are more planar. Collectively the results establish the intramolecular HB-XB as a tractable strategy to preorganize XB molecules and regulate XB strength.
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Affiliation(s)
| | - Daniel A Decato
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Jiyu Sun
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Casey J Massena
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
| | - Morly J Jessop
- University of Montana , 32 Campus Drive , Missoula , MT , USA .
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30
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Carlsson ACC, Scholfield MR, Rowe RK, Ford MC, Alexander AT, Mehl RA, Ho PS. Increasing Enzyme Stability and Activity through Hydrogen Bond-Enhanced Halogen Bonds. Biochemistry 2018; 57:4135-4147. [PMID: 29921126 PMCID: PMC6052408 DOI: 10.1021/acs.biochem.8b00603] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The construction of more stable proteins
is important in biomolecular
engineering, particularly in the design of biologics-based therapeutics.
We show here that replacing the tyrosine at position 18 (Y18) of T4
lysozyme with the unnatural amino acid m-chlorotyrosine
(mClY) increases both the thermal stability
(increasing the melting temperature by ∼1 °C and the melting
enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures
(15% higher than that of the parent enzyme at 40 °C) of this
classic enzyme. The chlorine of mClY forms
a halogen bond (XB) to the carbonyl oxygen of the peptide bond at
glycine 28 (G28) in a tight loop near the active site. In this case,
the XB potential of the typically weak XB donor Cl is shown from quantum
chemical calculations to be significantly enhanced by polarization
via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl
substituent of the tyrosyl side chain, resulting in a distinctive
synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger
halogens (bromine and iodine) are not well accommodated within this
same loop and, consequently, do not exhibit the effects on protein
stability or function associated with the HeX-B interaction. Thus,
we have for the first time demonstrated that an XB can be engineered
to stabilize and increase the activity of an enzyme, with the increased
stabilizing potential of the HeX-B further extending the application
of halogenated amino acids in the design of more stable protein therapeutics.
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Affiliation(s)
- Anna-Carin C Carlsson
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Matthew R Scholfield
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Rhianon K Rowe
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Melissa Coates Ford
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Austin T Alexander
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - Ryan A Mehl
- Department of Biochemistry & Biophysics , Oregon State University , Corvallis , Oregon 97333 , United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology , Colorado State University , Fort Collins , Colorado 80523 , United States
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31
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Gamekkanda JC, Sinha AS, Desper J, Đaković M, Aakeröy CB. Competition between hydrogen bonds and halogen bonds: a structural study. NEW J CHEM 2018. [DOI: 10.1039/c8nj00537k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O–H hydrogen-bond donors and R–CC–I halogen-bond donors are close competitors for suitable acceptor sites in solid-state assembly.
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Affiliation(s)
| | | | - John Desper
- Department of Chemistry
- Kansas State University
- Manhattan
- USA
| | - Marijana Đaković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
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32
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Abstract
The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br···S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single-crystal structure of the junction shows the geometry of the Br···S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to or slightly more stable than the analogous O acceptor, with a -3.5 kcal/mol difference in ΔΔH25°C and -0.4 kcal/mol ΔΔG25°C (including an entropic penalty ΔΔS25°C of -10 cal/(mol K)). Thus sulfur is shown to be a favorable acceptor for bromine X-bonds, extending the application of this interaction for the design of inhibitors and biological materials.
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Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - Matthew Saxton
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University , 1870 Campus Delivery, Fort Collins, Colorado 80523-1870, United States
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33
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Abstract
Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.
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Affiliation(s)
- Michal H Kolář
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo 1, I-06123 Perugia, Italy
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