1
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Winiewska-Szajewska M, Czapinska H, Kaus-Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J. Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes. Sci Rep 2022; 12:18964. [PMID: 36347916 PMCID: PMC9641685 DOI: 10.1038/s41598-022-23611-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
CK2 is a member of the CMGC group of eukaryotic protein kinases and a cancer drug target. It can be efficiently inhibited by halogenated benzotriazoles and benzimidazoles. Depending on the scaffold, substitution pattern, and pH, these compounds are either neutral or anionic. Their binding poses are dictated by a hydrophobic effect (desolvation) and a tug of war between a salt bridge/hydrogen bond (to K68) and halogen bonding (to E114 and V116 backbone oxygens). Here, we test the idea that binding poses might be controllable by pH for ligands with near-neutral pKa, using the conditionally anionic 5,6-DBBt and constitutively anionic TBBt as our models. We characterize the binding by low-volume Differential Scanning Fluorimetry (nanoDSF), Isothermal Calorimetry (ITC), Hydrogen/Deuterium eXchange (HDX), and X-ray crystallography (MX). The data indicate that the ligand pose away from the hinge dominates for the entire tested pH range (5.5-8.5). The insensitivity of the binding mode to pH is attributed to the perturbation of ligand pKa upon binding that keeps it anionic in the ligand binding pocket at all tested pH values. However, a minor population of the ligand, detectable only by HDX, shifts towards the hinge in acidic conditions. Our findings demonstrate that electrostatic (ionic) interactions predominate over halogen bonding.
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Affiliation(s)
- Maria Winiewska-Szajewska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | - Honorata Czapinska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena Kaus-Drobek
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Fricke
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Kinga Mieczkowska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Michał Dadlez
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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2
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Dammann M, Stahlecker J, Zimmermann MO, Klett T, Rotzinger K, Kramer M, Coles M, Stehle T, Boeckler FM. Screening of a Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes. J Med Chem 2022; 65:14539-14552. [DOI: 10.1021/acs.jmedchem.2c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel Dammann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Jason Stahlecker
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus O. Zimmermann
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Kilian Rotzinger
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Markus Kramer
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076Tübingen, Germany
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3
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Khursheed S, Rafiq Wani M, Shadab G, Tabassum S, Arjmand F. Synthesis, Structure Elucidation by Multi-spectroscopic Techniques and Single-crystal X-ray Diffraction of Promising Fluoro/Bromo-substituted-chromone(bpy)copper(II) Anticancer Drug Entities. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Targeting the DIO3 enzyme using first-in-class inhibitors effectively suppresses tumor growth: a new paradigm in ovarian cancer treatment. Oncogene 2021; 40:6248-6257. [PMID: 34556811 DOI: 10.1038/s41388-021-02020-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023]
Abstract
The enzyme iodothyronine deiodinase type 3 (DIO3) contributes to cancer proliferation by inactivating the tumor-suppressive actions of thyroid hormone (T3). We recently established DIO3 involvement in the progression of high-grade serous ovarian cancer (HGSOC). Here we provide a link between high DIO3 expression and lower survival in patients, similar to common disease markers such as Ki67, PAX8, CA-125, and CCNE1. These observations suggest that DIO3 is a logical target for inhibition. Using a DIO3 mimic, we developed original DIO3 inhibitors that contain a core of dibromomaleic anhydride (DBRMD) as scaffold. Two compounds, PBENZ-DBRMD and ITYR-DBRMD, demonstrated attenuated cell counts, induction in apoptosis, and a reduction in cell proliferation in DIO3-positive HGSOC cells (OVCAR3 and KURAMOCHI), but not in DIO3-negative normal ovary cells (CHOK1) and OVCAR3 depleted for DIO3 or its substrate, T3. Potent tumor inhibition with a high safety profile was further established in HGSOC xenograft model, with no effect in DIO3-depleted tumors. The antitumor effects are mediated by downregulation in an array of pro-cancerous proteins, the majority of which known to be repressed by T3. To conclude, using small molecules that specifically target the DIO3 enzyme we present a new treatment paradigm for ovarian cancer and potentially other DIO3-dependent malignancies.
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5
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Winiewska-Szajewska M, Maciejewska AM, Speina E, Poznański J, Paprocki D. Synthesis of Novel Halogenated Heterocycles Based on o-Phenylenediamine and Their Interactions with the Catalytic Subunit of Protein Kinase CK2. Molecules 2021; 26:molecules26113163. [PMID: 34070615 PMCID: PMC8198750 DOI: 10.3390/molecules26113163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 01/07/2023] Open
Abstract
Protein kinase CK2 is a highly pleiotropic protein kinase capable of phosphorylating hundreds of protein substrates. It is involved in numerous cellular functions, including cell viability, apoptosis, cell proliferation and survival, angiogenesis, or ER-stress response. As CK2 activity is found perturbed in many pathological states, including cancers, it becomes an attractive target for the pharma. A large number of low-mass ATP-competitive inhibitors have already been developed, the majority of them halogenated. We tested the binding of six series of halogenated heterocyclic ligands derived from the commercially available 4,5-dihalo-benzene-1,2-diamines. These ligand series were selected to enable the separation of the scaffold effect from the hydrophobic interactions attributed directly to the presence of halogen atoms. In silico molecular docking was initially applied to test the capability of each ligand for binding at the ATP-binding site of CK2. HPLC-derived ligand hydrophobicity data are compared with the binding affinity assessed by low-volume differential scanning fluorimetry (nanoDSF). We identified three promising ligand scaffolds, two of which have not yet been described as CK2 inhibitors but may lead to potent CK2 kinase inhibitors. The inhibitory activity against CK2α and toxicity against four reference cell lines have been determined for eight compounds identified as the most promising in nanoDSF assay.
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6
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Nandy A, Kazi I, Guha S, Sekar G. Visible-Light-Driven Halogen-Bond-Assisted Direct Synthesis of Heteroaryl Thioethers Using Transition-Metal-Free One-Pot C–I Bond Formation/C–S Cross-Coupling Reaction. J Org Chem 2021; 86:2570-2581. [DOI: 10.1021/acs.joc.0c02672] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Anuradha Nandy
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Imran Kazi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Somraj Guha
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
| | - Govindasamy Sekar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036 Tamil Nadu, India
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7
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Kasperowicz S, Marzec E, Maciejewska AM, Trzybiński D, Bretner M, Woźniak K, Poznański J, Mieczkowska K. A competition between hydrophobic and electrostatic interactions in protein-ligand systems. Binding of heterogeneously halogenated benzotriazoles by the catalytic subunit of human protein kinase CK2. IUBMB Life 2020; 72:1211-1219. [PMID: 32162783 DOI: 10.1002/iub.2271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/29/2020] [Indexed: 01/15/2023]
Abstract
A series of chlorine-substituted benzotriazole derivatives, representing all possible substitution patterns of halogen atoms attached to the benzotriazole benzene ring, were synthetized as potential inhibitors of human protein kinase CK2. Basic ADME parameters for the free solutes (hydrophobicity, electronic properties) together with their binding affinity to the catalytic subunit of protein kinase CK2 were determined with reverse-phase HPLC, spectrophotometric titration, and Thermal Shift Assay Method, respectively. The analysis of position-dependent thermodynamic contribution of a chlorine atom attached to the benzotriazole ring confirmed the previous observation for brominated benzotriazoles, in which substitution at positions 5 and 6 with bromine was found crucial for ligand binding. In all tested halogenated benzotriazoles the replacement of Br with Cl decreases the hydrophobicity, while the electronic properties remain virtually unaffected. Supramolecular architecture identified in the just resolved crystal structures of three of the four possible dichloro-benzotriazoles shows how substitution distant from the triazole ring affects the pattern of intermolecular interactions. Summarizing, the benzotriazole benzene ring substitution pattern has been identified as the main driver of ligand binding, predominating the non-specific hydrophobic effect.
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Affiliation(s)
- Sławomir Kasperowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Ewa Marzec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Damian Trzybiński
- Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Maria Bretner
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kinga Mieczkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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8
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Marzec E, Poznański J, Paprocki D. Thermodynamic contribution of iodine atom to the binding of heterogeneously polyhalogenated benzotriazoles by the catalytic subunit of human protein kinase CK2. IUBMB Life 2020; 72:1203-1210. [PMID: 32083806 DOI: 10.1002/iub.2257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/09/2020] [Indexed: 12/29/2022]
Abstract
A series of novel benzotriazole derivatives containing iodine atom(s) were synthesized. The binding of these compounds to the catalytic subunit of human protein kinase CK2 was evaluated using differential scanning fluorimetry. The obtained thermodynamic data were compared with those determined previously for the brominated and chlorinated benzotriazole analogues to get a deeper insight into the thermodynamic contribution of iodine substitution to the free energy of ligand binding. We have shown that iodine atom(s) attached to the benzene ring of benzotriazole enhance(s) its binding by the target protein. This effect is the strongest when two iodine atoms are attached at positions peripheral to the triazole ring, which according to the structures deposited in protein data bank may be indicative for the formation of the halogen bond between iodine and carbonyl groups of residues located in the hinge region of the protein. Finally, quantitative structure-activity relationship analysis pointed the solute hydrophobicity as the main factor contributing to the binding affinity.
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Affiliation(s)
- Ewa Marzec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Daniel Paprocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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9
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El-Kardocy A, Mostafa YA, Mohamed NG, Abo-Zeid MN, Hassan NA, Hetta HF, Abdel-Aal ABM. CK2 inhibition, lipophilicity and anticancer activity of new N1versus N2-substituted tetrabromobenzotriazole regioisomers. NEW J CHEM 2020. [DOI: 10.1039/d0nj01194k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Both the type and position of polar group substitutions in polybrominated benzotriazoles dramatically change their lipophilicity, kinase inhibition and anticancer activity.
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Affiliation(s)
- Ahmed El-Kardocy
- Student Research Unit
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Yaser A. Mostafa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Noha G. Mohamed
- Student Research Unit
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Mohammad Nabil Abo-Zeid
- Department of Pharmaceutical Analytical Chemistry
- Faculty of Pharmacy
- Assiut University
- Assiut 71526
- Egypt
| | - Nivin A. Hassan
- Cancer Biology Department
- South Egypt Cancer Institute, Assiut University
- Assiut
- Egypt
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology
- Faculty of Medicine
- Assiut University
- Assiut
- Egypt
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10
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Ageshina AA, Chesnokov GA, Topchiy MA, Alabugin IV, Nechaev MS, Asachenko AF. Making endo-cyclizations favorable again: a conceptually new synthetic approach to benzotriazoles via azide group directed lithiation/cyclization of 2-azidoaryl bromides. Org Biomol Chem 2019; 17:4523-4534. [PMID: 30994147 DOI: 10.1039/c9ob00615j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although benzotriazoles are important and ubiquitous, currently there is only one conceptual approach to their synthesis: bridging the two ortho-amino groups with an electrophilic nitrogen atom. Herein, we disclose a new practical alternative - the endo-cyclization of 2-azidoaryl lithiums obtained in situ from 2-azido-aryl bromides. The scope of the reaction is illustrated using twenty-four examples with a variety of alkyl, alkoxy, perfluoroalkyl, and halogen substituents. We found that the directing effect of the azide group allows selective metal-halogen exchange in aryl azides containing several bromine atoms. Furthermore, (2-bromophenyl)diazomethane undergoes similar cyclization to give an indazole. Thus, cyclizations of aryl lithiums containing an ortho-X = Y = Z group emerge as a new general approach for the synthesis of aromatic heterocycles. DFT computations suggested that the observed endo-selectivity applies to the anionic cyclizations of other functionalities that undergo "1,1-additions" (i.e., azides, diazo compounds, and isonitriles). In contrast, cyclizations with the heteroatomic functionalities that follow the "1,2-addition" pattern (cyanates, thiocyanates, isocyanates, isothiocyanates, and nitriles) prefer the exo-cyclization path. Hence, such reactions expand the current understanding of stereoelectronic factors in anionic cyclizations.
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Affiliation(s)
- Alexandra A Ageshina
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Leninskiy prospect 29, Russian Federation.
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11
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Szymaniec-Rutkowska A, Bugajska E, Kasperowicz S, Mieczkowska K, Maciejewska AM, Poznański J. Does the partial molar volume of a solute reflect the free energy of hydrophobic solvation? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Rational drug-design approach supported with thermodynamic studies - a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Sci Rep 2019; 9:11018. [PMID: 31358826 PMCID: PMC6662822 DOI: 10.1038/s41598-019-47404-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/15/2019] [Indexed: 12/24/2022] Open
Abstract
Numerous inhibitors of protein kinases act on the basis of competition, targeting the ATP binding site. In this work, we present a procedure of rational design of a bi-substrate inhibitor, complemented with biophysical assays. The inhibitors of this type are commonly engineered by combining ligands carrying an ATP-like part with a peptide or peptide-mimicking fragment that determines specificity. Approach presented in this paper led to generation of a specific system for independent screening for efficient ligands and peptides, by means of thermodynamic measurements, that assessed the ability of the identified ligand and peptide to combine into a bi-substrate inhibitor. The catalytic subunit of human protein kinase CK2 was used as the model target. Peptide sequence was optimized using peptide libraries [KGDE]-[DE]-[ST]-[DE]3-4-NH2, originated from the consensus CK2 sequence. We identified KESEEE-NH2 peptide as the most promising one, whose binding affinity is substantially higher than that of the reference RRRDDDSDDD peptide. We assessed its potency to form an efficient bi-substrate inhibitor using tetrabromobenzotriazole (TBBt) as the model ATP-competitive inhibitor. The formation of ternary complex was monitored using Differential Scanning Fluorimetry (DSF), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC).
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13
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Kuznetsov ML. Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A) nY-X···X-Z(B) m] Type (X = Cl, Br, I). Molecules 2019; 24:E2733. [PMID: 31357615 PMCID: PMC6695802 DOI: 10.3390/molecules24152733] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/25/2019] [Indexed: 01/31/2023] Open
Abstract
Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.
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Affiliation(s)
- Maxim L Kuznetsov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal.
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14
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Govindaraj V, Ungati H, Jakka SR, Bose S, Mugesh G. Directing Traffic: Halogen‐Bond‐Mediated Membrane Transport. Chemistry 2019; 25:11180-11192. [DOI: 10.1002/chem.201902243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/15/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Vijayakumar Govindaraj
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Harinarayana Ungati
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Surendar R. Jakka
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Sritama Bose
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
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15
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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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16
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Wang PF, Neiner A, Lane TR, Zorn KM, Ekins S, Kharasch ED. Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches. Mol Pharm 2019; 16:898-906. [PMID: 30589555 PMCID: PMC9121441 DOI: 10.1021/acs.molpharmaceut.8b01214] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ketamine is analgesic at anesthetic and subanesthetic doses, and it has been used recently to treat depression. Biotransformation mediates ketamine effects, influencing both systemic elimination and bioactivation. CYP2B6 is the major catalyst of hepatic ketamine N-demethylation and metabolism at clinically relevant concentrations. Numerous CYP2B6 substrates contain halogens. CYP2B6 readily forms halogen-protein (particularly Cl-π) bonds, which influence substrate selectivity and active site orientation. Ketamine is chlorinated, but little is known about the metabolism of halogenated analogs. This investigation evaluated halogen substitution effects on CYP2B6-catalyzed ketamine analogs N-demethylation in vitro and modeled interactions with CYP2B6 using various computational approaches. Ortho phenyl ring halogen substituent changes caused substantial (18-fold) differences in Km, on the order of Br (bromoketamine, 10 μM) < Cl < F < H (deschloroketamine, 184 μM). In contrast, Vmax varied minimally (83-103 pmol/min/pmol CYP). Thus, apparent substrate binding affinity was the major consequence of halogen substitution and the major determinant of N-demethylation. Docking poses of ketamine and analogs were similar, sharing a π-stack with F297. Libdock scores were deschloroketamine < bromoketamine < ketamine < fluoroketamine. A Bayesian log Km model generated with Assay Central had a ROC of 0.86. The probability of activity at 15 μM for ketamine and analogs was predicted with this model. Deschloroketamine scores corresponded to the experimental Km, but the model was unable to predict activity with fluoroketamine. The binding pocket of CYP2B6 also suggested a hydrophobic component to substrate docking, on the basis of a strong linear correlation ( R2 = 0.92) between lipophilicity ( Alog P) and metabolism (log Km) of ketamine and analogs. This property may be the simplest design criteria to use when considering similar compounds and CYP2B6 affinity.
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Affiliation(s)
- Pan-Fen Wang
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC
| | - Alicia Neiner
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO
| | - Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510, Raleigh, NC
| | - Kimberley M. Zorn
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510, Raleigh, NC
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510, Raleigh, NC
| | - Evan D. Kharasch
- Department of Anesthesiology, Duke University School of Medicine, Durham, NC
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17
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Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM. De novo active sites for resurrected Precambrian enzymes. Nat Commun 2017; 8:16113. [PMID: 28719578 PMCID: PMC5520109 DOI: 10.1038/ncomms16113] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/30/2017] [Indexed: 11/22/2022] Open
Abstract
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
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Affiliation(s)
- Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Adela M. Candel
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | - Dennis M. Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - David Pantoja-Uceda
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Quimica Organica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Eric A. Gaucher
- School of Biology, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30322, USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marta Bruix
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada Avenida de la Palmeras 4, Granada, 18100 Armilla, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
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18
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1,N 6-α-hydroxypropanoadenine, the acrolein adduct to adenine, is a substrate for AlkB dioxygenase. Biochem J 2017; 474:1837-1852. [PMID: 28408432 DOI: 10.1042/bcj20161008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022]
Abstract
1,N6-α-hydroxypropanoadenine (HPA) is an exocyclic DNA adduct of acrolein - an environmental pollutant and endocellular oxidative stress product. Escherichia coli AlkB dioxygenase belongs to the superfamily of α-ketoglutarate (αKG)- and iron-dependent dioxygenases which remove alkyl lesions from bases via an oxidative mechanism, thereby restoring native DNA structure. Here, we provide in vivo and in vitro evidence that HPA is mutagenic and is effectively repaired by AlkB dioxygenase. HPA generated in plasmid DNA caused A → C and A → T transversions and, less frequently, A → G transitions. The lesion was efficiently repaired by purified AlkB protein; the optimal pH, Fe(II), and αKG concentrations for this reaction were determined. In vitro kinetic data show that the protonated form of HPA is preferentially repaired by AlkB, albeit the reaction is stereoselective. Moreover, the number of reaction cycles carried out by an AlkB molecule remains limited. Molecular modeling of the T(HPA)T/AlkB complex demonstrated that the R stereoisomer in the equatorial conformation of the HPA hydroxyl group is strongly preferred, while the S stereoisomer seems to be susceptible to AlkB-directed oxidative hydroxylation only when HPA adopts the syn conformation around the glycosidic bond. In addition to the biochemical activity assays, substrate binding to the protein was monitored by differential scanning fluorimetry allowing identification of the active protein form, with cofactor and cosubstrate bound, and monitoring of substrate binding. In contrast FTO, a human AlkB homolog, failed to bind an ssDNA trimer carrying HPA.
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19
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ITC-derived binding affinity may be biased due to titrant (nano)-aggregation. Binding of halogenated benzotriazoles to the catalytic domain of human protein kinase CK2. PLoS One 2017; 12:e0173260. [PMID: 28273138 PMCID: PMC5342230 DOI: 10.1371/journal.pone.0173260] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/17/2017] [Indexed: 12/13/2022] Open
Abstract
The binding of four bromobenzotriazoles to the catalytic subunit of human protein kinase CK2 was assessed by two complementary methods: Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC). New algorithm proposed for the global analysis of MST pseudo-titration data enabled reliable determination of binding affinities for two distinct sites, a relatively strong one with the Kd of the order of 100 nM and a substantially weaker one (Kd > 1 μM). The affinities for the strong binding site determined for the same protein-ligand systems using ITC were in most cases approximately 10-fold underestimated. The discrepancy was assigned directly to the kinetics of ligand nano-aggregates decay occurring upon injection of the concentrated ligand solution to the protein sample. The binding affinities determined in the reverse ITC experiment, in which ligands were titrated with a concentrated protein solution, agreed with the MST-derived data. Our analysis suggests that some ITC-derived Kd values, routinely reported together with PDB structures of protein-ligand complexes, may be biased due to the uncontrolled ligand (nano)-aggregation, which may occur even substantially below the solubility limit.
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20
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Jin RZ, Li YL, Wang XS. One-Pot Ullmann C-N Coupling Cyclization Toward Domino Synthesis of Fused Hexacyclic Quinolinotriazoloacridinones Catalyzed by CuI/L-Proline. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Rong-Zhang Jin
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthesis for Functional Materials; Jiangsu Normal University; Xuzhou Jiangsu 221116 China
| | - Yu-Ling Li
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthesis for Functional Materials; Jiangsu Normal University; Xuzhou Jiangsu 221116 China
| | - Xiang-Shan Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthesis for Functional Materials; Jiangsu Normal University; Xuzhou Jiangsu 221116 China
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21
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Abstract
The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
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Affiliation(s)
- Gabriella Cavallo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Pierangelo Metrangolo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Roberto Milani
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Tullio Pilati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Arri Priimagi
- Department
of Chemistry and Bioengineering, Tampere
University of Technology, Korkeakoulunkatu 8, FI-33101 Tampere, Finland
| | - Giuseppe Resnati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Giancarlo Terraneo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
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22
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Zhuang S, Wang H, Ding K, Wang J, Pan L, Lu Y, Liu Q, Zhang C. Interactions of benzotriazole UV stabilizers with human serum albumin: Atomic insights revealed by biosensors, spectroscopies and molecular dynamics simulations. CHEMOSPHERE 2016; 144:1050-9. [PMID: 26454115 DOI: 10.1016/j.chemosphere.2015.09.085] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 05/08/2023]
Abstract
Benzotriazole UV stabilizers (BZTs) belong to one prominent group of ultraviolet (UV) stabilizers and are widely used in various plastics materials. Their large production volumes, frequent detections in the environment and potential toxicities have raised increasing public concern. BZTs can be transported in vivo by transport proteins in plasma and the binding association to transport proteins may serve as a significant parameter to evaluate the bioaccumulative potential. We utilized a novel HSA biosensor, circular dichroism spectroscopy, fluorescence spectroscopy to detect the dynamic interactions of six BZTs (UV-326, UV-327, UV-328, UV-329, UV-P, and BZT) with human serum albumin (HSA), and characterized the corresponding structure-activity relationships (SAR) by molecular dynamics simulations. All test BZTs potently bind at Sudlow site I of HSA with a binding constant of 10(4) L/mol at 298 K. Minor changes in the moieties of BZTs affect their interactions with HSA and differently induce conformations of HSA. Their binding reduced electrochemical impedance spectra and α-helix content of HSA, caused slight red-shifted emission, and changed fluorescence lifetime components of HSA in a concentration-dependent mode. UV-327 and UV-329 form hydrogen bonds with HSA, while UV-329, UV-P and BZT bind HSA with more favorable electrostatic interactions. Our in vitro and in silico study offered a significant framework toward the understanding of risk assessment of BZTs and provides guide for future design of environmental benign BZTs-related materials.
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Affiliation(s)
- Shulin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316022, China.
| | - Haifei Wang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316022, China
| | - Keke Ding
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiaying Wang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liumeng Pan
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanli Lu
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Qingjun Liu
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Chunlong Zhang
- Department of Environmental Sciences, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX 77058, USA
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23
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Machara A, Konvalinka J, Kotora M. A MODULAR SYNTHESIS OFN-BENZOTRIAZOLE UREAS USING ALKYLATION OF 5-NITROBENZOTRIAZOLE. ChemistrySelect 2016. [DOI: 10.1002/slct.201600025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Aleš Machara
- Department of Organic Chemistry, Faculty of Science; Charles University in Prague, Hlavova 8; 128 43 Prague 2 Czech Republic
| | - Jan Konvalinka
- Department of Biochemistry, Faculty of Science; Charles University in Prague; Hlavova 8 128 43 Prague 2
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo n.2 166 10 Prague 6 Czech Republic
| | - Martin Kotora
- Department of Organic Chemistry, Faculty of Science; Charles University in Prague, Hlavova 8; 128 43 Prague 2 Czech Republic
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24
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Jin RZ, Li YL, Wang XS. An efficient synthesis of 11-aryl-10-oxo-7,8,10,11-tetrahydro-1H-[1,2,3]triazolo [4′,5′:3,4]benzo[1,2-b][1,6]naphthyridine derivatives under catalyst-free conditions. HETEROCYCL COMMUN 2015. [DOI: 10.1515/hc-2015-0050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA three-component reaction of an aromatic aldehyde, 1H-benzo[d][1,2,3]triazol-5-amine and tert-butyl 2,4-dioxopiperidine-1-carboxylate in refluxing EtOH under catalyst-free conditions furnishes the title compounds in high yields.
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Affiliation(s)
- Rong-Zhang Jin
- 1School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou, Jiangsu 221116, P.R. China
| | - Yu-Ling Li
- 1School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou, Jiangsu 221116, P.R. China
| | - Xiang-Shan Wang
- 1School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou, Jiangsu 221116, P.R. China
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25
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Winiewska M, Kucińska K, Makowska M, Poznański J, Shugar D. Thermodynamics parameters for binding of halogenated benzotriazole inhibitors of human protein kinase CK2α. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1708-17. [PMID: 25891901 DOI: 10.1016/j.bbapap.2015.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
The interaction of human CK2α (hCK2α) with nine halogenated benzotriazoles, TBBt and its analogues representing all possible patterns of halogenation on the benzene ring of benzotriazole, was studied by biophysical methods. Thermal stability of protein-ligand complexes, monitored by calorimetric (DSC) and optical (DSF) methods, showed that the increase in the mid-point temperature for unfolding of protein-ligand complexes (i.e. potency of ligand binding to hCK2α) follow the inhibitory activities determined by biochemical assays. The dissociation constant for the ATP-hCK2α complex was estimated with the aid of microscale thermophoresis (MST) as 4.3±1.8 μM, and MST-derived dissociation constants determined for halogenated benzotriazoles, when converted according to known ATP concentrations, perfectly reconstruct IC50 values determined by the biochemical assays. Ligand-dependent quenching of tyrosine fluorescence, together with molecular modeling and DSC-derived heats of unfolding, support the hypothesis that halogenated benzotriazoles bind in at least two alternative orientations, and those that are efficient hCK2α inhibitors bind in the orientation which TBBt adopts in its complex with maize CK2α. DSC-derived apparent heat for ligand binding (ΔΔHbind) is driven by intermolecular electrostatic interactions between Lys68 and the triazole ring of the ligand, as indicated by a good correlation between ΔΔHbind and ligand pKa. Overall results, additionally supported by molecular modeling, confirm that a balance of hydrophobic and electrostatic interactions contribute predominantly (~40 kJ/mol), relative to possible intermolecular halogen/hydrogen bonding (less than 10 kJ/mol), in binding of halogenated benzotriazoles to the ATP-binding site of hCK2α. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Maria Winiewska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Katarzyna Kucińska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Małgorzata Makowska
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
| | - David Shugar
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
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26
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Winiewska M, Makowska M, Maj P, Wielechowska M, Bretner M, Poznański J, Shugar D. Thermodynamic parameters for binding of some halogenated inhibitors of human protein kinase CK2. Biochem Biophys Res Commun 2014; 456:282-7. [PMID: 25450618 DOI: 10.1016/j.bbrc.2014.11.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 11/19/2014] [Indexed: 01/20/2023]
Abstract
The interaction of human CK2α with a series of tetrabromobenzotriazole (TBBt) and tetrabromobenzimidazole (TBBz) analogs, in which one of the bromine atoms proximal to the triazole/imidazole ring is replaced by a methyl group, was studied by biochemical (IC50) and biophysical methods (thermal stability of protein-ligand complex monitored by DSC and fluorescence). Two newly synthesized tri-bromo derivatives display inhibitory activity comparable to that of the reference compounds, TBBt and TBBz, respectively. DSC analysis of the stability of protein-ligand complexes shows that the heat of ligand binding (Hbind) is driven by intermolecular electrostatic interactions involving the triazole/imidazole ring, as indicated by a strong correlation between Hbind and ligand pKa. Screening, based on fluorescence-monitored thermal unfolding of protein-ligand complexes, gave comparable results, clearly identifying ligands that most strongly bind to the protein. Overall results, additionally supported by molecular modeling, confirm that a balance of hydrophobic and electrostatic interactions contribute predominantly, relative to possible intermolecular halogen bonding, in binding of the ligands to the CK2α ATP-binding site.
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Affiliation(s)
- Maria Winiewska
- Institute of Biochemistry and Biophysics PAS, Warszawa, Poland
| | | | - Piotr Maj
- Institute of Biochemistry and Biophysics PAS, Warszawa, Poland; Nencki Institute of Experimental Biology PAS, Warszawa, Poland
| | | | - Maria Bretner
- Warsaw University of Technology, Faculty of Chemistry, Warszawa, Poland
| | | | - David Shugar
- Institute of Biochemistry and Biophysics PAS, Warszawa, Poland
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27
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Poznański J, Poznańska A, Shugar D. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor. PLoS One 2014; 9:e99984. [PMID: 24933273 PMCID: PMC4059718 DOI: 10.1371/journal.pone.0099984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 05/21/2014] [Indexed: 01/13/2023] Open
Abstract
Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.
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Affiliation(s)
- Jarosław Poznański
- Biophysics Department, Institute of Biochemistry and Biophysics PAS, Warszawa, Poland
- * E-mail: (JP); (DS)
| | - Anna Poznańska
- Centre for Monitoring and Analyses of Population Health Status, National Institute of Public Health - National Institute of Hygiene, Warszawa, Poland
| | - David Shugar
- Institute of Biochemistry and Biophysics PAS, Warszawa, Poland
- * E-mail: (JP); (DS)
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Abstract
Halogens are atypical elements in biology, but are common as substituents in ligands, including thyroid hormones and inhibitors, which bind specifically to proteins and nucleic acids. The short-range, stabilizing interactions of halogens - now seen as relatively common in biology - conform generally to halogen bonds characterized in small molecule systems and as described by the σ-hole model. The unique properties of biomolecular halogen bonds (BXBs), particularly in their geometric and energetic relationship to classic hydrogen bonds, make them potentially powerful tools for inhibitor design and molecular engineering. This chapter reviews the current research on BXBs, focusing on experimental studies on their structure-energy relationships, how these studies inform the development of computational methods to model BXBs, and considers how BXBs can be applied to the rational design of more effective inhibitors against therapeutic targets and of new biological-based materials.
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Affiliation(s)
- P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA,
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29
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Gyenis L, Kuś A, Bretner M, Litchfield DW. Functional proteomics strategy for validation of protein kinase inhibitors reveals new targets for a TBB-derived inhibitor of protein kinase CK2. J Proteomics 2013; 81:70-9. [DOI: 10.1016/j.jprot.2012.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/13/2012] [Accepted: 09/16/2012] [Indexed: 01/01/2023]
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30
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Poznański J, Shugar D. Halogen bonding at the ATP binding site of protein kinases: preferred geometry and topology of ligand binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1381-6. [PMID: 23376187 DOI: 10.1016/j.bbapap.2013.01.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/23/2013] [Indexed: 11/25/2022]
Abstract
Halogenated ligands have been widely developed as potent, and frequently selective, inhibitors of protein kinases (PK). Herein, all structures of protein kinases complexed with a halogenated ligand, identified in the PDB, were analyzed in the context of eventual contribution of halogen bonding to protein-ligand interactions. Global inspection shows that two carbonyl groups of residues located in the hinge region are the most abundant halogen bond acceptors. In contrast to solution data, well-defined water molecules, located at sites conserved across most PK structures, are also involved in halogen bonding. Analysis of cumulative distributions of halogen-acceptor distances shows that structures displaying short contacts involving a halogen atom are overpopulated, contributing together to clearly defined maxima of 2.82, 2.91 and 2.94Å for chlorine, bromine and iodine, respectively. The angular preference of a halogen bond favors ideal topology (180°, 120°) for iodine. For bromine the distribution is much more dispersed, and no such preference was found for chlorine. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland.
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Monbaliu JCM, Beagle LK, Hansen FK, Stevens CV, McArdle C, Katritzky AR. Capture of benzotriazole-based Mannich electrophiles by CH-acidic compounds. RSC Adv 2013. [DOI: 10.1039/c3ra22826f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Isomeric mono-, di-, and tri-bromobenzo-1H-triazoles as inhibitors of human protein kinase CK2α. PLoS One 2012; 7:e48898. [PMID: 23155426 PMCID: PMC3498355 DOI: 10.1371/journal.pone.0048898] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 10/03/2012] [Indexed: 02/03/2023] Open
Abstract
To further clarify the role of the individual bromine atoms of 4,5,6,7-tetrabromotriazole (TBBt), a relatively selective inhibitor of protein kinase CK2, we have examined the inhibition (IC(50)) of human CK2α by the two mono-, the four di-, and the two tri- bromobenzotriazoles relative to that of TBBt. Halogenation of the central vicinal C(5)/C(6) atoms proved to be a key factor in enhancing inhibitory activity, in that 5,6-di-Br(2)Bt and 4,5,6-Br(3)Bt were almost as effective inhibitors as TBBt, notwithstanding their marked differences in pK(a) for dissociation of the triazole proton. The decrease in pK(a) on halogenation of the peripheral C(4)/C(7) atoms virtually nullifies the gain due to hydrophobic interactions, and does not lead to a decrease in IC(50). Molecular modeling of structures of complexes of the ligands with the enzyme, as well as QSAR analysis, pointed to a balance of hydrophobic and electrostatic interactions as a discriminator of inhibitory activity. The role of halogen bonding remains debatable, as originally noted for the crystal structure of TBBt with CK2α (pdb1j91). Finally we direct attention to the promising applicability of our series of well-defined halogenated benzotriazoles to studies on inhibition of kinases other than CK2.
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Maciejewska AM, Poznanski J, Kaczmarska Z, Krowisz B, Nieminuszczy J, Polkowska-Nowakowska A, Grzesiuk E, Kusmierek JT. AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action. J Biol Chem 2012; 288:432-41. [PMID: 23148216 DOI: 10.1074/jbc.m112.353342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Efficient repair by Escherichia coli AlkB dioxygenase of exocyclic DNA adducts 3,N(4)-ethenocytosine, 1,N(6)-ethenoadenine, 3,N(4)-α-hydroxyethanocytosine, and reported here for the first time 3,N(4)-α-hydroxypropanocytosine requires higher Fe(II) concentration than the reference 3-methylcytosine. The pH optimum for the repair follows the order of pK(a) values for protonation of the adduct, suggesting that positively charged substrates favorably interact with the negatively charged carboxylic group of Asp-135 side chain in the enzyme active center. This interaction is supported by molecular modeling, indicating that 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine are bound to AlkB more favorably in their protonated cationic forms. An analysis of the pattern of intermolecular interactions that stabilize the location of the ligand points to a role of Asp-135 in recognition of the adduct in its protonated form. Moreover, ab initio calculations also underline the role of substrate protonation in lowering the free energy barrier of the transition state of epoxidation of the etheno adducts studied. The observed time courses of repair of mixtures of stereoisomers of 3,N(4)-α-hydroxyethanocytosine or 3,N(4)-α-hydroxypropanocytosine are unequivocally two-exponential curves, indicating that the respective isomers are repaired by AlkB with different efficiencies. Molecular modeling of these adducts bound by AlkB allowed evaluation of the participation of their possible conformational states in the enzymatic reaction.
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Wąsik R, Wińska P, Poznański J, Shugar D. Synthesis and physico-chemical properties in aqueous medium of all possible isomeric bromo analogues of benzo-1H-triazole, potential inhibitors of protein kinases. J Phys Chem B 2012; 116:7259-68. [PMID: 22632480 DOI: 10.1021/jp301561x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In ongoing studies on the role of the individual bromine atoms of 4,5,6,7-tetrabromobenzotriazole (TBBt) in its relatively selective inhibition of protein kinase CK2α, we have prepared all the possible two mono-, four di-, and two tri-bromobenzotriazoles and determined their physicochemical properties in aqueous medium. They exhibited a general trend of a decrease in solubility with an increase in the number of bromines on the benzene ring, significantly modulated by the pattern of substitution. For a given number of attached bromines, this was directly related to the electronic effects resulting from different sites of substitution, leading to marked variations of pK(a) values for dissociation of the triazole proton. Experimental data (pK(a), solubility) and ab initio calculations demonstrated that hydration of halogenated benzotriazoles is driven by a subtle balance of hydrophobic and polar interactions. The combination of QM-derived free energies for solvation and proton dissociations was found to be a reasonably good predictor of inhibitory activity of halogenated benzotriazoles vs CK2α. Since the pattern of halogenation of the benzene ring of benzotriazole has also been shown to be one of the determinants of inhibitory potency vs some viruses and viral enzymes, the present comprehensive description of their physicochemical properties should prove helpful in efforts to elucidate reaction mechanisms, including possible halogen bonding, and the search for more selective and potent inhibitors.
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Affiliation(s)
- Romualda Wąsik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warszawa, Poland
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Shirman T, Kaminker R, Freeman D, van der Boom ME. Halogen-bonding mediated stepwise assembly of gold nanoparticles onto planar surfaces. ACS NANO 2011; 5:6553-6563. [PMID: 21749110 DOI: 10.1021/nn201923q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study halogen bonding (XB) is used as the driving force for the noncovalent assembly of gold nanoparticles (AuNPs) on silicon and quartz substrates functionalized with organic monolayers. The AuNPs are functionalized with XB-donor ligands, whereas the monolayers have pyridine groups as XB-acceptors. The surface-confined systems are formed by iteratively exposing the monolayers to solutions of organic cross-linkers having 2-4 pyridine groups and functionalized AuNPs. UV-vis spectroscopy, atomic force microscopy (AFM), and scanning electron microscopy (SEM) reveal how the structure of the resulting surface-bound assemblies are controlled by (i) the properties of the monolayers, (ii) the molecular structure and the number of XB binding sites of the organic cross-linker, and (iii) the number of functionalized AuNP and cross-linker deposition steps. Moreover, these structures exhibit surface-enhanced Raman scattering and significant changes are observed in the morphology of some of the surface-bound assemblies upon aging.
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Affiliation(s)
- Tanya Shirman
- Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot 76100, Israel
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Dobeš P, Řezáč J, Fanfrlík J, Otyepka M, Hobza P. Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails. J Phys Chem B 2011; 115:8581-9. [DOI: 10.1021/jp202149z] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Petr Dobeš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic
- Center of Molecular Biology and Gene Therapy, Department of Internal Medicine − Hematooncology, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
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Lu Y, Li H, Zhu X, Zhu W, Liu H. How Does Halogen Bonding Behave in Solution? A Theoretical Study Using Implicit Solvation Model. J Phys Chem A 2011; 115:4467-75. [DOI: 10.1021/jp111616x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yunxiang Lu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Haiying Li
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Xiang Zhu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglai Liu
- Key Laboratory for Advanced Material and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
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