351
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Schmidt C, Karge B, Misgeld R, Prokop A, Franke R, Brönstrup M, Ott I. Gold(I) NHC Complexes: Antiproliferative Activity, Cellular Uptake, Inhibition of Mammalian and Bacterial Thioredoxin Reductases, and Gram-Positive Directed Antibacterial Effects. Chemistry 2017; 23:1869-1880. [DOI: 10.1002/chem.201604512] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Claudia Schmidt
- Institute of Medicinal and Pharmaceutical Chemistry; Technische Universität Braunschweig; Beethovenstrasse 55 38106 Braunschweig Germany
| | - Bianka Karge
- Department of Chemical Biology; Helmholtz Centre for Infection Research GmbH; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Rainer Misgeld
- Department of Paedriatric Oncology; Children's Hospital Cologne; Amsterdamer Strasse 59 50735 Cologne Germany
| | - Aram Prokop
- Department of Paedriatric Oncology; Children's Hospital Cologne; Amsterdamer Strasse 59 50735 Cologne Germany
| | - Raimo Franke
- Department of Chemical Biology; Helmholtz Centre for Infection Research GmbH; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Mark Brönstrup
- Department of Chemical Biology; Helmholtz Centre for Infection Research GmbH; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Ingo Ott
- Institute of Medicinal and Pharmaceutical Chemistry; Technische Universität Braunschweig; Beethovenstrasse 55 38106 Braunschweig Germany
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352
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Borges NM, Kenny PW, Montanari CA, Prokopczyk IM, Ribeiro JFR, Rocha JR, Sartori GR. The influence of hydrogen bonding on partition coefficients. J Comput Aided Mol Des 2017; 31:163-181. [PMID: 28054187 DOI: 10.1007/s10822-016-0002-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.
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Affiliation(s)
- Nádia Melo Borges
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Peter W Kenny
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil.
| | - Carlos A Montanari
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Igor M Prokopczyk
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Jean F R Ribeiro
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Josmar R Rocha
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
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353
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Schoder S, Schalley CA. Orthogonal switching of self-sorting processes in a stimuli-responsive library of cucurbit[8]uril complexes. Chem Commun (Camb) 2017; 53:9546-9549. [DOI: 10.1039/c7cc05469f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-sorting processes in dynamic libraries of cucurbit[8]uril complexes can be switched orthogonally by pH and redox stimuli.
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Affiliation(s)
- Stefan Schoder
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- 14195 Berlin
- Germany
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354
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Paikar A, Pramanik A, Das T, Haldar D. A self-assembled peptide mimetic of a tubular host and a supramolecular polymer. Polym Chem 2017. [DOI: 10.1039/c6py01955b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A tripeptide self-assembles in a helical manner to form a tubular host-like supramolecular nanotube. The tube with a hydrophobic core has been used to develop a supramolecular polymer.
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Affiliation(s)
- Arpita Paikar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur 741246
- India
| | - Apurba Pramanik
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur 741246
- India
| | - Tanmay Das
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur 741246
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur 741246
- India
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355
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Pitchaimani J, Kundu A, Karthikeyan S, Anthony SP, Moon D, Madhu V. A crab claw shaped molecular receptor for selective recognition of picric acid: supramolecular self-assembly mediated aggregation induced emission and color change. CrystEngComm 2017. [DOI: 10.1039/c7ce00642j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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356
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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357
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Kinoshita M, Hayashi T. Unified elucidation of the entropy-driven and -opposed hydrophobic effects. Phys Chem Chem Phys 2017; 19:25891-25904. [DOI: 10.1039/c7cp05160c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The association of nonpolar solutes is generally believed to be entropy driven, which has been shown to be true for the contact of small molecules, ellipsoids, and plates.
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358
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Dumele O, Schreib B, Warzok U, Trapp N, Schalley CA, Diederich F. Halogen-Bonded Supramolecular Capsules in the Solid State, in Solution, and in the Gas Phase. Angew Chem Int Ed Engl 2016; 56:1152-1157. [DOI: 10.1002/anie.201610884] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Oliver Dumele
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
- Department of Chemistry; Northwestern University; 2145 Sheridan Rd Evanston IL 60208 USA
| | - Benedikt Schreib
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Ulrike Warzok
- Institut für Chemie und Biochemie der; Freien Universität; Takustrasse 3 14195 Berlin Germany
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie der; Freien Universität; Takustrasse 3 14195 Berlin Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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359
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Dumele O, Schreib B, Warzok U, Trapp N, Schalley CA, Diederich F. Halogenverbrückte supramolekulare Kapseln im Festkörper, in Lösung und in der Gasphase. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610884] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Oliver Dumele
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
- Department of Chemistry; Northwestern University; 2145 Sheridan Rd Evanston IL 60208 USA
| | - Benedikt Schreib
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Ulrike Warzok
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
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360
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Zhang Q, Xu Z, Zhu W. The Underestimated Halogen Bonds Forming with Protein Side Chains in Drug Discovery and Design. J Chem Inf Model 2016; 57:22-26. [DOI: 10.1021/acs.jcim.6b00628] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Qian Zhang
- Department
of Computer Science and Technology, East China Normal University, Shanghai 200241, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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361
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Ishikawa Y. Crystal structure of 7-iodo-4-oxo-4 H-chromene-3-carbaldehyde. Acta Crystallogr E Crystallogr Commun 2016; 72:1724-1727. [PMID: 27980816 PMCID: PMC5137594 DOI: 10.1107/s2056989016016972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 11/10/2022]
Abstract
In the title compound, C10H5IO3, an iodinated 3-formyl-chromone derivative, the non-H atoms are essentially coplanar (r.m.s. deviation = 0.0344 Å), with the largest deviation from the least-squares plane [0.101 (3) Å] being found for the formyl O atom. In the crystal, mol-ecules are linked through stacking inter-actions [centroid-centroid distance between the benzene rings = 3.700 (3) Å] and C-H⋯O hydrogen bonds. Halogen bonds between the I atoms at 7-position and the formyl O atoms [I1⋯O3 = 3.056 (2) Å, C6-I1⋯O3 = 173.18 (8)° and I1⋯O3-C10 = 111.12 (18)°] are also formed along [110], resulting in sheets perpendicular to the c axis, constructed by C-H⋯O hydrogen bonds and I⋯O halogen bonds.
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Affiliation(s)
- Yoshinobu Ishikawa
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku Shizuoka 422-8526, Japan
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362
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Zhang SY, Li J, Zeng Y, Wen HR, Du ZY. Hydrogen-bond-directed assemblies of [La(18-crown-6)(H 2 O) 4 ](BiCl 6 )·3H 2 O and [Nd(18-crown-6)(H 2 O) 4 ](BiCl 6 )·3.5H 2 O regulated by different symmetries. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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363
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Bell DR, Qi R, Jing Z, Xiang JY, Mejias C, Schnieders MJ, Ponder JW, Ren P. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field. Phys Chem Chem Phys 2016; 18:30261-30269. [PMID: 27254477 PMCID: PMC5102783 DOI: 10.1039/c6cp02509a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.
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Affiliation(s)
- David R Bell
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jin Yu Xiang
- Computational and Molecular Biophysics Program, Washington Univ. School of Medicine, Saint Louis, Missouri 63130, United States
| | - Christopher Mejias
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Michael J Schnieders
- Department of Biomedical Engineering and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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364
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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365
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Shawon J, Khan AM, Rahman A, Hoque MM, Khan MAK, Sarwar MG, Halim MA. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations. Interdiscip Sci 2016; 10:525-537. [PMID: 27696206 DOI: 10.1007/s12539-016-0186-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/20/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Abstract
Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.
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Affiliation(s)
- Jakaria Shawon
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Adhip Rahman
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Abdul Kader Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961, Saudi Arabia
| | - Mohammed G Sarwar
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh.
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
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366
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Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res 2016; 44:8052-64. [PMID: 27566147 PMCID: PMC5041495 DOI: 10.1093/nar/gkw725] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/12/2022] Open
Abstract
RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
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Affiliation(s)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Karen Mercier
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Jonas Nascimento Conde
- Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Daniella M Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Fatima-Ezzahra Hibti
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Tom Hassell
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Carlos Martinez
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Anil K Sood
- Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Terry P Lybrand
- Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chiraz Frydman
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Robson Q Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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367
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Lazar AI, Biedermann F, Mustafina KR, Assaf KI, Hennig A, Nau WM. Nanomolar Binding of Steroids to Cucurbit[n]urils: Selectivity and Applications. J Am Chem Soc 2016; 138:13022-13029. [DOI: 10.1021/jacs.6b07655] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alexandra I. Lazar
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Frank Biedermann
- Institute
of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz
Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kamila R. Mustafina
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Khaleel I. Assaf
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Andreas Hennig
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Werner M. Nau
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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368
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Ivanov DM, Novikov AS, Ananyev IV, Kirina YV, Kukushkin VY. Halogen bonding between metal centers and halocarbons. Chem Commun (Camb) 2016; 52:5565-8. [PMID: 27020251 DOI: 10.1039/c6cc01107a] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal-involving halogen bonding was detected in a series of associates of CHI3 with trans-[PtX2(NCNAlk2)2] (X = Cl, Br). The HI2C-Iη(1)(Pt) halogen bonding and the bifurcated HI2C-Iη(2)(Pt-Cl) halogen bonding - the latter undergoes the thermally induced reversible HI2C-I∙∙∙η(2)(Pt-Cl) ⇄ HI2C-I∙∙∙η(1)(Pt) transformation - were observed and confirmed theoretically.
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Affiliation(s)
- Daniil M Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034, Saint Petersburg, Russian Federation.
| | - Alexander S Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034, Saint Petersburg, Russian Federation.
| | - Ivan V Ananyev
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova St., 28, 119991, Moscow, Russian Federation
| | - Yulia V Kirina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034, Saint Petersburg, Russian Federation.
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034, Saint Petersburg, Russian Federation.
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369
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Shah R, Strom A, Zhou A, Maize KM, Finzel BC, Wagner CR. Design, Synthesis, and Characterization of Sulfamide and Sulfamate Nucleotidomimetic Inhibitors of hHint1. ACS Med Chem Lett 2016; 7:780-4. [PMID: 27563403 DOI: 10.1021/acsmedchemlett.6b00169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Hint1 has recently emerged to be an important target of interest due to its involvement in the regulation of a broad range of CNS functions including opioid signaling, tolerance, neuropathic pain, and nicotine dependence. A series of inhibitors were rationally designed, synthesized, and tested for their inhibitory activity against hHint1 using isothermal titration calorimetry (ITC). The studies resulted in the development of the first small-molecule inhibitors of hHint1 with submicromolar binding affinities. A combination of thermodynamic and high-resolution X-ray crystallographic studies provides an insight into the biomolecular recognition of ligands by hHint1. These novel inhibitors have potential utility as molecular probes to better understand the role and function of hHint1 in the CNS.
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Affiliation(s)
- Rachit Shah
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Alexander Strom
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew Zhou
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kimberly M. Maize
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Barry C. Finzel
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carston R. Wagner
- Departments
of Medicinal Chemistry and §Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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370
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Bulfield D, Huber SM. Halogen Bonding in Organic Synthesis and Organocatalysis. Chemistry 2016; 22:14434-50. [PMID: 27465662 DOI: 10.1002/chem.201601844] [Citation(s) in RCA: 390] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 12/16/2022]
Abstract
Halogen bonding is a noncovalent interaction similar to hydrogen bonding, which is based on electrophilic halogen substituents. Hydrogen-bonding-based organocatalysis is a well-established strategy which has found numerous applications in recent years. In light of this, halogen bonding has recently been introduced as a key interaction for the design of activators or organocatalysts that is complementary to hydrogen bonding. This Concept features a discussion on the history and electronic origin of halogen bonding, summarizes all relevant examples of its application in organocatalysis, and provides an overview on the use of cationic or polyfluorinated halogen-bond donors in halide abstraction reactions or in the activation of neutral organic substrates.
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Affiliation(s)
- David Bulfield
- Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Stefan M Huber
- Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany.
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371
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Pinalli R, Brancatelli G, Pedrini A, Menozzi D, Hernández D, Ballester P, Geremia S, Dalcanale E. The Origin of Selectivity in the Complexation of N-Methyl Amino Acids by Tetraphosphonate Cavitands. J Am Chem Soc 2016; 138:8569-80. [PMID: 27310660 DOI: 10.1021/jacs.6b04372] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the eligibility of tetraphosphonate resorcinarene cavitands for the molecular recognition of amino acids. We determined the crystal structure of 13 complexes of the tetraphosphonate cavitand Tiiii[H, CH3, CH3] with amino acids. (1)H NMR and (31)P NMR experiments and ITC analysis were performed to probe the binding between cavitand Tiiii[C3H7, CH3, C2H5] or the water-soluble counterpart Tiiii[C3H6Py(+)Cl(-), CH3, C2H5] and a selection of representative amino acids. The reported studies and results allowed us (i) to highlight the noncovalent interactions involved in the binding event in each case; (ii) to investigate the ability of tetraphosphonate cavitand receptors to discriminate between the different amino acids; (iii) to calculate the Ka values of the different complexes formed and evaluate the thermodynamic parameters of the complexation process, dissecting the entropic and enthalpic contributions; and (iv) to determine the solvent influence on the complexation selectivity. By moving from methanol to water, the complexation changed from entropy driven to entropy opposed, leading to a drop of almost three orders in the magnitude of the Ka. However, this reduction in binding affinity is associated with a dramatic increase in selectivity, since in aqueous solutions only N-methylated amino acids are effectively recognized. The thermodynamic profile of the binding does not change in PBS solution. The pivotal role played by cation-π interactions is demonstrated by the linear correlation found between the log Ka in methanol solution and the depth of (+)N-CH3 cavity inclusion in the molecular structures. These findings are relevant for the potential use of phosphonate cavitands as synthetic receptors for the detection of epigenetic modifications of histones in physiological media.
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Affiliation(s)
- Roberta Pinalli
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Giovanna Brancatelli
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Alessandro Pedrini
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniela Menozzi
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniel Hernández
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Pablo Ballester
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16, 43007 Tarragona, Spain
| | - Silvano Geremia
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Enrico Dalcanale
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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372
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Suponitsky KY, Burakov NI, Kanibolotsky AL, Mikhailov VA. Multiple Noncovalent Bonding in Halogen Complexes with Oxygen Organics. I. Tertiary Amides. J Phys Chem A 2016; 120:4179-90. [PMID: 27228362 DOI: 10.1021/acs.jpca.6b02192] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present work describes the structure and binding of adducts of N,N'-diacetylpiperazine with halogens and interhalogens based on combination of different experimental methods and quantum chemical calculations. On the basis of conductometric and spectro-photometric experimental results, behavior of complexes in the acetonitrile solution was described. The iodine adduct with N,N'-diacetylpiperazine fully degrades into components. Adducts of interhalogens I-X (X = Cl or Br) with N,N'-diacetylpiperazine in acetonitrile partially dissociate to anionic [X-I-X](-) and cationic species. In the solid state, molecules are connected via C═O···I, C-H···I, and Cl···Cl attractive interactions. N,N'-diacetylpiperazine···dihalogen complex is stabilized by simultaneous C═O···I and C-H···I interactions. Such binding mode allows to explain the problems of the direct halogenation of acetyl-containing compounds with molecular halogens as reagents. We believe that the observed binding pattern can be used as prototypical for future design of halogeno complexes.
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Affiliation(s)
- Kyrill Yu Suponitsky
- X-ray Structural Centre, A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , 28 Vavilov Street, Moscow 119991, Russia
| | - N I Burakov
- L. M. Litvinenko Institute of Physical Organic and Coal Chemistry , R. Luxemburg Street 70, 83114 Donetsk, Ukraine
| | - Alexander L Kanibolotsky
- L. M. Litvinenko Institute of Physical Organic and Coal Chemistry , R. Luxemburg Street 70, 83114 Donetsk, Ukraine.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Vasilii A Mikhailov
- L. M. Litvinenko Institute of Physical Organic and Coal Chemistry , R. Luxemburg Street 70, 83114 Donetsk, Ukraine
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373
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Changes in hydration structure are necessary for collective motions of a multi-domain protein. Sci Rep 2016; 6:26302. [PMID: 27193111 PMCID: PMC4872039 DOI: 10.1038/srep26302] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 01/27/2023] Open
Abstract
Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
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374
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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375
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Gao ZZ, Lu JH, Tao Z, Zhu QJ, Xue SF, Liu JX, Xiao X. Hybrid nitrate-water cluster in the hydrophobic cavity of cucurbit[8]uril. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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376
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Ballistreri FP, Brancatelli G, Demitri N, Geremia S, Guldi DM, Melchionna M, Pappalardo A, Prato M, Tomaselli GA, Trusso Sfrazzetto G. Recognition of C60 by tetra- and tri-quinoxaline cavitands. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1150594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - Giovanna Brancatelli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza in Biocristallografia, Università di Trieste, Trieste, Italy
| | | | - Silvano Geremia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza in Biocristallografia, Università di Trieste, Trieste, Italy
| | - Dirk M. Guldi
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials, Frierich-Alexander Universität Erlangen-Nűrnberg, Erlangen, Germany
| | - Michele Melchionna
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza in Biocristallografia, Università di Trieste, Trieste, Italy
| | - Andrea Pappalardo
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
- I.N.S.T.M. UdR of Catania, Catania, Italy
| | - Maurizio Prato
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza in Biocristallografia, Università di Trieste, Trieste, Italy
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377
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Kenny PW, Montanari CA, Prokopczyk IM, Ribeiro JFR, Sartori GR. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design. J Med Chem 2016; 59:4278-88. [DOI: 10.1021/acs.jmedchem.5b01946] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter W. Kenny
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Carlos A. Montanari
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Igor M. Prokopczyk
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Jean F. R. Ribeiro
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
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378
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Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Körner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem 2016; 59:4087-102. [PMID: 26878596 DOI: 10.1021/acs.jmedchem.5b01875] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Guba
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jérôme Hert
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Simona Ceccarelli
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Matthias Körner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christian Lerner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Patrizio Mattei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Werner Neidhart
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Emmanuel Pinard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tanja Schulz-Gasch
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Thomas Woltering
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Martin Stahl
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
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379
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Krautwald S, Nilewski C, Mori M, Shiomi K, Ōmura S, Carreira EM. Bioisosteric Exchange of Csp3 -Chloro and Methyl Substituents: Synthesis and Initial Biological Studies of Atpenin A5 Analogues. Angew Chem Int Ed Engl 2016; 55:4049-53. [PMID: 26891236 DOI: 10.1002/anie.201511672] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 11/06/2022]
Abstract
Asymmetric synthesis and initial biological studies of two analogues of a naturally occurring chlorinated antifungal agent, atpenin A5, are described. These analogues were selected on the basis of Cl→CH3 or H3 C→Cl exchanges in the side-chain of atpenin A5. The interchange of chloro and methyl substituents led to complex II inhibitors with equal IC50 values. This suggests that Cl↔Me bioisosteric exchange can be realized in aliphatic settings.
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Affiliation(s)
- Simon Krautwald
- Laboratorium für Organische Chemie, HCI H335, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Christian Nilewski
- Laboratorium für Organische Chemie, HCI H335, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Mihoko Mori
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kazuro Shiomi
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Satoshi Ōmura
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Erick M Carreira
- Laboratorium für Organische Chemie, HCI H335, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
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380
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Krautwald S, Nilewski C, Mori M, Shiomi K, Ōmura S, Carreira EM. Bioisosteric Exchange of Csp3
-Chloro and Methyl Substituents: Synthesis and Initial Biological Studies of Atpenin A5 Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Simon Krautwald
- Laboratorium für Organische Chemie, HCI H335; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christian Nilewski
- Laboratorium für Organische Chemie, HCI H335; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Mihoko Mori
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences; Kitasato University; 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Kazuro Shiomi
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences; Kitasato University; 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Satoshi Ōmura
- Department of Drug Discovery Sciences, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences; Kitasato University; 5-9-1 Shirokane, Minato-ku Tokyo 108-8641 Japan
| | - Erick M. Carreira
- Laboratorium für Organische Chemie, HCI H335; Eidgenössische Technische Hochschule Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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381
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Li X, Zhang Q, Li Z, Wang X, Liu J, Cui S, Xu S, Zhao C, Chen C, Guo K. Thiourea binding with carboxylic acid promoted cationic ring-opening polymerization. POLYMER 2016. [DOI: 10.1016/j.polymer.2015.12.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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382
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Pérez C, Krin A, Steber AL, López JC, Kisiel Z, Schnell M. Wetting Camphor: Multi-Isotopic Substitution Identifies the Complementary Roles of Hydrogen Bonding and Dispersive Forces. J Phys Chem Lett 2016; 7:154-160. [PMID: 26689110 DOI: 10.1021/acs.jpclett.5b02541] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Using broadband rotational spectroscopy, we report here on the delicate interplay between hydrogen bonds and dispersive forces when an unprecedentedly large organic molecule (camphor, C10H16O) is microsolvated with up to three molecules of water. Unambiguous assignment was achieved by performing multi H2(18)O isotopic substitution of clustered water molecules. The observation of all possible mono- and multi-H2(18)O insertions in the cluster structure yielded accurate structural information that is not otherwise achievable with single-substitution experiments. The observed clusters exhibit water chains starting with a strong hydrogen bond to the C═O group and terminated by a mainly van der Waals (dispersive) contact to one of the available sites at the monomer moiety. The effect of hydrogen bond cooperativity is noticeable, and the O···O distances between the clustered water subunits decrease with the number of attached water molecules. The results reported here will further contribute to reveal the hydrophobic and hydrophilic interactions in systems of increasing size.
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Affiliation(s)
- Cristóbal Pérez
- Max Planck Institute for the Structure and Dynamics of Matter , D-22761 Hamburg, Germany
- The Center for Free-Electron Laser Science , D-22761 Hamburg, Germany
| | - Anna Krin
- Max Planck Institute for the Structure and Dynamics of Matter , D-22761 Hamburg, Germany
- The Center for Free-Electron Laser Science , D-22761 Hamburg, Germany
| | - Amanda L Steber
- Max Planck Institute for the Structure and Dynamics of Matter , D-22761 Hamburg, Germany
- The Center for Free-Electron Laser Science , D-22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging at the University of Hamburg , D-22761 Hamburg, Germany
| | - Juan C López
- Max Planck Institute for the Structure and Dynamics of Matter , D-22761 Hamburg, Germany
- Departamento de Quimica Fisica y Quimica Inorganica, Facultad de Ciencias, Universidad de Valladolid , 47011 Valladolid, Spain
| | - Zbigniew Kisiel
- Institute of Physics, Polish Academy of Sciences , 02-668 Warszawa, Poland
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter , D-22761 Hamburg, Germany
- The Center for Free-Electron Laser Science , D-22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging at the University of Hamburg , D-22761 Hamburg, Germany
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383
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Li X, Zhang Q, Li Z, Xu S, Zhao C, Chen C, Zhi X, Wang H, Zhu N, Guo K. Tripodal hydrogen bond donor binding with sulfonic acid enables ring-opening polymerization. Polym Chem 2016. [DOI: 10.1039/c5py01931a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The first Brønsted acidic catalysis platform workable in all of the three major types of cyclic ester monomers including lactides, cyclic carbonates, and lactones, is described in this paper.
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384
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Nguyen TB, Al-Mourabit A. Remarkably high homoselectivity in [2 + 2] photodimerization of trans-cinnamic acids in multicomponent systems. Photochem Photobiol Sci 2016; 15:1115-1119. [PMID: 27459036 DOI: 10.1039/c6pp00201c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
[2 + 2] homoadducts were exclusively obtained with total regio- and stereo-selectivities when a suspension of several solid photoactive trans-cinnamic acids in cyclohexane was stirred and irradiated.
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Affiliation(s)
- Thanh Binh Nguyen
- Institut de Chimie des Substances Naturelles
- CNRS UPR 2301
- Université Paris-Sud
- Université Paris-Saclay
- 91198 Gif-sur-Yvette
| | - Ali Al-Mourabit
- Institut de Chimie des Substances Naturelles
- CNRS UPR 2301
- Université Paris-Sud
- Université Paris-Saclay
- 91198 Gif-sur-Yvette
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385
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Xu L, Wang J, Sun N, Liu M, Cao Y, Wang Z, Pei R. Neutral red as a specific light-up fluorescent probe for i-motif DNA. Chem Commun (Camb) 2016; 52:14330-14333. [DOI: 10.1039/c6cc07674b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neutral red as the first specific light-up fluorescent probe for i-motif DNA is presented.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Min Liu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Yi Cao
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Zhili Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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386
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Garcia Martin S, Prins LJ. Dynamic nanoproteins: self-assembled peptide surfaces on monolayer protected gold nanoparticles. Chem Commun (Camb) 2016; 52:9387-90. [DOI: 10.1039/c6cc04786f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small peptides self-assemble on gold nanoparticles to form a dynamic multivalent peptide surface.
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Affiliation(s)
| | - Leonard J. Prins
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
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387
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Ariga K, Minami K, Shrestha LK. Nanoarchitectonics for carbon-material-based sensors. Analyst 2016; 141:2629-38. [DOI: 10.1039/c6an00057f] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recently, the nanoarchitectonics concept has been proposed to fabricate functional materials on the basis of concerted harmonization actions to control materials organization.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
| | - Kosuke Minami
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
| | - Lok Kumar Shrestha
- World Premier International Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
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388
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Oliveira R, Groni S, Fave C, Branca M, Mavré F, Lorcy D, Fourmigué M, Schöllhorn B. Electrochemical activation of a tetrathiafulvalene halogen bond donor in solution. Phys Chem Chem Phys 2016; 18:15867-73. [DOI: 10.1039/c6cp02219g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrochemistry: a powerful tool for probing and controlling halogen bonding in solution.
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Affiliation(s)
- R. Oliveira
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
| | - S. Groni
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
| | - C. Fave
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
| | - M. Branca
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
| | - F. Mavré
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
| | - D. Lorcy
- Institut des Sciences Chimiques de Rennes
- Université Rennes 1
- CNRS UMR 6226 Campus de Beaulieu
- 35042 Rennes
- France
| | - M. Fourmigué
- Institut des Sciences Chimiques de Rennes
- Université Rennes 1
- CNRS UMR 6226 Campus de Beaulieu
- 35042 Rennes
- France
| | - B. Schöllhorn
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- Sorbonne Paris Cité
- Bâtiment La-voisier
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389
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Schmidt A, Hollering M, Han J, Casini A, Kühn FE. Self-assembly of highly luminescent heteronuclear coordination cages. Dalton Trans 2016; 45:12297-300. [DOI: 10.1039/c6dt02708c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A promising approach is described to enhance the luminescence of palladium(ii) cages resulting in one of the highest fluorescence qunatum yields for metallosupramolecular complexes.
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Affiliation(s)
- Andrea Schmidt
- Molecular Catalysis
- Catalysis Research Center and Department of Chemistry
- Technische Universität München
- 85747 Garching bei München
- Germany
| | - Manuela Hollering
- Molecular Catalysis
- Catalysis Research Center and Department of Chemistry
- Technische Universität München
- 85747 Garching bei München
- Germany
| | - Jiaying Han
- Groningen Research Institute of Pharmacy
- University of Groningen
- 9713 AV Groningen
- The Netherlands
| | - Angela Casini
- Medicinal and Bioinorganic Chemistry
- School of Chemistry
- Cardiff University
- CF103AT Cardiff
- UK
| | - Fritz E. Kühn
- Molecular Catalysis
- Catalysis Research Center and Department of Chemistry
- Technische Universität München
- 85747 Garching bei München
- Germany
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390
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Hayashi T, Kinoshita M. Statistical thermodynamics of aromatic–aromatic interactions in aqueous solution. Phys Chem Chem Phys 2016; 18:32406-32417. [DOI: 10.1039/c6cp06000e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To elucidate the interactions between aromatic rings, which are believed to play essential roles in a variety of biological processes, we analyze the water-mediated interactions between toluene molecules along face-to-face stacked (FF) and point-to-face T-shaped (TS) paths using a statistical-mechanical theory of liquids combined with a molecular model for water.
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391
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Sure R, Grimme S. Halogen bonded supramolecular capsules: a challenging test case for quantum chemical methods. Chem Commun (Camb) 2016; 52:9893-6. [DOI: 10.1039/c6cc03664c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By state-of-the-art dispersion corrected density functional theory, the complexation properties of a recently synthesized halogen-bonded capsule with about 400 atoms are investigated and predictions for improved binding affinities are made.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical Chemistry
- Institut für Physikalische und Theoretische Chemie
- Universität Bonn
- D-53115 Bonn
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institut für Physikalische und Theoretische Chemie
- Universität Bonn
- D-53115 Bonn
- Germany
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392
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Rauch M, Ruccolo S, Mester JP, Rong Y, Parkin G. Synthesis, structure and reactivity of a terminal magnesium fluoride compound, [Tp But,Me]MgF: hydrogen bonding, halogen bonding and C-F bond formation. Chem Sci 2016; 7:142-149. [PMID: 29861975 PMCID: PMC5950829 DOI: 10.1039/c5sc03504j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022] Open
Abstract
The bulky tris(3-tert-butyl-5-pyrazolyl)hydroborato ligand, [TpBut,Me], has been employed to obtain the first structurally characterized example of a molecular magnesium compound that features a terminal fluoride ligand, namely [TpBut,Me]MgF, via the reaction of [TpBut,Me]MgMe with Me3SnF. The chloride, bromide and iodide complexes, [TpBut,Me]MgX (X = Cl, Br, I), can also be obtained by an analogous method using Me3SnX. The molecular structures of the complete series of halide derivatives, [TpBut,Me]MgX (X = F, Cl, Br, I) have been determined by X-ray diffraction. In each case, the Mg-X bond lengths are shorter than the sum of the covalent radii, thereby indicating that there is a significant ionic component to the bonding, in agreement with density functional theory calculations. The fluoride ligand of [TpBut,Me]MgF undergoes halide exchange with Me3SiX (X = Cl, Br, I) to afford [TpBut,Me]MgX and Me3SiF. The other halide derivatives [TpBut,Me]MgX undergo similar exchange reactions, but the thermodynamic driving forces are much smaller than those involving fluoride transfer, a manifestation of the often discussed silaphilicity of fluorine. In accord with the highly polarized Mg-F bond, the fluoride ligand of [TpBut,Me]MgF is capable of serving as a hydrogen bond and halogen bond acceptor, such that it forms adducts with indole and C6F5I. [TpBut,Me]MgF also reacts with Ph3CCl to afford Ph3CF, thereby demonstrating that [TpBut,Me]MgF may be used to form C-F bonds.
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Affiliation(s)
- Michael Rauch
- Department of Chemistry , Columbia University , New York , New York 10027 , USA .
| | - Serge Ruccolo
- Department of Chemistry , Columbia University , New York , New York 10027 , USA .
| | - John Paul Mester
- Department of Chemistry , Columbia University , New York , New York 10027 , USA .
| | - Yi Rong
- Department of Chemistry , Columbia University , New York , New York 10027 , USA .
| | - Gerard Parkin
- Department of Chemistry , Columbia University , New York , New York 10027 , USA .
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393
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Marafon G, Mosconi D, Mazzier D, Biondi B, De Zotti M, Moretto A. Shaping bioinspired photo-responsive microstructures by the light-driven modulation of selective interactions. RSC Adv 2016. [DOI: 10.1039/c6ra17673a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The selective adenine–thymine binding occurring between complementary self-organized complex systems can be modulated by the activation of the plasmon resonance.
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Affiliation(s)
- Giulia Marafon
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Dario Mosconi
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Daniela Mazzier
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry
- Padova Unit
- CNR
- 35131 Padova
- Italy
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Alessandro Moretto
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
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394
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Yang L, Brazier JB, Hubbard TA, Rogers DM, Cockroft SL. Can Dispersion Forces Govern Aromatic Stacking in an Organic Solvent? Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508056] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lixu Yang
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - John B. Brazier
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Thomas A. Hubbard
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - David M. Rogers
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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395
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Yang L, Brazier JB, Hubbard TA, Rogers DM, Cockroft SL. Can Dispersion Forces Govern Aromatic Stacking in an Organic Solvent? Angew Chem Int Ed Engl 2015; 55:912-6. [DOI: 10.1002/anie.201508056] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/13/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Lixu Yang
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - John B. Brazier
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Thomas A. Hubbard
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - David M. Rogers
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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396
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Alamiddine Z, Selvam B, Cerón-Carrasco JP, Mathé-Allainmat M, Lebreton J, Thany SH, Laurent AD, Graton J, Le Questel JY. Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation. J Comput Aided Mol Des 2015; 29:1151-67. [PMID: 26589615 DOI: 10.1007/s10822-015-9884-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/16/2015] [Indexed: 11/29/2022]
Abstract
The binding of thiaclopride (THI), a neonicotinoid insecticide, with Aplysia californica acetylcholine binding protein (Ac-AChBP), the surrogate of the extracellular domain of insects nicotinic acetylcholine receptors, has been studied with a QM/QM' hybrid methodology using the ONIOM approach (M06-2X/6-311G(d):PM6). The contributions of Ac-AChBP key residues for THI binding are accurately quantified from a structural and energetic point of view. The importance of water mediated hydrogen-bond (H-bond) interactions involving two water molecules and Tyr55 and Ser189 residues in the vicinity of the THI nitrile group, is specially highlighted. A larger stabilization energy is obtained with the THI-Ac-AChBP complex compared to imidacloprid (IMI), the forerunner of neonicotinoid insecticides. Pairwise interaction energy calculations rationalize this result with, in particular, a significantly more important contribution of the pivotal aromatic residues Trp147 and Tyr188 with THI through CH···π/CH···O and π-π stacking interactions, respectively. These trends are confirmed through a complementary non-covalent interaction (NCI) analysis of selected THI-Ac-AChBP amino acid pairs.
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Affiliation(s)
- Zakaria Alamiddine
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Balaji Selvam
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.,Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, 61801, USA
| | - José P Cerón-Carrasco
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.,Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Campus de los Jerónimos, 30107, Murcia, Spain
| | - Monique Mathé-Allainmat
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jacques Lebreton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Steeve H Thany
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d'Orléans, UPRES EA 1207. Rue de Chartres, BP 6759, 45067, Orléans Cedex 2, France
| | - Adèle D Laurent
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, BP 92208, Nantes, 44322, France.
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397
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Lauber BS, Hardegger LA, Asraful AK, Lund BA, Dumele O, Harder M, Kuhn B, Engh RA, Diederich F. Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of PKA and a PKB Mimic. Chemistry 2015; 22:211-21. [DOI: 10.1002/chem.201503552] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 12/25/2022]
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398
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Kamps JJ, Huang J, Poater J, Xu C, Pieters BJ, Dong A, Min J, Sherman W, Beuming T, Matthias Bickelhaupt F, Li H, Mecinović J. Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins. Nat Commun 2015; 6:8911. [PMID: 26578293 PMCID: PMC4673829 DOI: 10.1038/ncomms9911] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/15/2015] [Indexed: 01/02/2023] Open
Abstract
A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation-π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain. These results have implications in rational drug design by specifically targeting the aromatic cage of readers of trimethyllysine.
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Affiliation(s)
- Jos J.A.G. Kamps
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jiaxin Huang
- Department of Basic Medical Sciences, Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jordi Poater
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Bas J.G.E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, Canada M5G 1L7
| | - Woody Sherman
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036 USA
| | - Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036 USA
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Haitao Li
- Department of Basic Medical Sciences, Center for Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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399
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Intriguing Electrostatic Potential of CO: Negative Bond-ends and Positive Bond-cylindrical-surface. Sci Rep 2015; 5:16307. [PMID: 26542890 PMCID: PMC4635358 DOI: 10.1038/srep16307] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022] Open
Abstract
The strong electronegativity of O dictates that the ground state of singlet CO has positively charged C and negatively charged O, in agreement with ab initio charge analysis, but in disagreement with the dipole direction. Though this unusual phenomenon has been fairly studied, the study of electrostatic potential (EP) for noncovalent interactions of CO is essential for better understanding. Here we illustrate that both C and O atom-ends show negative EP (where the C end gives more negative EP), favoring positively charged species, whereas the cylindrical surface of the CO bond shows positive EP, favoring negatively charged ones. This is demonstrated from the interactions of CO with Na+, Cl–, H2O, CO and benzene. It can be explained by the quadrupole driven electrostatic nature of CO (like N2) with very weak dipole moment. The EP is properly described by the tripole model taking into account the electrostatic multipole moments, which has a large negative charge at a certain distance protruded from C, a large positive charge on C, and a small negative charge on O. We also discuss the EP of the first excited triplet CO.
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400
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Zhang L, Zhang SY, Wang HZ, Sun YZ, Du ZY. Deformation of the four-membered supramolecular ring in a series of dialkylammonium hydrogen 2,2′-biphenyldicarboxylates. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.06.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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