751
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Effect of stepwise microhydration on the guanidinium···π interaction. J Mol Model 2014; 20:2209. [PMID: 24691534 DOI: 10.1007/s00894-014-2209-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
The characteristics of the interaction of microhydrated guanidinium cation with the aromatic moieties present in the aromatic amino acids side chains have been studied by means of computational methods. The most stable minima found for non-hydrated complexes correspond in all cases to structures with guanidinium oriented toward the ring and interacting by means of N-H···π hydrogen bonds. The interaction becomes stronger when going from benzene (-14 kcal mol⁻¹) to phenol (-17 kcal mol⁻¹) to indole (-21 kcal mol⁻¹). These complexes are held together mainly by electrostatics, but with important contributions from induction and dispersion. The presence of a small number of water molecules significantly affects the characteristics of the complexes. Hydrogen bonds formed by water with the cation, another water molecule, or the aromatic units become more and more similar in intensity as water molecules are included in the complex, leading to a great variety of minima with similar stability but showing very different structural patterns. The behavior is similar with the three aromatic units, the differences in stability mainly being a consequence of the different strength of the cation···π contact.
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Affiliation(s)
- Ana A Rodríguez-Sanz
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X El Sabio s/n, 27002, Lugo, Spain
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752
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Exploration of heterometallic systems containing silver(I) in acyclic Schiff base ligands: Finite and infinite self-assemblies as a result of silver(I)–carbon bond and silver(I)⋯silver(I) interaction. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.01.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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753
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Pudlo M, Luzet V, Ismaïli L, Tomassoli I, Iutzeler A, Refouvelet B. Quinolone–benzylpiperidine derivatives as novel acetylcholinesterase inhibitor and antioxidant hybrids for Alzheimer Disease. Bioorg Med Chem 2014; 22:2496-507. [DOI: 10.1016/j.bmc.2014.02.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
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754
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Binding of acetylcholine and quaternary ammonium compounds to a C3-symmetric bowl-shaped tripeptide of 2-(3-aminophenoxy)propanoic acids acting as a ditopic receptor. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.02.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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755
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Reishus KN, Brathwaite AD, Mosley JD, Duncan MA. Coordination versus Solvation in Al+(benzene)n Complexes Studied with Infrared Spectroscopy. J Phys Chem A 2014; 118:7516-25. [DOI: 10.1021/jp500778w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kimberly N. Reishus
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Antonio D. Brathwaite
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Jonathan D. Mosley
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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756
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Narumi T, Tsuzuki S, Tamamura H. Imidazolium Salt-Catalyzed Friedel-Crafts-Type Conjugate Addition of Indoles: Analysis of Indole/Imidazolium Complex by High Level ab Initio Calculations. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201400026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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757
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Van Arnam EB, Dougherty DA. Functional probes of drug-receptor interactions implicated by structural studies: Cys-loop receptors provide a fertile testing ground. J Med Chem 2014; 57:6289-300. [PMID: 24568098 PMCID: PMC4136689 DOI: 10.1021/jm500023m] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Structures
of integral membrane receptors provide valuable models
for drug–receptor interactions across many important classes
of drug targets and have become much more widely available in recent
years. However, it remains to be determined to what extent these images
are relevant to human receptors in their biological context and how
subtle issues such as subtype selectivity can be informed by them.
The high precision structural modifications enabled by unnatural amino
acid mutagenesis on mammalian receptors expressed in vertebrate cells
allow detailed tests of predictions from structural studies. Using
the Cys-loop superfamily of ligand-gated ion channels, we show that
functional studies lead to detailed binding models that, at times,
are significantly at odds with the structural studies on related invertebrate
proteins. Importantly, broad variations in binding interactions are
seen for very closely related receptor subtypes and for varying drugs
at a given binding site. These studies highlight the essential interplay
between structural studies and functional studies that can guide efforts
to develop new pharmaceuticals.
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Affiliation(s)
- Ethan B Van Arnam
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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758
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Dub PA, Henson NJ, Martin RL, Gordon JC. Unravelling the mechanism of the asymmetric hydrogenation of acetophenone by [RuX2(diphosphine)(1,2-diamine)] catalysts. J Am Chem Soc 2014; 136:3505-21. [PMID: 24524727 DOI: 10.1021/ja411374j] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanism of catalytic hydrogenation of acetophenone by the chiral complex trans-[RuCl2{(S)-binap}{(S,S)-dpen}] and KO-t-C4H9 in propan-2-ol is revised on the basis of DFT computations carried out in dielectric continuum and the most recent experimental observations. The results of these collective studies suggest that neither a six-membered pericyclic transition state nor any multibond concerted transition states are involved. Instead, a hydride moiety is transferred in an outer-sphere manner to afford an ion-pair, and the corresponding transition state is both enantio- and rate-determining. Heterolytic dihydrogen cleavage proceeds neither by a (two-bond) concerted, four-membered transition state, nor by a (three-bond) concerted, six-membered transition state mediated by a solvent molecule. Instead, cleavage of the H-H bond is achieved via deprotonation of the η(2)-H2 ligand within a cationic Ru complex by the chiral conjugate base of (R)-1-phenylethanol. Thus, protonation of the generated (R)-1-phenylethoxide anion originates from the η(2)-H2 ligand of the cationic Ru complex and not from NH protons of a neutral Ru trans-dihydride complex, as initially suggested within the framework of a metal-ligand bifunctional mechanism. Detailed computational analysis reveals that the 16e(-) Ru amido complex [RuH{(S)-binap}{(S,S)-HN(CHPh)2NH2}] and the 18e(-) Ru alkoxo complex trans-[RuH{OCH(CH3)(R)}{(S)-binap}{(S,S)-dpen}] (R = CH3 or C6H5) are not intermediates within the catalytic cycle, but rather are off-loop species. The accelerative effect of KO-t-C4H9 is explained by the reversible formation of the potassium amidato complexes trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH2}] or trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH(K)}]. The three-dimensional (3D) cavity observed within these molecules results in a chiral pocket stabilized via several different noncovalent interactions, including neutral and ionic hydrogen bonding, cation-π interactions, and π-π stacking interactions. Cooperatively, these interactions modify the catalyst structure, in turn lowering the relative activation barrier of hydride transfer by ~1-2 kcal mol(-1) and the following H-H bond cleavage by ~10 kcal mol(-1), respectively. A combined computational study and analysis of recent experimental data of the reaction pool results in new mechanistic insight into the catalytic cycle for hydrogenation of acetophenone by Noyori's catalyst, in the presence or absence of KO-t-C4H9.
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Affiliation(s)
- Pavel A Dub
- Chemistry Division, MS J582, and ‡Theoretical Division, MS B268, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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759
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Scola PM, Wang AX, Good AC, Sun LQ, Combrink KD, Campbell JA, Chen J, Tu Y, Sin N, Venables BL, Sit SY, Chen Y, Cocuzza A, Bilder DM, D’Andrea S, Zheng B, Hewawasam P, Ding M, Thuring J, Li J, Hernandez D, Yu F, Falk P, Zhai G, Sheaffer AK, Chen C, Lee MS, Barry D, Knipe JO, Li W, Han YH, Jenkins S, Gesenberg C, Gao Q, Sinz MW, Santone KS, Zvyaga T, Rajamani R, Klei HE, Colonno RJ, Grasela DM, Hughes E, Chien C, Adams S, Levesque PC, Li D, Zhu J, Meanwell NA, McPhee F. Discovery and Early Clinical Evaluation of BMS-605339, a Potent and Orally Efficacious Tripeptidic Acylsulfonamide NS3 Protease Inhibitor for the Treatment of Hepatitis C Virus Infection. J Med Chem 2014; 57:1708-29. [DOI: 10.1021/jm401840s] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paul M. Scola
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Alan Xiangdong Wang
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew C. Good
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Li-Qiang Sun
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Keith D. Combrink
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jeffrey A. Campbell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jie Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yong Tu
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ny Sin
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Brian L. Venables
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yan Chen
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Anthony Cocuzza
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Donna M. Bilder
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Stanley D’Andrea
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Barbara Zheng
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Piyasena Hewawasam
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min Ding
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jan Thuring
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jianqing Li
- Department
of Discovery Chemical Synthesis, Bristol-Myers Squibb Research and Development, P.O.
Box 4000, Princeton, New Jersey 08543, United States
| | - Dennis Hernandez
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fei Yu
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul Falk
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Guangzhi Zhai
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Amy K. Sheaffer
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Chaoqun Chen
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min S. Lee
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Diana Barry
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jay O. Knipe
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Wenying Li
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yong-Hae Han
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Susan Jenkins
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Christoph Gesenberg
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Qi Gao
- Department of Pharmaceutical Development, Bristol-Myers Squibb Research and Development, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael W. Sinz
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kenneth S. Santone
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Tatyana Zvyaga
- Department of
Lead Discovery and Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ramkumar Rajamani
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Herbert E. Klei
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Richard J. Colonno
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Dennis M. Grasela
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Eric Hughes
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Caly Chien
- Department of Early Clinical and Translational
Research, Discovery Medicine—Virology, Bristol-Myers Squibb Research and Development, Hopewell, New Jersey 08543, United States
| | - Stephen Adams
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Paul C. Levesque
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Danshi Li
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jialong Zhu
- Department
of Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Fiona McPhee
- Department
of Virology Discovery Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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760
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Rapp C, Goldberger E, Tishbi N, Kirshenbaum R. Cation-π interactions of methylated ammonium ions: a quantum mechanical study. Proteins 2014; 82:1494-502. [PMID: 24464782 DOI: 10.1002/prot.24519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/12/2014] [Accepted: 01/16/2014] [Indexed: 11/05/2022]
Abstract
Cation-π interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylate these sites, and neurotransmitter receptor complexes which bind choline-derived ligands. Recognition in these systems is achieved through an 'aromatic cage' motif in the binding site. Here we use high-level quantum mechanical calculations to address how cation-π interactions of methylated ammonium ions are modulated by a change in methylation state and interaction geometry. We survey methyl-lysine and choline-derived complexes in the Protein Databank to validate our results against available structural data. A quantitative description of cation-π interactions of methylated ammonium systems is critical to structure-based efforts to target methyl-lysine binding proteins and demethylase enzymes in the treatment of unregulated transcriptional control, and neurotransmitter receptors in the treatment of neurological disease. It is our hope that our work will serve as a benchmark for the development of physical chemistry based force fields that can accurately model the contribution of cation-π interactions to binding and specificity in these systems.
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Affiliation(s)
- Chaya Rapp
- Department of Chemistry and Biochemistry, Stern College for Women, Yeshiva University, New York, New York
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761
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Berger G, Soubhye J, van der Lee A, Vande Velde C, Wintjens R, Dubois P, Clément S, Meyer F. Interplay between Halogen Bonding and Lone Pair-π Interactions: A Computational and Crystal Packing Study. Chempluschem 2014; 79:552-558. [DOI: 10.1002/cplu.201400005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/10/2022]
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762
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Rodríguez-Romero A, Hernández-Santoyo A, Fuentes-Silva D, Palomares LA, Muñoz-Cruz S, Yépez-Mulia L, Orozco-Martínez S. Structural analysis of the endogenous glycoallergen Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis and its recognition by human basophils. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:329-41. [PMID: 24531467 PMCID: PMC3940204 DOI: 10.1107/s1399004713027673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022]
Abstract
Endogenous glycosylated Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis is an important latex allergen that is recognized by IgE antibodies from patients who suffer from latex allergy. The carbohydrate moieties of Hev b 2 constitute a potentially important IgE-binding epitope that could be responsible for its cross-reactivity. Here, the structure of the endogenous isoform II of Hev b 2 that exhibits three post-translational modifications, including an N-terminal pyroglutamate and two glycosylation sites at Asn27 and at Asn314, is reported from two crystal polymorphs. These modifications form a patch on the surface of the molecule that is proposed to be one of the binding sites for IgE. A structure is also proposed for the most important N-glycan present in this protein as determined by digestion with specific enzymes. To analyze the role of the carbohydrate moieties in IgE antibody binding and in human basophil activation, the glycoallergen was enzymatically deglycosylated and evaluated. Time-lapse automated video microscopy of basophils stimulated with glycosylated Hev b 2 revealed basophil activation and degranulation. Immunological studies suggested that carbohydrates on Hev b 2 represent an allergenic IgE epitope. In addition, a dimer was found in each asymmetric unit that may reflect a regulatory mechanism of this plant defence protein.
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Affiliation(s)
- Adela Rodríguez-Romero
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, CU, 04310 Coyoacán, DF, Mexico
| | - Alejandra Hernández-Santoyo
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, CU, 04310 Coyoacán, DF, Mexico
| | - Deyanira Fuentes-Silva
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, CU, 04310 Coyoacán, DF, Mexico
| | - Laura A. Palomares
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, MOR, Mexico
| | - Samira Muñoz-Cruz
- UMAE–Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Avenida Cuauhtémoc 330, Colonia Doctores, Mexico, DF, Mexico
| | - Lilian Yépez-Mulia
- UMAE–Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Avenida Cuauhtémoc 330, Colonia Doctores, Mexico, DF, Mexico
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763
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Marotta CB, Dilworth CN, Lester HA, Dougherty DA. Probing the non-canonical interface for agonist interaction with an α5 containing nicotinic acetylcholine receptor. Neuropharmacology 2014; 77:342-9. [PMID: 24144909 PMCID: PMC3934363 DOI: 10.1016/j.neuropharm.2013.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 11/18/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) containing the α5 subunit are of interest because genome-wide association studies and candidate gene studies have identified polymorphisms in the α5 gene that are linked to an increased risk for nicotine dependence, lung cancer, and/or alcohol addiction. To probe the functional impact of an α5 subunit on nAChRs, a method to prepare a homogeneous population of α5-containing receptors must be developed. Here we use a gain of function (9') mutation to isolate populations of α5-containing nAChRs for characterization by electrophysiology. We find that the α5 subunit modulates nAChR rectification when co-assembled with α4 and β2 subunits. We also probe the α5-α4 interface for possible ligand-binding interactions. We find that mutations expected to ablate an agonist-binding site involving the α5 subunit have no impact on receptor function. The most straightforward interpretation of this observation is that agonists do not bind at the α5-α4 interface, in contrast to what has recently been demonstrated for the α4-α4 interface in related receptors. In addition, our mutational results suggest that the α5 subunit does not replace the α4 or β2 subunits and is relegated to occupying only the auxiliary position of the pentameric receptor.
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Affiliation(s)
- Christopher B Marotta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA
| | - Crystal N Dilworth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
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764
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Ivanova B, Spiteller M. Evodiamine and rutaecarpine alkaloids as highly selective transient receptor potential vanilloid 1 agonists. Int J Biol Macromol 2014; 65:314-24. [PMID: 24495556 DOI: 10.1016/j.ijbiomac.2014.01.059] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/24/2014] [Indexed: 10/25/2022]
Abstract
Despite that among non-camptothecin natural products promising anticancer therapeutics are evodiamine derivatives, involved into mechanism of physiological function of topoisomerase-I. But, more recent findings have been shown that substituted quinazole alkaloids act as transient receptor potential vanilloid 1 agonists. The TRP(V1) is a calcium ion channel, activated by pH, heat and inflammatory activators. I is implicated in pain sensing. TRPV1 agonist is capsaicine (1). Both 1 and evodiamine (2), therefore, produce same physiological response, but are structurally unrelated from chemical viewpoint. Furthermore precise mechanistic aspects of drugs receptor interactions are still not fully understood. This study is the first one, which provides assessment of molecular factors contributing significantly to selectivity of 2 and rutaecarpine (3) as well as their twenty-two new functionalized derivatives towards (TRP)V1. The suggested new functionalization type of molecular skeleton, which is completely different one in respect the known derivatives, which is implicated in treatment of variety of cancer cell lines interacting preferably with topoisomerase-I. It resulted to increasing of the binding affinity and selectivity of the functionalized derivatives specifically to (TRP)V1∈1.36-1.72 and ∈2.50-3.16 higher than 1-3.
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany.
| | - Michael Spiteller
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany
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765
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Zhao Y, Beuchat C, Domoto Y, Gajewy J, Wilson A, Mareda J, Sakai N, Matile S. Anion−π Catalysis. J Am Chem Soc 2014; 136:2101-11. [DOI: 10.1021/ja412290r] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yingjie Zhao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - César Beuchat
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Yuya Domoto
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jadwiga Gajewy
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Adam Wilson
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jiri Mareda
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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766
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Li Q, Zhuo H, Yang X, Cheng J, Li W, Loffredo RE. Cooperative and Diminutive Effects of Pnicogen Bonds and Cation-π Interactions. Chemphyschem 2014; 15:500-6. [DOI: 10.1002/cphc.201300965] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 11/22/2013] [Indexed: 11/05/2022]
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767
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Haridas V, Praveen Kumar PP, Suresh CH. Cysteine-based fluorescence “turn-on” sensors for Cu2+ and Ag+. RSC Adv 2014. [DOI: 10.1039/c4ra10936h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amino acid cysteine was transformed to fluorescent turn-on sensors for Cu+2 and Ag+. The metal ion binding was studied in detail by spectroscopic, microscopic, calorimetric and computational methods.
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Affiliation(s)
- V. Haridas
- Department of Chemistry
- Indian Institute of Technology Delhi
- Hauz Khas-110016, India
| | - P. P. Praveen Kumar
- Department of Chemistry
- Indian Institute of Technology Delhi
- Hauz Khas-110016, India
| | - Cherumuttathu H. Suresh
- Inorganic and Theoretical Chemistry Section, CSTD, CSIR-National Institute for Interdisciplinary Science and Technology
- Thiruvananthapuram – 695019, India
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768
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769
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Gamez P. The anion–π interaction: naissance and establishment of a peculiar supramolecular bond. Inorg Chem Front 2014. [DOI: 10.1039/c3qi00055a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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770
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McGovern RE, McCarthy AA, Crowley PB. Protein assembly mediated by sulfonatocalix[4]arene. Chem Commun (Camb) 2014; 50:10412-5. [DOI: 10.1039/c4cc04897k] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The binding of anionic p-sulfonatocalix[4]arene to cationic lysozyme results in self assembly and the formation of protein tetramer chains, as revealed by X-ray crystallography.
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Affiliation(s)
- Róise E. McGovern
- School of Chemistry
- National University of Ireland Galway
- Galway, Ireland
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory and Unit of Virus Host-Cell Interactions
- UJF-EMBL-CNRS
- Grenoble Outstation
- 38042 Grenoble Cedex 9, France
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway, Ireland
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771
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Li ZF, Li HX, Yang XP. The mutual interactions based on amphipathic tetraoxacalix[2]arene[2]triazine: recognition cases of anion and cation investigated by a computational study. Phys Chem Chem Phys 2014; 16:25876-82. [DOI: 10.1039/c4cp03551h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This work provides insights into the interaction nature of amphiphilic tetraoxacalix[2]arene[2]triazine with the system (J. Am. Chem. Soc., 2013, 135, 892) as well as the recognition cases of anion and cation.
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Affiliation(s)
- Zhi-Feng Li
- College of Life Science and Chemistry
- Key Laboratory for New Molecule Design and Function of Gansu Universities
- Tianshui Normal University
- Tianshui 741001, China
| | - Hui-Xue Li
- College of Life Science and Chemistry
- Key Laboratory for New Molecule Design and Function of Gansu Universities
- Tianshui Normal University
- Tianshui 741001, China
| | - Xiao-Ping Yang
- College of Life Science and Chemistry
- Key Laboratory for New Molecule Design and Function of Gansu Universities
- Tianshui Normal University
- Tianshui 741001, China
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772
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Jana A, Mohanta S. A tale of crystal engineering of metal complexes derived from a special ligand family having a cosmopolitan compartment. CrystEngComm 2014. [DOI: 10.1039/c3ce41911h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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773
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Cation⋯π interaction and microhydration effects in complexes formed by pyrrolidinium cation and aromatic species in amino acid side chains. Org Biomol Chem 2014; 12:2938-49. [DOI: 10.1039/c3ob42388c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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774
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Chan EJ, Grabowsky S, Harrowfield JM, Shi MW, Skelton BW, Sobolev AN, White AH. Hirshfeld surface analysis of crystal packing in aza-aromatic picrate salts. CrystEngComm 2014. [DOI: 10.1039/c4ce00095a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures of picrate salts of extended aza-aromatic bases have been determined and systematically analyzed using the Hirshfeld surface approach.
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Affiliation(s)
- Eric J. Chan
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Jack M. Harrowfield
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Ming W. Shi
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Brian W. Skelton
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
| | - Allan H. White
- School of Chemistry and Biochemistry
- M310
- The University of Western Australia
- Crawley, Australia
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775
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Bauzá A, Deyà PM, Frontera A, Quiñonero D. Substituent effects in cation–π interactions revisited: a general approach based on intrinsic properties of the arenes. Phys Chem Chem Phys 2014; 16:1322-6. [DOI: 10.1039/c3cp54147a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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776
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Wilson A, Gasparini G, Matile S. Functional systems with orthogonal dynamic covalent bonds. Chem Soc Rev 2014; 43:1948-62. [DOI: 10.1039/c3cs60342c] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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777
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Han M, Wang GC, Duan HQ. Construction of supramolecular nanofibers through electrostatic interaction between perylene and cholesterol derivatives. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2013.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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778
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Ion enrichment on the hydrophobic carbon-based surface in aqueous salt solutions due to cation-π interactions. Sci Rep 2013; 3:3436. [PMID: 24310448 PMCID: PMC3853681 DOI: 10.1038/srep03436] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/12/2013] [Indexed: 11/17/2022] Open
Abstract
By incorporating cation-π interactions to classic all-atoms force fields, we show that there is a clear enrichment of Na+ on a carbon-based π electron-rich surface in NaCl solutions using molecular dynamics simulations. Interestingly, Cl− is also enriched to some extend on the surface due to the electrostatic interaction between Na+ and Cl−, although the hydrated Cl−-π interaction is weak. The difference of the numbers of Na+ and Cl− accumulated at the interface leads to a significant negatively charged behavior in the solution, especially in nanoscale systems. Moreover, we find that the accumulation of the cations at the interfaces is universal since other cations (Li+, K+, Mg2+, Ca2+, Fe2+, Co2+, Cu2+, Cd2+, Cr2+, and Pb2+) have similar adsorption behaviors. For comparison, as in usual force field without the proper consideration of cation-π interactions, the ions near the surfaces have a similar density of ions in the solution.
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779
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Cherny I, Greisen P, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS. Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries. ACS Chem Biol 2013; 8:2394-403. [PMID: 24041203 DOI: 10.1021/cb4004892] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
VX and its Russian (RVX) and Chinese (CVX) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. These organophosphates have a thiol leaving group with a choline-like moiety and are hydrolyzed very slowly by natural enzymes. We used an integrated computational and experimental approach to increase Brevundimonas diminuta phosphotriesterase's (PTE) detoxification rate of V-agents by 5000-fold. Computational models were built of the complex between PTE and V-agents. On the basis of these models, the active site was redesigned to be complementary in shape to VX and RVX and to include favorable electrostatic interactions with their choline-like leaving group. Small libraries based on designed sequences were constructed. The libraries were screened by a direct assay for V-agent detoxification, as our initial studies showed that colorimetric surrogates fail to report the detoxification rates of the actual agents. The experimental results were fed back to improve the computational models. Overall, five rounds of iterating between experiment and model refinement led to variants that hydrolyze the toxic SP isomers of all three V-agents with kcat/KM values of up to 5 × 10(6) M(-1) min(-1) and also efficiently detoxify G-agents. These new catalysts provide the basis for broad spectrum nerve agent detoxification.
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Affiliation(s)
- Izhack Cherny
- Department
of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Per Greisen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yacov Ashani
- Department
of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagar D. Khare
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Haim Leader
- Department
of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dan S. Tawfik
- Department
of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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780
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Yamada S, Iwaoka A, Fujita Y, Tsuzuki S. Tetraalkylammonium-Templated Stereoselective Norrish–Yang Cyclization. Org Lett 2013; 15:5994-7. [DOI: 10.1021/ol4028732] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Azusa Iwaoka
- Department of Chemistry, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Yuka Fujita
- Department of Chemistry, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
| | - Seiji Tsuzuki
- Department of Chemistry, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
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781
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Qiao JX, Wang TC, Ruel R, Thibeault C, L'Heureux A, Schumacher WA, Spronk SA, Hiebert S, Bouthillier G, Lloyd J, Pi Z, Schnur DM, Abell LM, Hua J, Price LA, Liu E, Wu Q, Steinbacher TE, Bostwick JS, Chang M, Zheng J, Gao Q, Ma B, McDonnell PA, Huang CS, Rehfuss R, Wexler RR, Lam PYS. Conformationally constrained ortho-anilino diaryl ureas: discovery of 1-(2-(1'-neopentylspiro[indoline-3,4'-piperidine]-1-yl)phenyl)-3-(4-(trifluoromethoxy)phenyl)urea, a potent, selective, and bioavailable P2Y1 antagonist. J Med Chem 2013; 56:9275-95. [PMID: 24164581 DOI: 10.1021/jm4013906] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Preclinical antithrombotic efficacy and bleeding models have demonstrated that P2Y1 antagonists are efficacious as antiplatelet agents and may offer a safety advantage over P2Y12 antagonists in terms of reduced bleeding liabilities. In this article, we describe the structural modification of the tert-butyl phenoxy portion of lead compound 1 and the subsequent discovery of a novel series of conformationally constrained ortho-anilino diaryl ureas. In particular, spiropiperidine indoline-substituted diaryl ureas are described as potent, orally bioavailable small-molecule P2Y1 antagonists with improved activity in functional assays and improved oral bioavailability in rats. Homology modeling and rat PK/PD studies on benchmark compound 3l will also be presented. Compound 3l was our first P2Y1 antagonist to demonstrate a robust oral antithrombotic effect with mild bleeding liability in the rat thrombosis and hemostasis models.
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Affiliation(s)
- Jennifer X Qiao
- Research and Development, Bristol-Myers Squibb Company , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
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782
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Ito R, Hashimoto I, Masukawa Y, Hoshino T. Effect of Cation-π Interactions and Steric Bulk on the Catalytic Action of Oxidosqualene Cyclase: A Case Study of Phe728 of β-Amyrin Synthase fromEuphorbia tirucalli L. Chemistry 2013; 19:17150-8. [DOI: 10.1002/chem.201301917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/31/2013] [Indexed: 11/06/2022]
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783
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Grishin AA, Cuny H, Hung A, Clark RJ, Brust A, Akondi K, Alewood PF, Craik DJ, Adams DJ. Identifying key amino acid residues that affect α-conotoxin AuIB inhibition of α3β4 nicotinic acetylcholine receptors. J Biol Chem 2013; 288:34428-42. [PMID: 24100032 DOI: 10.1074/jbc.m113.512582] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
α-Conotoxin AuIB is a selective α3β4 nicotinic acetylcholine receptor (nAChR) subtype inhibitor. Its analgesic properties are believed to result from it activating GABAB receptors and subsequently inhibiting CaV2.2 voltage-gated calcium channels. The structural determinants that mediate diverging AuIB activity at these targets are unknown. We performed alanine scanning mutagenesis of AuIB and α3β4 nAChR, homology modeling, and molecular dynamics simulations to identify the structural determinants of the AuIB·α3β4 nAChR interaction. Two alanine-substituted AuIB analogues, [P6A]AuIB and [F9A]AuIB, did not inhibit the α3β4 nAChR. NMR and CD spectroscopy studies demonstrated that [F9A]AuIB retains its native globular structure, so its activity loss is probably due to loss of specific toxin-receptor residue pairwise contacts. Compared with AuIB, the concentration-response curve for inhibition of α3β4 by [F9A]AuIB shifted rightward more than 10-fold, and its subtype selectivity profile changed. Homology modeling and molecular dynamics simulations suggest that Phe-9 of AuIB interacts with a two-residue binding pocket on the β4 nAChR subunit. This hypothesis was confirmed by site-directed mutagenesis of the β4-Trp-59 and β4-Lys-61 residues of loop D, which form a putative binding pocket. AuIB analogues with Phe-9 substitutions corroborated the finding of a binding pocket on the β4 subunit and gave further insight into how AuIB Phe-9 interacts with the β4 subunit. In summary, we identified critical residues that mediate interactions between AuIB and its cognate nAChR subtype. These findings might help improve the design of analgesic conopeptides that selectively "avoid" nAChR receptors while targeting receptors involved with nociception.
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Affiliation(s)
- Anton A Grishin
- From the Health Innovations Research Institute, RMIT University, Melbourne, Victoria 3083, Australia and
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784
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Nicholson BK, Clark CJ, Jameson GB, Telfer SG. Rubidium-templated bowl-shaped isopolyoxoantimonates [RbH11−x(RSb)14O34]x− derived from arylstibonic acids. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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785
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Mayeux C, Tammiku-Taul J, Massi L, Gal JF, Burk P. Interaction between the Cesium Cation and Cesium Carboxylates: An Extended Cs+Basicity Scale. Chempluschem 2013; 78:1195-1204. [DOI: 10.1002/cplu.201300181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/05/2013] [Indexed: 11/06/2022]
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786
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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787
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Zhao Y, Domoto Y, Orentas E, Beuchat C, Emery D, Mareda J, Sakai N, Matile S. Catalysis with Anion-π Interactions. Angew Chem Int Ed Engl 2013; 52:9940-3. [DOI: 10.1002/anie.201305356] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Indexed: 12/12/2022]
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788
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Zhao Y, Domoto Y, Orentas E, Beuchat C, Emery D, Mareda J, Sakai N, Matile S. Catalysis with Anion-π Interactions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305356] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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789
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Kadlubanski P, Calderón-Mojica K, Rodriguez WA, Majumdar D, Roszak S, Leszczynski J. Role of the Multipolar Electrostatic Interaction Energy Components in Strong and Weak Cation−π Interactions. J Phys Chem A 2013; 117:7989-8000. [DOI: 10.1021/jp404245q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Pawel Kadlubanski
- Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katherine Calderón-Mojica
- Universidad de Puerto Rico en Humacao, Estacidn Postal CUH 100 Carr.908,
Humacao PR00791-4300, Puerto Rico
| | | | - D. Majumdar
- Department of Chemistry and
Biochemistry, Jackson State University,
Jackson, Mississippi 39217, United States
| | - Szczepan Roszak
- Institute of Physical and Theoretical
Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jerzy Leszczynski
- Department of Chemistry and
Biochemistry, Jackson State University,
Jackson, Mississippi 39217, United States
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790
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Chen M, Al-lami N, Janvier M, D'Antonio EL, Faraldos JA, Cane DE, Allemann RK, Christianson DW. Mechanistic insights from the binding of substrate and carbocation intermediate analogues to aristolochene synthase. Biochemistry 2013; 52:5441-53. [PMID: 23905850 PMCID: PMC3755762 DOI: 10.1021/bi400691v] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Aristolochene synthase, a metal-dependent sesquiterpene cyclase from Aspergillus terreus, catalyzes the ionization-dependent cyclization of farnesyl diphosphate (FPP) to form the bicyclic eremophilane (+)-aristolochene with perfect structural and stereochemical precision. Here, we report the X-ray crystal structure of aristolochene synthase complexed with three Mg(2+) ions and the unreactive substrate analogue farnesyl-S-thiolodiphosphate (FSPP), showing that the substrate diphosphate group is anchored by metal coordination and hydrogen bond interactions identical to those previously observed in the complex with three Mg(2+) ions and inorganic pyrophosphate (PPi). Moreover, the binding conformation of FSPP directly mimics that expected for productively bound FPP, with the exception of the precise alignment of the C-S bond with regard to the C10-C11 π system that would be required for C1-C10 bond formation in the first step of catalysis. We also report crystal structures of aristolochene synthase complexed with Mg(2+)3-PPi and ammonium or iminium analogues of bicyclic carbocation intermediates proposed for the natural cyclization cascade. Various binding orientations are observed for these bicyclic analogues, and these orientations appear to be driven by favorable electrostatic interactions between the positively charged ammonium group of the analogue and the negatively charged PPi anion. Surprisingly, the active site is sufficiently flexible to accommodate analogues with partially or completely incorrect stereochemistry. Although this permissiveness in binding is unanticipated, based on the stereochemical precision of catalysis that leads exclusively to the (+)-aristolochene stereoisomer, it suggests the ability of the active site to enable controlled reorientation of intermediates during the cyclization cascade. Taken together, these structures illuminate important aspects of the catalytic mechanism.
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Affiliation(s)
- Mengbin Chen
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323 USA
| | - Naeemah Al-lami
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, United Kingdom
| | - Marine Janvier
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, United Kingdom
| | - Edward L. D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323 USA
| | - Juan A. Faraldos
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, United Kingdom
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108 USA
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, Wales, United Kingdom
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323 USA,To whom correspondence should be addressed: Department of Chemistry, University of Pennsylvania, 2001 Roy and Diana Vagelos Laboratories, 231 South 34th Street, Philadelphia, PA, 19104-6323 USA. Tel: 215-898-5714;
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791
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Rivas-Pardo JA, Herrera-Morande A, Castro-Fernandez V, Fernandez FJ, Vega MC, Guixé V. Crystal structure, SAXS and kinetic mechanism of hyperthermophilic ADP-dependent glucokinase from Thermococcus litoralis reveal a conserved mechanism for catalysis. PLoS One 2013; 8:e66687. [PMID: 23818958 PMCID: PMC3688580 DOI: 10.1371/journal.pone.0066687] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Thermococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.
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Affiliation(s)
| | - Alejandra Herrera-Morande
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, España
| | | | | | | | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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792
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Monakhov KY, Gourlaouen C, Zessin T, Linti G. Synthesis and Crystal Structure of a “FeBi” Cluster Compound with Noncovalent Low-Valent Bi···πArene Interactions. Inorg Chem 2013; 52:6782-4. [DOI: 10.1021/ic401001f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirill Yu. Monakhov
- Institut für Anorganische
Chemie, RWTH Aachen University, Landoltweg
1, 52074 Aachen, Germany
| | - Christophe Gourlaouen
- Laboratoire de Chimie Quantique, Institut de Chimie (UMR 7177 CNRS), Université de Strasbourg, 1 rue Blaise Pascal,
67008 Strasbourg, France
| | - Thomas Zessin
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg,
Germany
| | - Gerald Linti
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg,
Germany
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793
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Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
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Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
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794
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Substituted benzo[i]phenanthridines as promising topoisomerase-I non-camptothecin targeting agents: an experimental and theoretical study. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0515-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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795
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Krenske EH. Aromatic interactions in asymmetric catalysis: control of enantioselectivity in Diels–Alder reactions catalysed by camphor-derived hydrazides. Org Biomol Chem 2013; 11:5226-32. [DOI: 10.1039/c3ob40850g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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796
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Hassan A, Dinadayalane TC, Grabowski SJ, Leszczynski J. Structural, energetic, spectroscopic and QTAIM analyses of cation–π interactions involving mono- and bi-cyclic ring fused benzene systems. Phys Chem Chem Phys 2013; 15:20839-56. [PMID: 24196371 DOI: 10.1039/c3cp53927j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ayorinde Hassan
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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797
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Recent Advancements in Chiral Porphyrin Self-Assembly. TOPICS IN HETEROCYCLIC CHEMISTRY 2013. [DOI: 10.1007/7081_2013_110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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798
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Bianchini G, Sorella GL, Canever N, Scarso A, Strukul G. Efficient isonitrile hydration through encapsulation within a hexameric self-assembled capsule and selective inhibition by a photo-controllable competitive guest. Chem Commun (Camb) 2013; 49:5322-4. [DOI: 10.1039/c3cc42233j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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799
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Bhattacharya S, Jana A, Mohanta S. Crystal structures of discrete, one-dimensional and cocrystalline copper(ii)–uranyl(vi) systems: the influence of the reactant ratio in the competition between hydrogen bonds and coordinate bonds. CrystEngComm 2013. [DOI: 10.1039/c3ce41625a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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