1
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Pinto CB, Dos Santos LHR, Rodrigues BL. Further evaluation of the shape of atomic Hirshfeld surfaces: M...H contacts and homoatomic bonds. Acta Crystallogr C Struct Chem 2024; 80:478-486. [PMID: 39115535 DOI: 10.1107/s2053229624007125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
It is well known that Hirshfeld surfaces provide an easy and straightforward way of analysing intermolecular interactions in the crystal environment. The use of atomic Hirshfeld surfaces has also demonstrated that such surfaces carry information related to chemical bonds which allow a deeper evaluation of the structures. Here we briefly summarize the approach of atomic Hirshfeld surfaces while further evaluating the kind of information that can be retrieved from them. We show that the analysis of the metal-centre Hirshfeld surfaces from structures refined via Hirshfeld Atom Refinement (HAR) allow accurate evaluation of contacts of type M...H, and that such contacts can be related to the overall shape of the surfaces. The compounds analysed were tetraaquabis(3-carboxypropionato)metal(II), [M(C4H3O4)2(H2O)4], for metal(II)/M = manganese/Mn, cobalt/Co, nickel/Ni and zinc/Zn. We also evaluate the sensitivity of the surfaces by an investigation of seemingly flat surfaces through analysis of the curvature functions in the direction of C-C bonds. The obtained values not only demonstrate variations in curvature but also show a correlation with the hybridization of the C atoms involved in the bond.
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Affiliation(s)
- Camila B Pinto
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Leonardo H R Dos Santos
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Bernardo L Rodrigues
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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2
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Estrogenic flavonoids and their molecular mechanisms of action. J Nutr Biochem 2023; 114:109250. [PMID: 36509337 DOI: 10.1016/j.jnutbio.2022.109250] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Flavonoids are a major group of phytoestrogens associated with physiological effects, and ecological and social impacts. Although the estrogenic activity of flavonoids was reported by researchers in the fields of medical, environmental and food studies, their molecular mechanisms of action have not been comprehensively reviewed. The estrogenic activity of the respective classes of flavonoids, anthocyanidins/anthocyanins, 2-arylbenzofurans/3-arylcoumarins/α-methyldeoxybenzoins, aurones/chalcones/dihydrochalcones, coumaronochromones, coumestans, flavans/flavan-3-ols/flavan-4-ols, flavanones/dihydroflavonols, flavones/flavonols, homoisoflavonoids, isoflavans, isoflavanones, isoflavenes, isoflavones, neoflavonoids, oligoflavonoids, pterocarpans/pterocarpenes, and rotenone/rotenoids, was summarized through a comprehensive literature search, and their structure-activity relationship, biological activities, signaling pathways, and applications were discussed. Although the respective classes of flavonoids contained at least one chemical mimicking estrogen, the mechanisms varied, such as those with estrogenic, anti-estrogenic, non-estrogenic, and biphasic activities, and additional activities through crosstalk/bypassing, which exert biological activities through cell signaling pathways. Such mechanistic variations of estrogen action are not limited to flavonoids and are observed among other broad categories of chemicals, thus this group of chemicals can be termed as the "estrogenome". This review article focuses on the connection of estrogen action mainly between the outer and the inner environments, which represent variations of chemicals and biological activities/signaling pathways, respectively, and form the basis to understand their applications. The applications of chemicals will markedly progress due to emerging technologies, such as artificial intelligence for precision medicine, which is also true of the study of the estrogenome including estrogenic flavonoids.
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3
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Gobbi S, Martini S, Rozza R, Spinello A, Caciolla J, Rampa A, Belluti F, Zaffaroni N, Magistrato A, Bisi A. Switching from Aromatase Inhibitors to Dual Targeting Flavonoid-Based Compounds for Breast Cancer Treatment. Molecules 2023; 28:3047. [PMID: 37049810 PMCID: PMC10096035 DOI: 10.3390/molecules28073047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Despite the significant outcomes attained by scientific research, breast cancer (BC) still represents the second leading cause of death in women. Estrogen receptor-positive (ER+) BC accounts for the majority of diagnosed BCs, highlighting the disruption of estrogenic signalling as target for first-line treatment. This goal is presently pursued by inhibiting aromatase (AR) enzyme or by modulating Estrogen Receptor (ER) α. An appealing strategy for fighting BC and reducing side effects and resistance issues may lie in the design of multifunctional compounds able to simultaneously target AR and ER. In this paper, previously reported flavonoid-related potent AR inhibitors were suitably modified with the aim of also targeting ERα. As a result, homoisoflavone derivatives 3b and 4a emerged as well-balanced submicromolar dual acting compounds. An extensive computational study was then performed to gain insights into the interactions the best compounds established with the two targets. This study highlighted the feasibility of switching from single-target compounds to balanced dual-acting agents, confirming that a multi-target approach may represent a valid therapeutic option to counteract ER+ BC. The homoisoflavone core emerged as a valuable natural-inspired scaffold for the design of multifunctional compounds.
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Affiliation(s)
- Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Martini
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Via Amadeo 42, 20113 Milano, Italy
| | - Alessandra Magistrato
- National Research Council of Italy Institute of Materials (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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4
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Real-Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields. Chemistry 2022; 28:e202200985. [PMID: 35638164 DOI: 10.1002/chem.202200985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/09/2022]
Abstract
Intricate behaviour of one-electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic ϕ e s r and kinetic ϕ k r potentials and electron density ρ r allowed partitioning any molecules and crystals into atomic ρ - and potential-based ϕ -basins; ϕ k -basins explicitly account for the electron exchange effect, which is missed for ϕ e s -ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero-flux surfaces of ρ - and ϕ -basins. The gap between ϕ e s - and ρ -basins represents the charge transfer, while the gap between ϕ k - and ρ -basins is a real-space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of ρ -, ϕ e s -, and ϕ k - basin boundaries between interacting atoms was proposed. The position of ϕ k -boundary between ϕ e s - and ρ -ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an H⋅⋅⋅O hydrogen bond is, the deeper hydrogen atom's ϕ k -basin penetrates oxygen atom's ρ -basin, while for covalent bonds a ϕ k -boundary closely approaches a ϕ e s -one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the ρ -basin of an electron occupier atom.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation.,South Ural State University, 76 Lenin Avenue, Chelyabinsk, 454080, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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5
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Paciotti R, Chiavarino B, Coletti C, Scuderi D, Re N, Corinti D, Rotari L, Fornarini S, Crestoni ME. IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid. ACS OMEGA 2022; 7:19535-19544. [PMID: 35721943 PMCID: PMC9202291 DOI: 10.1021/acsomega.2c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/17/2022] [Indexed: 05/11/2023]
Abstract
Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Debora Scuderi
- Institut
de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Lucretia Rotari
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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6
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Comparative Study of Natural Antioxidants from Glycine max, Anethum graveolensand Pimpinella anisum Seed and Sprout Extracts Obtained by Ultrasound-Assisted Extraction. SEPARATIONS 2022. [DOI: 10.3390/separations9060152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The study aimed to evaluate the antioxidant potential of sprout and seed extracts from three species of plants, namely Glycine max (GMsp-sprouts, GMsd-seeds), Anethum graveolens (AGsp-sprouts, AGsd-seeds) and Pimpinella anisum (PAsp-sprouts, PAsd-seeds), which are widely accepted by consumers and have various applications in food flavoring, and also in natural medical treatments in the pharmaceutical industries. These plants are rich in valuable compounds that show a remarkable antioxidant power and are associated with many health benefits. Ethanol extracts were obtained by ultrasound-assisted extraction and they were comparatively evaluated for their in vitro antioxidant properties. The extracts were characterized by HPTLC, HPLC-DAD, total phenol content (TPC), total flavonoid content (TFC) analysis and antioxidant activities with different assays, such as total antioxidant capacity (TAC), 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) radical cation decolorization assay (ABTS), 1,1-diphenyl 1-2-picryl-hydrazyl (DPPH) and iron binding ability of chelators. Our results showed that the sprout and seed extracts of the studied plants exhibited a high content of phytochemicals and promising antioxidant properties. The highest polyphenols content was detected for AGsd (53.02 ± 0.57 mg/g DW), PAsd (48.75 ± 0.34 mg/g DW) and the highest flavonoids content for PAsp (26.84 ± 0.57 mg/g DW). Moreover, the presence of valuable compounds was demonstrated by using HPTLC, FT-IR and HPLC-DAD techniques. In order to have a better understanding of the relationship between the biological properties and the electronic structure, a molecular modelling study of genistein was also conducted. Our approach to the comparative assessment of these three plant species was based on a priori knowledge from literature data; however, this study demonstrated that these plant extracts of seeds and also sprouts are excellent sources of natural antioxidants. Significant additional differences that were found in the phytochemical composition could be exploited in future research for pharmaceutical purposes.
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7
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The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123690. [PMID: 35744821 PMCID: PMC9229234 DOI: 10.3390/molecules27123690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022]
Abstract
The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.
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8
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Li K, Zhang S, Sun Y, Chen Y, Chen W, Ruan W, Liu Y. Antiamyloid β toxicity effect of genistein via activation of DAF‐16 and HSP‐16.2 signal pathways in
Caenorhabditis elegans. J Biochem Mol Toxicol 2022; 36:e23055. [DOI: 10.1002/jbt.23055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Ke Li
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Saiya Zhang
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Yiyang Sun
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Yusi Chen
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Wenbo Chen
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Weibin Ruan
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
| | - Yanqiang Liu
- Department of Zoology and Developmental Biology, College of Life Sciences Nankai University Tianjin China
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9
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Akram S, Mehmood A, Noureen S, Ahmed M. Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis. Acta Crystallogr C Struct Chem 2022; 78:72-80. [DOI: 10.1107/s2053229621013607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/27/2021] [Indexed: 11/10/2022] Open
Abstract
Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.
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10
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Pinto CB, Rodrigues BL, Dos Santos LHR. Estimating electron density at the bond critical point through atomic Hirshfeld surfaces. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721009213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Interatomic surfaces often carry information related to the electron distribution in a molecule or crystal, not only being a visual aid but also enabling quantitative analyses. Under certain conditions, atomic Hirshfeld surfaces present a high resemblance to the interatomic surfaces obtained through the quantum theory of atoms in molecules (QTAIM), with the advantage of being easily calculated, even for crystal structures determined at low resolutions (i.e. when a charge-density refinement is not performed). Here an empirical relation between the curvedness property of the Hirshfeld surfaces and the electron density at the bond critical point for certain types of covalent and coordination interactions involving carbon atoms has been obtained. The exponential function was tested to estimate the electron density in different crystalline systems, and the highest deviation from reference values obtained through QTAIM was just 16%. Additionally, fine details of this fit may be salient to the difference in electronegativity of the atoms involved in the bond.
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11
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Delannoy López DM, Tran DT, Viault G, Dairi S, Peixoto PA, Capello Y, Minder L, Pouységu L, Génot E, Di Primo C, Deffieux D, Quideau S. Real-Time Analysis of Polyphenol-Protein Interactions by Surface Plasmon Resonance Using Surface-Bound Polyphenols. Chemistry 2021; 27:5498-5508. [PMID: 33443311 DOI: 10.1002/chem.202005187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 11/11/2022]
Abstract
A selection of bioactive polyphenols of different structural classes, such as the ellagitannins vescalagin and vescalin, the flavanoids catechin, epicatechin, epigallocatechin gallate (EGCG), and procyanidin B2, and the stilbenoids resveratrol and piceatannol, were chemically modified to bear a biotin unit for enabling their immobilization on streptavidin-coated sensor chips. These sensor chips were used to evaluate in real time by surface plasmon resonance (SPR) the interactions of three different surface-bound polyphenolic ligands per sensor chip with various protein analytes, including human DNA topoisomerase IIα, flavonoid leucoanthocyanidin dioxygenase, B-cell lymphoma 2 apoptosis regulator protein, and bovine serum albumin. The types and levels of SPR responses unveiled major differences in the association, or lack thereof, and dissociation between a given protein analyte and different polyphenolic ligands. Thus, this multi-analysis SPR technique is a valuable methodology to rapidly screen and qualitatively compare various polyphenol-protein interactions.
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Affiliation(s)
| | - Dong Tien Tran
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Guillaume Viault
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Sofiane Dairi
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | | | - Yoan Capello
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Laëtitia Minder
- INSERM, CNRS, IECB (US001, UMS 3033), Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Laurent Pouységu
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Elisabeth Génot
- Centre de Recherche Cardio-Thoracique de Bordeaux (INSERM U1045), Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Carmelo Di Primo
- INSERM, CNRS (U1212, UMR 5320), IECB, Univ. Bordeaux, 2 rue Robert Escarpit, 33607, Pessac Cedex, France
| | - Denis Deffieux
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Stéphane Quideau
- Univ. Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France.,Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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12
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Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
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Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
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Umereweneza D, Atilaw Y, Rudenko A, Gütlin Y, Bourgard C, Gupta AK, Orthaber A, Muhizi T, Sunnerhagen P, Erdélyi M, Gogoll A. Antibacterial and cytotoxic prenylated dihydrochalcones from Eriosema montanum. Fitoterapia 2021; 149:104809. [PMID: 33359421 DOI: 10.1016/j.fitote.2020.104809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022]
Abstract
Two new prenylated dihydrochalcones (1,2) and eighteen known secondary metabolites (3-20) were isolated from the CH2Cl2-MeOH (1:1) extracts of the roots, the stem bark and the leaves of Eriosema montanum Baker f. (Leguminosae). The structures of the isolated compounds were characterized by NMR, IR, and UV spectroscopic and mass spectrometric analyses. The structures of compounds 5, 10, 11 and 13 were confirmed by single crystal X-ray diffraction. The antibacterial activity of the crude extracts and the isolated constituents were established against Gram-positive and Gram-negative bacteria. Among the tested compounds, 1-4 and 10 showed strong activity against the Gram-positive bacterium Bacillus subtilis with minimum inhibitory concentration (MIC) ranging from 3.1 to 8.9 μM, as did the leaf crude extract with an MIC of 3.0 μg/mL. None of the crude extracts nor the isolated compounds were active against Escherichia coli. Compounds 1, 3 and 4 showed higher cytotoxicity, evaluated against the human breast cancer cell line MCF-7, with EC50 of 7.0, 18.0 and 18.0 μM, respectively. These findings contribute to the phytochemical understanding of the genus Eriosema, and highlight the pharmaceutical potential of prenylated dihydrochalcones.
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Affiliation(s)
- Daniel Umereweneza
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden; Department of Chemistry, College of Science and Technology, University of Rwanda, P.O Box 3900, Kigali, Rwanda
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Anastasia Rudenko
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Yukino Gütlin
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Catarina Bourgard
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Arvind Kumar Gupta
- Department of Chemistry - Ångström, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Andreas Orthaber
- Department of Chemistry - Ångström, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Théoneste Muhizi
- Department of Chemistry, College of Science and Technology, University of Rwanda, P.O Box 3900, Kigali, Rwanda
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden.
| | - Adolf Gogoll
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden.
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14
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Lu H, Qi Y, Zhao Y, Jin N. Effects of Hydroxyl Group on the Interaction of Carboxylated Flavonoid Derivatives with S. Cerevisiae α-Glucosidase. Curr Comput Aided Drug Des 2020; 16:31-44. [PMID: 30345924 PMCID: PMC6967131 DOI: 10.2174/1573409914666181022142553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023]
Abstract
Introduction Carboxyalkyl flavonoids derivatives are considered as effective inhibitors in reducing post-prandial hyperglycaemia. Methods Combined with Density Functional Theory (DFT) and the theory of Atoms in Molecules (AIM), molecular docking and charge density analysis are carried out to understand the molecular flexibility, charge density distribution and the electrostatic properties of these carboxyalkyl derivatives. Results Results show that the electron density of the chemical bond C14-O17 on B ring of molecule II increases while O17-H18 decreases at the active site, suggesting the existence of weak non-covalent interactions, most prominent of which are H-bonding and electrostatic interaction. When hydroxyl groups are introduced, the highest positive electrostatic potentials are distributed near the B ring hydroxyl hydrogen atom and the carboxyl hydrogen atom on the A ring. It was reported that quercetin has a considerably inhibitory activity to S. cerevisiae α-glucosidase, from the binding affinities, it is suggested that the position and number of hydroxyl groups on the B and C rings are also pivotal to the hypoglycemic activity when the long carboxyalkyl group is introduced into the A ring. Conclusion It is concluded that the presence of three well-defined zones in the structure, both hydrophobicity alkyl, hydrophilicity carboxyl and hydroxyl groups are necessary.
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Affiliation(s)
- Huining Lu
- Department of Life Sciences and Biological Engineering, Northwest Minzu University, Lanzhou 730124, China
| | - Yanjiao Qi
- Department of Chemical Engineering, Northwest Minzu University, Lanzhou 730124, China.,Key Laboratory for Utility of Environment-Friendly Composite Materials and Biomass in Universities of Gansu Province, Lanzhou, China
| | - Yaming Zhao
- Department of Chemical Engineering, Northwest Minzu University, Lanzhou 730124, China
| | - Nengzhi Jin
- Gansu Province Computing Center, Lanzhou 730000, China
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16
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Faroque MU, Mehmood A, Noureen S, Ahmed M. Crystal engineering and electrostatic properties of co-crystals of pyrimethamine with benzoic acid and gallic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Intermolecular interactions and charge density distribution of endocrine-disrupting molecules (xenoestrogens) with ERα: QM/MM perspective. Struct Chem 2020. [DOI: 10.1007/s11224-019-01452-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Costa JPL, Brito HO, Galvão-Moreira LV, Brito LGO, Costa-Paiva L, Brito LMO. Randomized double-blind placebo-controlled trial of the effect of Morus nigra L. (black mulberry) leaf powder on symptoms and quality of life among climacteric women. Int J Gynaecol Obstet 2019; 148:243-252. [PMID: 31736077 DOI: 10.1002/ijgo.13057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 09/03/2019] [Accepted: 11/15/2019] [Indexed: 01/20/2023]
Abstract
OBJECTIVE To test the efficacy of Morus nigra L. (MN) leaf powder for treating climacteric symptoms by comparison with hormone therapy (HT) and placebo. METHODS A randomized controlled trial among 62 climacteric women attending Hospital of the Federal University of Maranhão, Brazil. Women were divided into MN, HT, and placebo groups, and received 250 mg of MN leaf powder, 1 mg of estradiol, or placebo for 60 days. Primary outcomes were the Blatt-Kupperman index (BKI) for climacteric symptoms and SF-36 health questionnaire scores. RESULTS Baseline sociodemographic variables, BKI scores, symptoms, and SF-36 domains did not differ among the groups. There was a reduction in mean BKI in the MN (17.5 vs 9.7, P<0.001), HT (15.4 vs 8.6, P=0.001), and placebo (16.1 vs 12.4, P=0.040) groups. Analysis of quality of life (QoL) showed that functional capacity (P=0.006), vitality (P=0.031), mental health (P=0.017), and social aspect (P<0.01) improved after treatment in the MN group. The HT group showed improvement in emotional limitation (P=0.040), and the placebo group showed better functional capacity (P=0.030) after treatment. CONCLUSIONS Climacteric symptoms and QoL improved after administration of 250 mg of MN leaf powder for 60 days, similar to the effects of HT. The trial is registered in the Brazilian Registry of Clinical Trials (REBEC) under registration number RBR-9t4xxk.
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Affiliation(s)
- Joyce P L Costa
- Postgraduate Program in Adult Health, Federal University of Maranhão, São Luis, Maranhão, Brazil
| | - Haissa O Brito
- Postgraduate Program in Adult Health, Federal University of Maranhão, São Luis, Maranhão, Brazil
| | | | - Luiz G O Brito
- Department of Obstetrics and Gynecology, State University of Campinas, São Paulo, Brazil
| | - Lucia Costa-Paiva
- Department of Obstetrics and Gynecology, State University of Campinas, São Paulo, Brazil
| | - Luciane M O Brito
- Postgraduate Program in Adult Health, Federal University of Maranhão, São Luis, Maranhão, Brazil
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19
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Saravanan K, Sivanandam M, Hunday G, Pavan MS, Kumaradhas P. Exploring the different environments effect of piperine via combined crystallographic, QM/MM and molecular dynamics simulation study. J Mol Graph Model 2019; 92:280-295. [PMID: 31425905 DOI: 10.1016/j.jmgm.2019.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022]
Abstract
Piperine is a pungent alkaloid, largely present in the skin of pepper. It is the most active component of pepper and being used as a medicine in many Asian countries. The effect of piperine on memory impairment and neurodegeneration in Alzheimer's disease model has been investigated. In the present study, we aim to investigate the effect of piperine molecule in different environments (crystal and active site of proteins) from crystallography, molecular docking, QM/MM based charge density analysis and molecular dynamic simulation. The crystal structure of piperine has been used to determine the topological electron density of intermolecular interactions. The O-atoms of piperine is forming C-H⋅⋅⋅O interactions with the neighboring molecules in the crystal, these interactions also confirmed from the Hirshfeld surface. Further, to understand the nature of interactions and the conformational flexibility of piperine in the active site of recombinant human acetylcholinesterase (rhAChE), molecular docking analysis has been performed. The selected docked complex suggests favorable hydrogen bonding and hydrophobic interactions with rhAChE enzyme; notably, the O3 atom of piperine molecule forms strong hydrogen bonding interaction with Glu202 at 1.8 Å. To determine the charge density distribution and the electrostatic properties of piperine molecule in the active site of rhAChE, the piperine-rhAChE complex was minimized at QM/MM energy level; in which, the binding pocket with piperine was considered as QM region. The charge density analysis of piperine and the interacting amino acid groups have been carried out. The topological analysis of O3⋯H-O/Glu202 hydrogen bonding interaction exhibits strong interactions and the electron density ρcp(r): 0.242 eÅ-3 and the Laplacian ∇2ρcp(r): 3.176 eÅ-5 respectively. These results were compared with the corresponding molecule present in the crystal and gas phase environments of piperine. The comparison of active site structure with the corresponding crystal phase and gas phase structures reveal that piperine exhibits large conformational modification in the active site. The molecular dynamics simulation and binding free energy calculations were performed, this gives the stability, binding affinity of the molecule in the active site of rhAChE. The O3⋯H-O/Glu202 interaction shows the high stability (89.2%), this was confirmed from the stability of hydrogen bond analysis. The binding free energy was used to measure the rate of inhibition of enzyme in the presence of ligand molecule. The comparative study allows to understand the nature of piperine molecule in the gas and crystal phases, and amino acids environment.
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Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Mysore S Pavan
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India.
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20
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Hasil A, Mehmood A, Ahmed M. Experimental and theoretical charge-density analysis of hippuric acid: insight into its binding with human serum albumin. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:750-762. [PMID: 32830731 DOI: 10.1107/s2052520619007911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/02/2019] [Indexed: 11/10/2022]
Abstract
In order to comprehend the binding of an important metabolite, hippuric acid, with human serum albumin and to understand its chemical and electronic nature, an experimental charge-density analysis has been carried out using high-resolution diffraction data collected under cryogenic conditions, and all the results have been compared with theoretical findings using the B3LYP/6-311++g(2d,2p) level of theory. The structure displays very strong classical hydrogen bonds as well as other noncovalent interactions, which have been fully characterized using Hirshfeld surface analysis and Bader's quantum theory of atoms in molecules. Contact analysis on the Hirshfeld surfaces shows that the O...H, C...H and C...N intermolecular interactions are enriched and gives their relative strengths. Topological analysis of the electron density shows the charge concentration/depletion of hippuric acid bonds in the crystal structure. Electrostatic parameters such as atomic charges and dipole moments were calculated. The mapping of atomic basins and the calculation of respective charges show the atomic volumes of each atom as well as their charge contributions in the hippuric acid crystal structure. The dipole-moment calculations show that the molecule is very polar in nature. Calculations of the electrostatic potential show that the chain part of the molecule has a higher concentration of negative charge than the ring, which might be instrumental in its strong binding with the polar residues of site II of human serum albumin.
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Affiliation(s)
- Asma Hasil
- Materials Chemistry Laboratory, Department of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus 63100, Pakistan
| | - Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, Texas 76129, USA
| | - Maqsood Ahmed
- Materials Chemistry Laboratory, Department of Chemistry, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus 63100, Pakistan
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21
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Chinnasamy K, Saravanan M, Poomani K. Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations. J Biomol Struct Dyn 2019; 38:219-235. [DOI: 10.1080/07391102.2019.1574605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kalaiarasi Chinnasamy
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Manjula Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
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22
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Zhao H, Song X, Zhang Y, Sheng X. Molecular interaction between MeOH and genistein during soy extraction. RSC Adv 2019; 9:39170-39179. [PMID: 35540639 PMCID: PMC9076023 DOI: 10.1039/c9ra05976h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/22/2019] [Indexed: 11/23/2022] Open
Abstract
Genistein has received great attention due to its possible anti-oxidant properties. The interaction between genistein and the extraction solvent helps in understanding the extraction efficiency. Hydrogen bonding plays a crucial role in liquid systems. Density functional theory quantum chemical computations in both gas phase and solution were performed to investigate the molecular interaction between genistein and methanol. All the resulting complexes (MeOH : genistein = 1 : 1, 2 : 1, 3 : 1, 6 : 1) were studied using the B3LYP-D3 computational level and the cc-pVTZ basis set. Binding energies demonstrate that more MeOH molecules surrounding genistein could stabilize the system more. Geometry optimizations show that there are strong O–H⋯O interactions between MeOH and genistein. The electron density and the corresponding Laplacian of charge density at bond critical points were also calculated using AIM theory, and the results are in line with the structural and energetic analysis of the studied system. Moreover, energy decomposition analysis shows that the exchange energy term has the largest contribution to the attraction interaction energy as compared with other energy terms. Meanwhile, this study shows that the MeOH–genistein system is more stable under basic conditions. This study could help increase the efficiency of extraction. The interaction between genistein and extraction solvent helps in understanding the extraction efficiency.![]()
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Affiliation(s)
- Hailiang Zhao
- Province Key Laboratory of Cereal Resource Transformation and Utilization
- Henan University of Technology
- 450001 Zhengzhou
- China
- College of Chemistry, Chemical and Environmental Engineering
| | - Xue Song
- College of Chemistry, Chemical and Environmental Engineering
- Henan University of Technology
- 450001 Zhengzhou
- China
| | - Yingming Zhang
- College of Chemistry, Chemical and Environmental Engineering
- Henan University of Technology
- 450001 Zhengzhou
- China
| | - Xia Sheng
- College of Chemistry, Chemical and Environmental Engineering
- Henan University of Technology
- 450001 Zhengzhou
- China
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23
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Manjula S, Sivanandam M, Kumaradhas P. Probing the "fingers" domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations. J Biomol Struct Dyn 2018; 37:2440-2456. [PMID: 30047829 DOI: 10.1080/07391102.2018.1491419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the "fingers" sub-domain of NS5B. The "fingers" domain is a new emerging allosteric site for the HCV drug development. The inhibitors of the "fingers" sub-domain adopt a new antiviral mechanism called RNA intervention. The details of essential amino acid residues, binding mode of the ligand, and the active site intermolecular interactions of RNA intervention reflect that this mechanism is ambiguous in the experimental study. To elucidate these details, we performed molecular docking analysis of the fingers domain inhibitor quercetagetin (QGN) with NS5B polymerase. The detailed analysis of QGN-NS5B intermolecular interactions was carried out and found that QGN interacts with the binding pocket amino acid residues Ala97, Ala140, Ile160, Phe162, Gly283, Gly557, and Asp559; and also forms π⋯π stacking interaction with Phe162 and hydrogen bonding interaction with Gly283. These are found to be the essential interactions for the RNA intervention mechanism. Among the strong hydrogen bonding interactions, the QGN⋯Ala140 is a newly identified important hydrogen bonding interaction by the present work and this interaction was not resolved by the previously reported crystal structure. Since D559G mutation at the fingers domain was reported for reducing the inhibition percentage of QGN to sevenfold, we carried out molecular dynamics (MD) simulation for wild and D559G mutated complexes to study the stability of protein conformation and intermolecular interactions. At the end of 50 ns MD simulation, the π⋯π stacking interaction of Phe162 with QGN found in the wild-type complex is altered into T-shaped π stacking interaction, which reduces the inhibition strength. The origin of the D559G resistance mutation was studied using combined MD simulation, binding free energy calculations and principal component analysis. The results were compared with the wild-type complex. The mutation D559G reduces the binding affinity of the QGN molecule to the fingers domain. The free energy decomposition analysis of each residue of wild-type and mutated complexes revealed that the loss of non-polar energy contribution is the origin of the resistance. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saravanan Manjula
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
| | - Magudeeswaran Sivanandam
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
| | - Poomani Kumaradhas
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
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Qi YJ, Lu HN, Jin NZ, Zhang JY, Dong JQ. Understanding of the conformational flexibility and electrostatic properties of coumarin derivatives in the active site of S. cerevisiae α-glucosidase. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
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Szeja W, Grynkiewicz G, Rusin A. Isoflavones, their Glycosides and Glycoconjugates. Synthesis and Biological Activity. CURR ORG CHEM 2016; 21:218-235. [PMID: 28553156 PMCID: PMC5427819 DOI: 10.2174/1385272820666160928120822] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/20/2016] [Accepted: 09/22/2016] [Indexed: 11/22/2022]
Abstract
Glycosylation of small biologically active molecules, either of natural or synthetic origin, has a profound impact on their solubility, stability, and bioactivity, making glycoconjugates attractive compounds as therapeutic agents or nutraceuticals. A large proportion of secondary metabolites, including flavonoids, occur in plants as glycosides, which adds to the molecular diversity that is much valued in medicinal chemistry studies. The subsequent growing market demand for glycosidic natural products has fueled the development of various chemical and biotechnological methods of glycosides preparation. The review gives an extensive overview of the processes of the synthesis of isoflavones and discusses recently developed major routes towards isoflavone-sugar formation processes. Special attention is given to the derivatives of genistein, the main isoflavone recognized as a useful lead in several therapeutic categories, with particular focus on anticancer drug design. The utility of chemical glycosylations as well as glycoconjugates preparation is discussed in some theoretical as well as practical aspects. Since novel approaches to chemical glycosylations and glycoconjugations are abundant and many of them proved suitable for derivatization of polyphenols a new body of evidence has emerged, indicating that sugar moiety can play a much more significant role, when attached to a pharmacophore, then being a mere “solubilizer”. In many cases, it has been demonstrated that semisynthetic glycoconjugates are much more potent cytostatic and cytotoxic agents than reference isoflavones. Moreover, the newly designed glycosides or glycoside mimics can act through different mechanisms than the parent active molecule.
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Affiliation(s)
- Wiesław Szeja
- Silesian Technical University, Department of Chemistry, Krzywoustego 4, 44-100 Gliwice, Poland
| | | | - Aleksandra Rusin
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Wybrzeze AK 15, 44-100 Gliwice, Poland
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Exploring molecular flexibility and the interactions of Quercetin derivatives in the active site of α-glucosidase using molecular docking and charge density analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Qi Y, Zhao Y, Wang X, Lu H, Jin N. Comparative analysis of interactions between the hydropyridine dicarboxylate derivatives and different proteins by molecular docking and charge density analysis. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular docking and charge density analysis were carried out to understand the geometry, charge density distribution and electrostatic properties of one of newly synthesized 4-substituted-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylates (PDE), which is regarded as the best [Formula: see text]-Glucosidase inhibitor among the hydropyridine dicarboxylate derivatives. The different bonding models of the PDE molecule in the active sites of proteins Human serum albumin (HSA) and Saccharomyces cerevisiae [Formula: see text]-glucosidase (SAG) are firstly compared, which is important to understand the different intermolecular interactions between drug-transport protein and drug-target protein. The deformation density maps suggest that the electron densities of the PDE molecule are redistributed when it presents in the active sites. When the molecule presents in the active site of the SAG, it is evident to find that the negative region does not appear at the vicinity of the oxygen atoms on one of the carboxylic acid dimethyl ester group. Frontier molecular orbital density distributions for the PDE molecule are similar in all forms. The highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy gaps in the active sites are higher than that of the molecule in pure solution phase. It is generally noticed that all of the orientations of the dipole moment vectors are reoriented in both active sites. These fine details at electronic level allow to better understand the exact drug-transport protein and drug-target protein interactions.
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Affiliation(s)
- Yanjiao Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Yaming Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Xiaoe Wang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Huining Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou 730124, P. R. China
| | - Nengzhi Jin
- Gansu Province Computing Center, Lanzhou 730000, P. R. China
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Stolarczyk EU, Stolarczyk K, Łaszcz M, Kubiszewski M, Maruszak W, Olejarz W, Bryk D. Synthesis and characterization of genistein conjugated with gold nanoparticles and the study of their cytotoxic properties. Eur J Pharm Sci 2016; 96:176-185. [PMID: 27644892 DOI: 10.1016/j.ejps.2016.09.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 10/21/2022]
Abstract
Gold nanoparticles conjugated with drug substances are used in diagnostics and therapies. Apart from the combinations involving gold nanoparticles conjugated with drug substances through linkers, a direct bonding is also known. In our paper the example of such a direct bonding between gold nanoparticles and genistein (AuNPs-GE) is presented. This conjugate was obtained in a one-pot synthesis and the formation of AuNPs-GE was monitored in terms of color change and UV-Vis spectroscopy. It has been shown that genistein reduces Au3+ ions to spherical Au0 nanocrystallites and acts as a stabilizing agent. The efficiency of the purification of the conjugate from free genistein was controlled by the capillary electrophoresis. Gold nanoparticles are homogeneously shaped and have a narrow range of size from 14 to 33nm and the size of the nanoparticles modified with genistein is around 64.64±0.41nm, as measured by the TEM and DSL techniques, respectively. The zeta potential of the gold nanoparticles modified with genistein is -19.32±0.82mV and suggests a high stability of the nanoparticles and lower toxicity for the normal cells. The identity of genistein on the gold nanoparticles was proved by the electrochemistry, NMR and Raman spectroscopy. The mechanism of the conjugate forming has been proposed. The coverage of gold nanoparticles with genistein 5.09% (m/m) has been calculated from the TGA analysis. Moreover, it has been proved that the obtained conjugate is characterized by a high cytotoxic activity towards cancer cells, as observed in the cell line test.
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Affiliation(s)
- Elżbieta U Stolarczyk
- Pharmaceutical Research Institute, R&D Analytical Department, 8 Rydygiera Str., 01-793Warsaw, Poland.
| | - Krzysztof Stolarczyk
- University of Warsaw, Faculty of Chemistry, 1 Pasteura Str., 02-093 Warsaw, Poland.
| | - Marta Łaszcz
- Pharmaceutical Research Institute, R&D Analytical Department, 8 Rydygiera Str., 01-793Warsaw, Poland
| | - Marek Kubiszewski
- Pharmaceutical Research Institute, R&D Analytical Department, 8 Rydygiera Str., 01-793Warsaw, Poland
| | - Wioleta Maruszak
- Pharmaceutical Research Institute, R&D Analytical Department, 8 Rydygiera Str., 01-793Warsaw, Poland
| | - Wioletta Olejarz
- Warsaw Medical University, Department of Biochemistry and Clinical Chemistry, 1 Banacha Str, 02-097 Warsaw, Poland
| | - Dorota Bryk
- Warsaw Medical University, Department of Biochemistry and Clinical Chemistry, 1 Banacha Str, 02-097 Warsaw, Poland
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30
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Zhurova EA, Zhurov VV, Kumaradhas P, Cenedese S, Pinkerton AA. Charge Density and Electrostatic Potential Study of 16α,17β-Estriol and the Binding of Estrogen Molecules to the Estrogen Receptors ERα and ERβ. J Phys Chem B 2016; 120:8882-91. [PMID: 27504698 DOI: 10.1021/acs.jpcb.6b05961] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An accurate X-ray diffraction study at 20 K combined with DFT theoretical calculations has been performed for the estriol crystal with two conformationally different molecules in the asymmetric unit. The electron density has been modeled via a multipole expansion, using both experimental and theoretical structure factors, and a topological analysis has been performed. The experimental molecular geometry, hydrogen bonding, atomic charges, dipole moments, and other topological characteristics are compared with those calculated theoretically. In particular, the molecular electrostatic potential has been extracted and compared with those reported for other estrogen molecules exhibiting different binding affinities to the estrogen receptors (ERα and ERβ).
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Affiliation(s)
- Elizabeth A Zhurova
- Department of Chemistry, The University of Toledo , Toledo, Ohio 43606, United States
| | - Vladimir V Zhurov
- Department of Chemistry, The University of Toledo , Toledo, Ohio 43606, United States
| | - Poomani Kumaradhas
- Department of Chemistry, The University of Toledo , Toledo, Ohio 43606, United States.,Department of Physics, Laboratory of Biocrystallography and Computational Molecular Biology, Periyar University , Salem 636 011, India
| | - Simone Cenedese
- Department of Chemistry, The University of Toledo , Toledo, Ohio 43606, United States
| | - A Alan Pinkerton
- Department of Chemistry, The University of Toledo , Toledo, Ohio 43606, United States
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31
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Revised structure of trans-resveratrol: Implications for its proposed antioxidant mechanism. Bioorg Med Chem Lett 2016; 26:1416-8. [DOI: 10.1016/j.bmcl.2016.01.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 11/23/2022]
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32
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Kirby IL, Pitak MB, Coles SJ, Gale PA. Systematic Experimental Charge Density: Linking Structural Modifications to Electron Density Distributions. CHEM LETT 2015. [DOI: 10.1246/cl.140929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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Rajalakshmi G, Hathwar VR, Kumaradhas P. Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2014; 70:568-79. [DOI: 10.1107/s205252061303388x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 12/15/2013] [Indexed: 11/10/2022]
Abstract
An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin θ/λ)max= 1.1 Å−1] measured at 100 (2) K. The structure was solved by direct methods usingSHELXS97 and refined bySHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen–Coppens multipole formalism implemented in theXDsoftware. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained fromCRYSTAL09at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N—H...N and N—H...O hydrogen bonds, in which the N3—H3B...N1 and N3—H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the π-electron cloud.
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36
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Leclercq G, Jacquot Y. Interactions of isoflavones and other plant derived estrogens with estrogen receptors for prevention and treatment of breast cancer-considerations concerning related efficacy and safety. J Steroid Biochem Mol Biol 2014; 139:237-44. [PMID: 23274118 DOI: 10.1016/j.jsbmb.2012.12.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/07/2012] [Accepted: 12/18/2012] [Indexed: 12/20/2022]
Abstract
Phytoestrogens are natural endocrine disruptors that interfere with estrogenic pathways. They insert directly within the hormone-binding domain of ERα and β, with a preference for the β isoform of which the concentration predominates in the normal mammary epithelium. Since ERβ antagonizes the growth promoting effect of ERα, which is mainly expressed in estrogen-sensitive tumor cells, a potential protective action against breast cancer incidence has been ascribed to phytoestrogens. The fact that Asian women living in far-east countries who consume isoflavone-rich food are less subjected to breast cancer emergence than their congeners in the USA as well as Caucasian women has been advocated to justify such a concept. Overview of data concerning the mechanism of action phytoestrogens reveals that such a view is an oversimplification: Such compounds interfere with a huge panel of regulatory proteins, giving rise to both promoting and antagonizing carcinogenic effects. Moreover, various physiological and pathological factors able to amplify these effects are not often sufficiently taken into account, which increases the difficulty to interpret data. Nevertheless, this overview of data established that chemical structures and concentrations modulate such effects: at the micromolar level, isoflavones activate ERα-mediated transcription and breast cancer cell proliferation while flavones fail to induce any significant promoting effects. At higher doses, both classes of compounds may display an antitumor activity. Reasons for such distinct behaviors as well as their potential impact in therapeutic applications are analyzed here. Ability of isoflavones and flavones to antagonize the association of calmodulin to ERα, which is required for its enhanced transcriptional activity is evoked to justify the antitumor activity ascribed to some flavones. Finally, a suspicion that peculiar classes of phytoestrogens may adopt a SERM-like conformation is addressed in a context of selection and synthesis of compounds with non-equivocal therapeutic value. This article is part of a Special Issue entitled "Phytoestrogens".
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Affiliation(s)
- Guy Leclercq
- Laboratoire J.-C. Heuson de Cancérologie Mammaire, Université Libre de Bruxelles (U.L.B.), Institut Jules Bordet, 1, rue Héger Bordet, Brussels, B-1000, Belgium.
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37
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Copper(II) complexes with cyanoguanidine and o-phenanthroline: Theoretical studies, in vitro antimicrobial activity and alkaline phosphatase inhibitory effect. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Grabowsky S, Jayatilaka D, Fink RF, Schirmeister T, Engels B. Can Experimental Electron-Density Studies be Used as a Tool to Predict Biologically Relevant Properties of Low-Molecular Weight Enzyme Ligands? Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201200518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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39
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Devipriya B, Kumaradhas P. Molecular flexibility and the electrostatic moments of curcumin and its derivatives in the active site of p300: a theoretical charge density study. Chem Biol Interact 2013; 204:153-65. [PMID: 23684744 DOI: 10.1016/j.cbi.2013.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 04/15/2013] [Accepted: 05/05/2013] [Indexed: 01/07/2023]
Abstract
A molecular docking analysis and quantum chemical calculation coupled with the charge density analysis have been carried out to understand the conformational change, charge density distribution and the electrostatic properties of HAT inhibitors curcumin and its derivatives (cinnamoyl compounds) in the active site of p300. The nearest neighbours, the shortest intermolecular contacts between the inhibitors and receptor p300; their binding energies were calculated from molecular docking analysis. A high level quantum chemical calculations were performed using density functional theory (DFT-B3LYP) with the basis set 6-311G(∗∗) combined with the theory of atoms in molecules (AIM) for the inhibitors in gas phase and in the active site of p300. It is observed that, when the molecules present in the active site of p300, relatively, their geometrical, bond topological and the electrostatic properties are significantly altered. The comparative study on the geometrical and electrostatic properties of these three inhibitors in gas phase and amino acid environment gives an insight on the molecular flexibility and the exact modification of electrostatic interaction of the inhibitor in the active site of p300. These fine details at electronic level allow to understand the exact drug-receptor interaction.
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Affiliation(s)
- B Devipriya
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
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40
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Sowa M, Ślepokura K, Matczak-Jon E. Cocrystals of fisetin, luteolin and genistein with pyridinecarboxamide coformers: crystal structures, analysis of intermolecular interactions, spectral and thermal characterization. CrystEngComm 2013. [DOI: 10.1039/c3ce41285g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Whaley WL, Okoso-amaa EM, Womack CL, Vladimirova A, Rogers LB, Risher MJ, Abraham MH. Summation Solute Hydrogen Bonding Acidity Values for Hydroxyl Substituted Flavones Determined by NMR Spectroscopy. Nat Prod Commun 2013. [DOI: 10.1177/1934578x1300800121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The flavonoids are a structurally diverse class of natural products that exhibit a broad spectrum of biochemical activities. The flavones are one of the most studied flavonoid subclasses due to their presence in dietary plants and their potential to protect human cells from reactive oxygen species (ROS). Several flavone compounds also mediate beneficial actions by direct binding to protein receptors and regulatory enzymes. There is current interest in using Quantitative Structure Activity Relationships (QSARs) to guide drug development based on flavone lead structures. This approach is most informative when it involves the use of accurate physical descriptors. The Abraham summation solute hydrogen bonding acidity ( A) is a descriptor in the general solvation equation. It defines the tendency of a molecule to act as a hydrogen bond donor, or acid, when surrounded by solvent molecules that are hydrogen bonding acceptors, or bases. As a linear free energy relationship, it is useful for predicting the absorption and uptake of drug molecules. A previously published method, involving nuclear magnetic resonance (NMR) spectroscopy, was used to evaluate A for the monohydroxyflavones (MHFs). Values of A ranged from 0.02, for 5-hydroxyflavone, to 0.69 for 4′-hydroxyflavone. The ability to examine separate NMR signals for individual hydroxyl groups allowed the investigation of intramolecular interactions between functional groups. The value of A for the position 7 hydroxyl group of 7-hydroxyflavone was 0.67. The addition of a position 5 hydroxyl group (in 5,7-dihydroxyflavone) increased the value of A for the position 7 hydroxyl group to 0.76. Values of A for MHFs were also calculated by the program ACD-Absolve and these agreed well with values measured by NMR. These results should facilitate more accurate estimation of the values of A for structurally complex flavones with pharmacological activities.
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Affiliation(s)
- William L. Whaley
- Department of Chemistry, Geosciences and Environmental Science, Tarleton State University, Box T-0540, Stephenville, TX 76401, USA
| | | | - Cody L. Womack
- Department of Chemistry, Northeast Texas Community College, Mount Vernon, TX 75456, USA
| | - Anna Vladimirova
- Department of Chemistry, Texas A&M University-College Station, College Station, TX 77840, USA
| | - Laura B. Rogers
- Supplier Quality Management, Lockheed Martin, Fort Worth, TX 76126, USA
| | - Margaret J. Risher
- Department of Chemistry, Geosciences and Environmental Science, Tarleton State University, Box T-0540, Stephenville, TX 76401, USA
| | - Michael H. Abraham
- Department of Chemistry, University College of London, 20 Gordon Street, London, WC1H 0AJ, UK
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42
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Chopra D. Advances in understanding of chemical bonding: inputs from experimental and theoretical charge density analysis. J Phys Chem A 2012; 116:9791-801. [PMID: 22928665 DOI: 10.1021/jp306169f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of charge density analysis has undergone a major renaissance in the last two decades. In recent years, the characterization of bonding features associated with atoms in molecules and in crystals has been explored using high-resolution X-ray diffraction data (laboratory or synchrotron) complemented by high level ab initio theoretical calculations. The extraction of one electron topological properties, namely, electrostatic charges, dipole moment and higher moments, electrostatic potential, electric field gradients, in addition to evaluation of the local kinetic and potential energy densities, have contributed toward an understanding of the electron density distributions in molecular solids. New topological descriptors, namely, the source function (SF) and electron localization function (ELF) provide additional information as regards characterization of the topology of the electron density. In addition, delocalization indices have also been developed to account for bonding features pertinent to M-M bonds. The evaluation of these properties have contributed significantly toward the understanding of intra- and intermolecular bonding features in organic, inorganic, and biomolecules in the crystalline phase, with concomitant applications in the understanding of chemical reactivity and material/biological properties. In recent years, the focus has strongly shifted toward the understanding of structure-property relationships in organometallic complexes containing labile M-C bonds in the crystal structure with subsequent implications in catalysis. This perspective aims to highlight the major developments in electron density measurements in the past few years and provides pointers directed toward the potential use of this technique in future applications for an improved understanding of chemical bonding in systems that have been unexplored.
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Affiliation(s)
- Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462023, India.
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43
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Sigalov MV, Doronina EP, Sidorkin VF. CAr–H···O Hydrogen Bonds in Substituted Isobenzofuranone Derivatives: Geometric, Topological, and NMR Characterization. J Phys Chem A 2012; 116:7718-25. [DOI: 10.1021/jp304009g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mark V. Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, 84105 Beer-Sheva,
Israel
| | - Evgeniya P. Doronina
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
| | - Valery F. Sidorkin
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
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Devipriya B, Kumaradhas P. Probing the effect of intermolecular interaction and understanding the electrostatic moments of anacardic acid in the active site of p300 enzyme via DFT and charge density analysis. J Mol Graph Model 2011; 34:57-66. [PMID: 22306413 DOI: 10.1016/j.jmgm.2011.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/19/2011] [Accepted: 12/19/2011] [Indexed: 01/07/2023]
Abstract
A charge density analysis has been performed on gas phase and docked forms of anacardic acid molecule to understand its charge density distribution, electrostatic moments and the conformation in the active site of p300 enzyme. Here, we report the binding affinity of anacardic acid with the p300 enzyme calculated from docking analysis. The charge density distribution of anacardic acid molecule in the gas phase as well as the docked form has been determined from the high level quantum chemical calculations using HF and DFT methods coupled with AIM theory. The charge density study on both forms of anacardic acid differentiates its structural and the electrostatic properties in different environments. When the molecule enters into the active site of p300 its conformation, charge density distribution, dipole moment and electrostatic potential are significantly altered in comparison to its gas phase structure. In the active site, the molecule adopts different conformations, its pentadecyl chain is found to be highly twisted; the charges are redistributed and the dipole moment increases from 2.37 to 3.17D. Due to the charge redistribution, the electronegative region of carboxyl group increased as it is found small in the gas phase. The comparisons between both forms reveal the flexibility of anacardic acid in the active site.
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Affiliation(s)
- B Devipriya
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636011, India
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45
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David Stephen A, Srinivasan P, Kumaradhas P. Bond charge depletion, bond strength and the impact sensitivity of high energetic 1,3,5-triamino 2,4,6-trinitrobenzene (TATB) molecule: A theoretical charge density analysis. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.04.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Rajalakshmi G, Devipriya B, Parameswari AR, Stephen AD, Kumaradhas P. Understanding the NN bond cleavage and the electrostatic properties of isoniazid drug molecule via theoretical charge density study. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Quideau S, Deffieux D, Douat-Casassus C, Pouységu L. Pflanzliche Polyphenole: chemische Eigenschaften, biologische Aktivität und Synthese. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201000044] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Quideau S, Deffieux D, Douat-Casassus C, Pouységu L. Plant polyphenols: chemical properties, biological activities, and synthesis. Angew Chem Int Ed Engl 2011; 50:586-621. [PMID: 21226137 DOI: 10.1002/anie.201000044] [Citation(s) in RCA: 1515] [Impact Index Per Article: 116.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 03/29/2010] [Indexed: 01/16/2023]
Abstract
Eating five servings of fruits and vegetables per day! This is what is highly recommended and heavily advertised nowadays to the general public to stay fit and healthy! Drinking green tea on a regular basis, eating chocolate from time to time, as well as savoring a couple of glasses of red wine per day have been claimed to increase life expectancy even further! Why? The answer is in fact still under scientific scrutiny, but a particular class of compounds naturally occurring in fruits and vegetables is considered to be crucial for the expression of such human health benefits: the polyphenols! What are these plant products really? What are their physicochemical properties? How do they express their biological activity? Are they really valuable for disease prevention? Can they be used to develop new pharmaceutical drugs? What recent progress has been made toward their preparation by organic synthesis? This Review gives answers from a chemical perspective, summarizes the state of the art, and highlights the most significant advances in the field of polyphenol research.
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Affiliation(s)
- Stéphane Quideau
- Université de Bordeaux, Institut des Sciences Moléculaires (CNRS-UMR 5255), 2 rue Robert Escarpit, 33607 Pessac Cedex, France.
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Leclercq G, de Cremoux P, This P, Jacquot Y. Lack of sufficient information on the specificity and selectivity of commercial phytoestrogens preparations for therapeutic purposes. Maturitas 2011; 68:56-64. [DOI: 10.1016/j.maturitas.2010.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 10/11/2010] [Accepted: 10/12/2010] [Indexed: 12/16/2022]
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50
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Zhurova EA, Zhurov VV, Chopra D, Stash AI, Pinkerton AA. 17α-Estradiol·1/2 H2O: Super-Structural Ordering, Electronic Properties, Chemical Bonding, and Biological Activity in Comparison with Other Estrogens. J Am Chem Soc 2009; 131:17260-9. [DOI: 10.1021/ja906057z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth A. Zhurova
- Department of Chemistry, the University of Toledo, Toledo, Ohio 43606, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and Karpov’ Institute of Physical Chemistry, Moscow, Russia
| | - Vladimir V. Zhurov
- Department of Chemistry, the University of Toledo, Toledo, Ohio 43606, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and Karpov’ Institute of Physical Chemistry, Moscow, Russia
| | - Deepak Chopra
- Department of Chemistry, the University of Toledo, Toledo, Ohio 43606, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and Karpov’ Institute of Physical Chemistry, Moscow, Russia
| | - Adam I. Stash
- Department of Chemistry, the University of Toledo, Toledo, Ohio 43606, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and Karpov’ Institute of Physical Chemistry, Moscow, Russia
| | - A. Alan Pinkerton
- Department of Chemistry, the University of Toledo, Toledo, Ohio 43606, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462 023, India, and Karpov’ Institute of Physical Chemistry, Moscow, Russia
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