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Avramopoulos A, Reis H, Tzeli D, Zaleśny R, Papadopoulos MG. Photoswitchable Molecular Units with Tunable Nonlinear Optical Activity: A Theoretical Investigation. Molecules 2023; 28:5646. [PMID: 37570617 PMCID: PMC10419997 DOI: 10.3390/molecules28155646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
The first-, second-, and third-order molecular nonlinear optical properties, including two-photon absorption of a series of derivatives, involving two dithienylethene (DTE) groups connected by several molecular linkers (bis(ethylene-1,2-dithiolato)Ni- (NiBDT), naphthalene, quasilinear oligothiophene chains), are investigated by employing density functional theory (DFT). These properties can be efficiently controlled by DTE switches, in connection with light of appropriate frequency. NiBDT, as a linker, is associated with a greater contrast, in comparison to naphthalene, between the first and second hyperpolarizabilities of the "open-open" and the "closed-closed" isomers. This is explained by invoking the low-lying excited states of NiBDT. It is shown that the second hyperpolarizability can be used as an index, which follows the structural changes induced by photochromism. Assuming a Förster type transfer mechanism, the intramolecular excited-state energy transfer (EET) mechanism is studied. Two important parameters related to this are computed: the electronic coupling (VDA) between the donor and acceptor fragments as well as the overlap between the absorption and emission spectra of the donor and acceptor groups. NiBDT as a linker is associated with a low electronic coupling, VDA, value. We found that VDA is affected by molecular geometry. Our results predict that the linker strongly influences the communication between the open-closed DTE groups. The sensitivity of the molecular nonlinear optical properties could assist with identification of molecular isomers.
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Affiliation(s)
| | - Heribert Reis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece; (H.R.); (M.G.P.)
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece;
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland;
| | - Manthos G. Papadopoulos
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece; (H.R.); (M.G.P.)
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2
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Matis I, Delivoria DC, Mavroidi B, Papaevgeniou N, Panoutsou S, Bellou S, Papavasileiou KD, Linardaki ZI, Stavropoulou AV, Vekrellis K, Boukos N, Kolisis FN, Gonos ES, Margarity M, Papadopoulos MG, Efthimiopoulos S, Pelecanou M, Chondrogianni N, Skretas G. Publisher Correction: An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding. Nat Biomed Eng 2018; 2:49. [PMID: 31015658 DOI: 10.1038/s41551-017-0164-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, in Fig. 1c-e, on the x axes, the lines labelled 'Aβ42' and 'Aβ42(F19S;L34P)' grouped the data incorrectly; the line labelled Aβ42 should have grouped the data for Random 1-2 and Clones 1-10, and the line labelled Aβ42(F19S;L34P) should have only grouped the data for Random 1-2 on the right end of the plots and blots. These figures have now been corrected in all versions of the Article.
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Affiliation(s)
- Ilias Matis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Dafni Chrysanthi Delivoria
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Barbara Mavroidi
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Nikoletta Papaevgeniou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Faculty of Biology and Pharmacy, Institute of Nutrition, Friedrich Schiller University of Jena, 07743, Jena, Germany
| | - Stefania Panoutsou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Department of Biology, National and Kapodistrian University of Athens, 15701, Athens, Greece
| | - Stamatia Bellou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Zacharoula I Linardaki
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Department of Biology, University of Patras, 26504, Patras, Greece
| | | | - Kostas Vekrellis
- Department of Neuroscience, Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Nikos Boukos
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Fragiskos N Kolisis
- School of Chemical Engineering, National Technical University of Athens, 15780, Athens, Greece
| | - Efstathios S Gonos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.,Medical School, Örebro University, 70182, Örebro, Sweden
| | | | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Spiros Efthimiopoulos
- Department of Biology, National and Kapodistrian University of Athens, 15701, Athens, Greece
| | - Maria Pelecanou
- Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310, Athens, Greece
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635, Athens, Greece.
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Miletić T, Fermi A, Papadakis I, Orfanos I, Karampitsos N, Avramopoulos A, Demitri N, De Leo F, Pope SJA, Papadopoulos MG, Couris S, Bonifazi D. A Twisted Bay-Substituted Quaterrylene Phosphorescing in the NIR Spectral Region. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tanja Miletić
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
- Department of Chemical and Pharmaceutical Sciences; INSTM UdR Trieste; University of Trieste; Piazzale Europa 1 34127 Trieste Italy
| | - Andrea Fermi
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | - Ioannis Papadakis
- Department of Physics; University of Patras; 26504 Patras Greece
- Institute of Chemical Engineering Sciences (ICE-HT); Foundation for Research and Technology-Hellas (FORTH); P.O. Box 1414 Patras 26504 Greece
| | - Ioannis Orfanos
- Department of Physics; University of Patras; 26504 Patras Greece
- Institute of Chemical Engineering Sciences (ICE-HT); Foundation for Research and Technology-Hellas (FORTH); P.O. Box 1414 Patras 26504 Greece
| | - Nikolaos Karampitsos
- Department of Physics; University of Patras; 26504 Patras Greece
- Institute of Chemical Engineering Sciences (ICE-HT); Foundation for Research and Technology-Hellas (FORTH); P.O. Box 1414 Patras 26504 Greece
| | - Aggelos Avramopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology; National Hellenic Research Foundation; 48 Vas. Constantinou Avenue Athens 11635 Greece
- Department of Computer Engineering; Technological Education Institute (TEI) of Sterea Ellada; Lamia 35100 Greece
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste; S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza - Trieste Italy
| | - Federica De Leo
- San Raffaele Hospital; Scientific Institute-IRCCS; Via Olgettina 60 20132 Milan Italy
| | - Simon J. A. Pope
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology; National Hellenic Research Foundation; 48 Vas. Constantinou Avenue Athens 11635 Greece
| | - Stelios Couris
- Department of Physics; University of Patras; 26504 Patras Greece
- Institute of Chemical Engineering Sciences (ICE-HT); Foundation for Research and Technology-Hellas (FORTH); P.O. Box 1414 Patras 26504 Greece
| | - Davide Bonifazi
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
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Matis I, Delivoria DC, Mavroidi B, Papaevgeniou N, Panoutsou S, Bellou S, Papavasileiou KD, Linardaki ZI, Stavropoulou AV, Vekrellis K, Boukos N, Kolisis FN, Gonos ES, Margarity M, Papadopoulos MG, Efthimiopoulos S, Pelecanou M, Chondrogianni N, Skretas G. An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding. Nat Biomed Eng 2017; 1:838-852. [DOI: 10.1038/s41551-017-0144-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/06/2017] [Indexed: 01/31/2023]
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Papavasileiou KD, Avramopoulos A, Leonis G, Papadopoulos MG. Computational investigation of fullerene-DNA interactions: Implications of fullerene’s size and functionalization on DNA structure and binding energetics. J Mol Graph Model 2017; 74:177-192. [DOI: 10.1016/j.jmgm.2017.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 10/20/2022]
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Chatzidaki MD, Papavasileiou KD, Papadopoulos MG, Xenakis A. Reverse Micelles As Antioxidant Carriers: An Experimental and Molecular Dynamics Study. Langmuir 2017; 33:5077-5085. [PMID: 28481539 DOI: 10.1021/acs.langmuir.7b00213] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Water-in-oil microemulsions with biocompatible components were formulated to be used as carriers of natural antioxidants, such as hydroxytyrosol (HT) and gallic acid (GA). The system was composed of a mixture of natural surfactants, lecithin and monoglycerides, medium chain triglycerides, and aqueous phase. A dual approach was undertaken to study the structure and dynamics of these complicated systems. First, experimental data were collected by using adequate techniques, such as dynamic light scattering (DLS) and electron paramagnetic resonance (EPR) spectroscopy. Following this, a coarse-grained molecular dynamics (CGMD) study based on the experimental composition using the MARTINI force field was conducted. The simulations revealed the spontaneous formation of reverse micelles (RMs) starting from completely random initial conformations, underlying their enhanced thermodynamic stability. The location of the bioactive molecules, as well as the structure of the RM, were in accordance with the experimental findings. Furthermore, GA molecules were found to be located inside the water core, in contrast to the HT ones, which seem to lie at the surfactant interfacial layer. The difference in the antioxidants' molecular location was only revealed in detail from the computational analysis and explains the RM's swelling observed by GA in DLS measurements.
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Affiliation(s)
- Maria D Chatzidaki
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
- National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology , Aghia Paraskevi Attikis, 153 10 Athens, Greece
| | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
| | - Aristotelis Xenakis
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation , 116 35 Athens, Greece
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Miletić T, Fermi A, Orfanos I, Avramopoulos A, De Leo F, Demitri N, Bergamini G, Ceroni P, Papadopoulos MG, Couris S, Bonifazi D. Tailoring Colors by O Annulation of Polycyclic Aromatic Hydrocarbons. Chemistry 2017; 23:2363-2378. [PMID: 27897357 PMCID: PMC5324668 DOI: 10.1002/chem.201604866] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Indexed: 01/24/2023]
Abstract
The synthesis of O-doped polyaromatic hydro- carbons in which two polycyclic aromatic hydrocarbon sub units are bridged through one or two O atoms has been achieved. This includes high-yield ring-closure key steps that, depending on the reaction conditions, result in the formation of furanyl or pyranopyranyl linkages through intramolecular C-O bond formation. Comprehensive photophysical measurements in solution showed that these compounds have exceptionally high emission yields and tunable absorption properties throughout the UV/Vis spectral region. Electrochemical investigations showed that in all cases O annulation increases the electron-donor capabilities by raising the HOMO energy level, whereas the LUMO energy level is less affected. Moreover, third-order nonlinear optical (NLO) measurements on solutions or thin films containing the dyes showed very good values of the second hyperpolarizability. Importantly, poly(methyl methacrylate) films containing the pyranopyranyl derivatives exhibited weak linear absorption and NLO absorption compared to the nonlinearity and NLO refraction, respectively, and thus revealed them to be exceptional organic materials for photonic devices.
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Affiliation(s)
- Tanja Miletić
- Department of Chemical and Pharmaceutical SciencesINSTM UdR TriesteUniversity of TriestePiazzale Europa 134127TriesteItaly
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
| | - Andrea Fermi
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
| | - Ioannis Orfanos
- Department of PhysicsUniversity of Patras26504PatrasGreece
- Institute of Chemical Engineering Sciences (ICE-HT)Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414Patras26504Greece
| | - Aggelos Avramopoulos
- Institute of Biology, Medicinal Chemistry and BiotechnologyNational Hellenic Research Foundation48 Vas. Constantinou AvenueAthens11635Greece
| | - Federica De Leo
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
| | - Nicola Demitri
- Elettra-Sincrotrone TriesteS.S. 14 Km 163.5 in Area Science Park34149Basovizza-TriesteItaly
| | - Giacomo Bergamini
- Department of Chemistry “Giacomo Ciamician”University of BolognaVia Selmi 240126BolognaItaly
| | - Paola Ceroni
- Department of Chemistry “Giacomo Ciamician”University of BolognaVia Selmi 240126BolognaItaly
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal Chemistry and BiotechnologyNational Hellenic Research Foundation48 Vas. Constantinou AvenueAthens11635Greece
| | - Stelios Couris
- Department of PhysicsUniversity of Patras26504PatrasGreece
- Institute of Chemical Engineering Sciences (ICE-HT)Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414Patras26504Greece
| | - Davide Bonifazi
- Department of Chemical and Pharmaceutical SciencesINSTM UdR TriesteUniversity of TriestePiazzale Europa 134127TriesteItaly
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
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Richarz AN, Avramopoulos A, Benfenati E, Gajewicz A, Golbamaki Bakhtyari N, Leonis G, Marchese Robinson RL, Papadopoulos MG, Cronin MT, Puzyn T. Compilation of Data and Modelling of Nanoparticle Interactions and Toxicity in the NanoPUZZLES Project. Adv Exp Med Biol 2017; 947:303-324. [PMID: 28168672 DOI: 10.1007/978-3-319-47754-1_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The particular properties of nanomaterials have led to their rapidly increasing use in diverse fields of application. However, safety assessment is not keeping pace and there are still gaps in the understanding of their hazards. Computational models predicting nanotoxicity, such as (quantitative) structure-activity relationships ((Q)SARs), can contribute to safety evaluation, in line with general efforts to apply alternative methods in chemical risk assessment. Their development is highly dependent on the availability of reliable and high quality experimental data, both regarding the compounds' properties as well as the measured toxic effects. In particular, "nano-QSARs" should take the nano-specific characteristics into account. The information compiled needs to be well organized, quality controlled and standardized. Integrating the data in an overarching, structured data collection aims to (a) organize the data in a way to support modelling, (b) make (meta)data necessary for modelling available, and (c) add value by making a comparison between data from different sources possible.Based on the available data, specific descriptors can be derived to parameterize the nanomaterial-specific structure and physico-chemical properties appropriately. Furthermore, the interactions between nanoparticles and biological systems as well as small molecules, which can lead to modifications of the structure of the active nanoparticles, need to be described and taken into account in the development of models to predict the biological activity and toxicity of nanoparticles. The EU NanoPUZZLES project was part of a global cooperative effort to advance data availability and modelling approaches supporting the characterization and evaluation of nanomaterials.
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Affiliation(s)
- Andrea-Nicole Richarz
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Nazanin Golbamaki Bakhtyari
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Georgios Leonis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Mark Td Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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Jagiello K, Chomicz B, Avramopoulos A, Gajewicz A, Mikolajczyk A, Bonifassi P, Papadopoulos MG, Leszczynski J, Puzyn T. Size-dependent electronic properties of nanomaterials: How this novel class of nanodescriptors supposed to be calculated? Struct Chem 2016. [DOI: 10.1007/s11224-016-0838-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xanthopoulos D, Kritsi E, Supuran CT, Papadopoulos MG, Leonis G, Zoumpoulakis P. Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches. ChemMedChem 2016; 11:1646-52. [PMID: 27411556 DOI: 10.1002/cmdc.201600220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/07/2016] [Indexed: 12/28/2022]
Abstract
A combination of computational techniques and inhibition assay experiments was employed to identify hit compounds from commercial libraries with enhanced inhibitory potency against HIV type 1 aspartic protease (HIV PR). Extensive virtual screening with the aid of reliable pharmacophore models yielded five candidate protease inhibitors. Subsequent molecular dynamics and molecular mechanics Poisson-Boltzmann surface area free-energy calculations for the five ligand-HIV PR complexes suggested a high stability of the systems through hydrogen-bond interactions between the ligands and the protease's flaps (Ile50/50'), as well as interactions with residues of the active site (Asp25/25'/29/29'/30/30'). Binding-energy calculations for the three most promising compounds yielded values between -5 and -10 kcal mol(-1) and suggested that van der Waals interactions contribute most favorably to the total energy. The predicted binding-energy values were verified by in vitro inhibition assays, which showed promising results in the high nanomolar range. These results provide structural considerations that may guide further hit-to-lead optimization toward improved anti-HIV drugs.
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Affiliation(s)
- Dimitrios Xanthopoulos
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece
| | - Eftichia Kritsi
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.,School of Chemical Engineering, National Technical University of Athens (NTUA), Organic Synthesis Laboratory, Iroon-Polytechneiou-Str. 9, 15773, Athens, Greece
| | - Claudiu T Supuran
- Neurofarba Dept., Sezione di Scienze farmaceutiche e nutraceutiche, e Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via UgoSchiff 6, 50019, Sesto Fiorentino, Firenze, Italy
| | - Manthos G Papadopoulos
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece
| | - Georgios Leonis
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.
| | - Panagiotis Zoumpoulakis
- National Hellenic Research Foundation (NHRF), Institute of Biology, Medicinal Chemistry and Biotechnology (IBMCB), Vassileos-Constantinou-Ave. 48, 11635, Athens, Greece.
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Vasilakaki S, Barbayianni E, Leonis G, Papadopoulos MG, Mavromoustakos T, Gelb MH, Kokotos G. Development of a potent 2-oxoamide inhibitor of secreted phospholipase A2 guided by molecular docking calculations and molecular dynamics simulations. Bioorg Med Chem 2016; 24:1683-95. [PMID: 26970660 DOI: 10.1016/j.bmc.2016.02.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/24/2016] [Accepted: 02/27/2016] [Indexed: 10/22/2022]
Abstract
Inhibition of group IIA secreted phospholipase A2 (GIIA sPLA2) has been an important objective for medicinal chemists. We have previously shown that inhibitors incorporating the 2-oxoamide functionality may inhibit human and mouse GIIA sPLA2s. Herein, the development of new potent inhibitors by molecular docking calculations using the structure of the known inhibitor 7 as scaffold, are described. Synthesis and biological evaluation of the new compounds revealed that the long chain 2-oxoamide based on (S)-valine GK241 led to improved activity (IC50=143 nM and 68 nM against human and mouse GIIA sPLA2, respectively). In addition, molecular dynamics simulations were employed to shed light on GK241 potent and selective inhibitory activity.
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Affiliation(s)
- Sofia Vasilakaki
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Efrosini Barbayianni
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Georgios Leonis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Manthos G Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Michael H Gelb
- Department of Chemistry and Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
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12
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Avramopoulos A, Otero N, Karamanis P, Pouchan C, Papadopoulos MG. A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases. J Phys Chem A 2016; 120:284-98. [PMID: 26690053 DOI: 10.1021/acs.jpca.5b09813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG. A Hirshfeld-based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -26.98 kcal/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB), a study of the magnitude of the interaction-induced polarizability of C84H24-NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Nicolás Otero
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Panaghiotis Karamanis
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Claude Pouchan
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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Jagiello K, Grzonkowska M, Swirog M, Ahmed L, Rasulev B, Avramopoulos A, Papadopoulos MG, Leszczynski J, Puzyn T. Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives. J Nanopart Res 2016; 18:256. [PMID: 27642255 PMCID: PMC5003910 DOI: 10.1007/s11051-016-3564-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/18/2016] [Indexed: 05/19/2023]
Abstract
In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure-Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure-Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide the recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.
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Affiliation(s)
- Karolina Jagiello
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Monika Grzonkowska
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Swirog
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Lucky Ahmed
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
| | - Bakhtiyor Rasulev
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
- Center for Computationally Assisted Science and Technology, North Dakota State University, 1805 NDSU Research Park Drive, Post Office Box 6050, Fargo, ND 58108 USA
| | - Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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14
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Leonis G, Avramopoulos A, Papavasileiou KD, Reis H, Steinbrecher T, Papadopoulos MG. A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes. J Phys Chem B 2015; 119:14971-85. [PMID: 26523956 DOI: 10.1021/acs.jpcb.5b05998] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human serum albumin (HSA) is the most abundant blood plasma protein, which transports fatty acids, hormones, and drugs. We consider nanoparticle-HSA interactions by investigating the binding of HSA with three fullerene analogs. Long MD simulations, quantum mechanical (fragment molecular orbital, energy decomposition analysis, atoms-in-molecules), and free energy methods elucidated the binding mechanism in these complexes. Such a systematic study is valuable due to the lack of comprehensive theoretical approaches to date. The main elements of the mechanism include the following: binding to IIA site results in allosteric modulation of the IIIA and heme binding sites with an increase in α-helical structure of IIIA. Fullerenes displayed high binding affinities for HSA; therefore, HSA can be used as a fullerene carrier, facilitating any toxic function the fullerene may exert. Complex formation is driven by hydrogen bonding, van der Waals, nonpolar, charge transfer, and dispersion energy contributions. Proper functionalization of C60 has enhanced its binding to HSA by more than an order of magnitude. This feature may be important for biological applications (e.g., photodynamic therapy of cancer). Satisfactory agreement with relevant experimental and theoretical data has been obtained.
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Affiliation(s)
- Georgios Leonis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Heribert Reis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Thomas Steinbrecher
- Institut für Physikalische Chemie, KIT , Fritz-Haber Weg 2, 76131 Karlsruhe, Germany
| | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Ave., Athens 11635, Greece
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15
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Tzoupis H, Leonis G, Avramopoulos A, Reis H, Czyżnikowska Ż, Zerva S, Vergadou N, Peristeras LD, Papavasileiou KD, Alexis MN, Mavromoustakos T, Papadopoulos MG. Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays. J Mol Graph Model 2015; 62:138-149. [PMID: 26421414 DOI: 10.1016/j.jmgm.2015.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/14/2015] [Accepted: 09/16/2015] [Indexed: 12/01/2022]
Abstract
We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction.
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Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece; Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zographou 15771, Greece.
| | - Georgios Leonis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece.
| | - Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Heribert Reis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Faculty of Pharmacy, Wrocław Medical University, Szewska 38 PL-50139 Wrocław, Poland
| | - Sofia Zerva
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Niki Vergadou
- National Center for Scientific Research "Demokritos", Institute of Advanced Materials, Physicochemical Processes, Nanotechnology and Microsystems, Molecular Thermodynamics and Modelling of Materials Laboratory, GR-153 10, Aghia Paraskevi Attikis, Greece
| | | | - Konstantinos D Papavasileiou
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Michael N Alexis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zographou 15771, Greece
| | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 11635, Greece.
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16
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Koukoulitsa C, Villalonga-Barber C, Csonka R, Alexi X, Leonis G, Dellis D, Hamelink E, Belda O, Steele BR, Micha-Screttas M, Alexis MN, Papadopoulos MG, Mavromoustakos T. Biological and computational evaluation of resveratrol inhibitors against Alzheimer's disease. J Enzyme Inhib Med Chem 2015; 31:67-77. [PMID: 26147348 DOI: 10.3109/14756366.2014.1003928] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It has been reported that beta amyloid induces production of radical oxygen species and oxidative stress in neuronal cells, which in turn upregulates β-secretase (BACE-1) expression and beta amyloid levels, thereby propagating oxidative stress and increasing neuronal injury. A series of resveratrol derivatives, known to be inhibitors of oxidative stress-induced neuronal cell death (oxytosis) were biologically evaluated against BACE-1 using homogeneous time-resolved fluorescence (TRF) assay. Correlation between oxytosis inhibitory and BACE-1 inhibitory activity of resveratrol derivatives was statistically significant, supporting the notion that BACE-1 may act as pivotal mediator of neuronal cell oxytosis. Four of the biologically evaluated resveratrol analogs demonstrated considerably higher activity than resveratrol in either assay. The discovery of some "hits" led us to initiate detailed docking studies associated with Molecular Dynamics in order to provide a plausible explanation for the experimental results and understand their molecular basis of action.
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Affiliation(s)
| | - Caroline Villalonga-Barber
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Robert Csonka
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Xanthippi Alexi
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Georgios Leonis
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Dimitris Dellis
- c Institute of Accelerating Systems and Applications , Panepistimiopolis Zografou , Athens , Greece , and
| | | | | | - Barry R Steele
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Maria Micha-Screttas
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Michael N Alexis
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
| | - Manthos G Papadopoulos
- b Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation , Athens , Greece
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17
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Reis H, Rasulev B, Papadopoulos MG, Leszczynski J. Reliable but Timesaving: In Search of an Efficient Quantum-chemical Method for the Description of Functional Fullerenes. Curr Top Med Chem 2015; 15:1845-58. [PMID: 25961522 DOI: 10.2174/1568026615666150506150601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 11/22/2022]
Abstract
Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.
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Affiliation(s)
| | | | | | - J Leszczynski
- Interdisciplinary Center for Nanotoxicity, Jackson State University, 1325 J.R. Lynch St, PO Box 17910, Jackson, MS 39217, USA.
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18
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Kellici TF, Ntountaniotis D, Leonis G, Chatziathanasiadou M, Chatzikonstantinou AV, Becker-Baldus J, Glaubitz C, Tzakos AG, Viras K, Chatzigeorgiou P, Tzimas S, Kefala E, Valsami G, Archontaki H, Papadopoulos MG, Mavromoustakos T. Investigation of the Interactions of Silibinin with 2-Hydroxypropyl-β-cyclodextrin through Biophysical Techniques and Computational Methods. Mol Pharm 2015; 12:954-65. [DOI: 10.1021/mp5008053] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Tahsin F. Kellici
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
- Department
of Chemistry, University of Ioannina, Ioannina 45110, Greece
| | - Dimitrios Ntountaniotis
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
| | - Georgios Leonis
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | | | | | - Johanna Becker-Baldus
- Institute
of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt, Germany
| | - Clemens Glaubitz
- Institute
of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt, Germany
| | - Andreas G. Tzakos
- Department
of Chemistry, University of Ioannina, Ioannina 45110, Greece
| | - Kyriakos Viras
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
| | - Petros Chatzigeorgiou
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
| | - Stavros Tzimas
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
| | - Evangelia Kefala
- Department
of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou 15771, Greece
| | - Georgia Valsami
- Department
of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou 15771, Greece
| | - Helen Archontaki
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
| | - Manthos G. Papadopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Thomas Mavromoustakos
- Department
of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis
Zografou 15771, Greece
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19
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Vrontaki E, Leonis G, Avramopoulos A, Papadopoulos MG, Simčič M, Grdadolnik SG, Afantitis A, Melagraki G, Hadjikakou SK, Mavromoustakos T. Stability and binding effects of silver(I) complexes at lipoxygenase-1. J Enzyme Inhib Med Chem 2014; 30:539-49. [DOI: 10.3109/14756366.2014.951348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Tzoupis H, Leonis G, Avramopoulos A, Mavromoustakos T, Papadopoulos MG. Systematic molecular dynamics, MM-PBSA, and ab initio approaches to the saquinavir resistance mechanism in HIV-1 PR due to 11 double and multiple mutations. J Phys Chem B 2014; 118:9538-52. [PMID: 25036111 DOI: 10.1021/jp502687q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in the human immunodeficiency virus (HIV) enable virus replication even when appropriate antiretroviral therapy is followed, thus leading to the emergence of drug resistance. In a previous work, we systematically examined seven single mutations that are associated with saquinavir (SQV) resistance in HIV-1 protease (Tzoupis, H.; Leonis, G.; Mavromoustakos, T.; Papadopoulos, M. G. J. Chem. Theory Comput. 2013, 9, 1754-1764). Herein, we extend our analysis, which includes seven double (G48V-V82A, L10I-G48V, G48V-L90M, I84V-L90M, L10I-V82A, L10I-L63P, A71V-G73S) and four multiple (L10I-L63P-A71V, L10I-G48V-V82A, G73S-I84V-L90M, L10I-L63P-A71V-G73S-I84V-L90M) SQV-HIV-1 PR mutant complexes, in an attempt to generalize our findings and formulate the main elements of the SQV resistance mechanism in the protease. On the basis of molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and ab initio computational approaches, we identified specific features that constitute the HIV-1 PR mechanism of resistance at the molecular level: the low flexibility of SQV in the binding cavity and the preservation of hydrogen bonding (HB) and van der Waals interactions between SQV and several active-site (Gly27/27', Asp29/29'/30/30', especially Asp25/25') and flap (Ile50/50', Gly48/48') residues of the protease contribute significantly to efficient binding. The total enthalpy loss in all mutants is mostly due to the loss in enthalpy of the active-site region. Furthermore, it was observed that mutation accumulation may induce stabilization to SQV and to the flaps through enhanced HB interactions that lead to improved inhibition (e.g., accumulation of mutations in complexes containing L10I, G48V, L63P, I84V, or L90M single mutations). It was also concluded that permanent flap closure is obtained independently of mutations and SQV binding is mostly driven by van der Waals, nonpolar, and exchange-energy contributions. Importantly, it was indicated that the optimal positioning of SQV and the structure of the binding cavity are tightly coupled, since small changes in geometry may affect the binding energy greatly. The results of our theoretical approaches are in agreement with experimental evidence and provide a reliable description of SQV resistance in HIV-1 PR.
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Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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21
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Leonis G, Avramopoulos A, Salmas RE, Durdagi S, Yurtsever M, Papadopoulos MG. Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. J Chem Inf Model 2014; 54:2294-308. [DOI: 10.1021/ci5002873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Georgios Leonis
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Aggelos Avramopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Ramin Ekhteiari Salmas
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Serdar Durdagi
- Department
of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Istanbul 34349, Turkey
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Manthos G. Papadopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
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22
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Karamanis P, Otero N, Pouchan C, Torres JJ, Tiznado W, Avramopoulos A, Papadopoulos MG. Significant nonlinear-optical switching capacity in atomic clusters built from silicon and lithium: A combinedab initioand density functional study. J Comput Chem 2014. [DOI: 10.1002/jcc.23549] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Panaghiotis Karamanis
- Equipe de Chimie Physique; IPREM Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254. Hélioparc Pau Pyrénées 2 avenue du Président Angot; 64053 PAU Cedex 09 France
| | - Nicolás Otero
- Equipe de Chimie Physique; IPREM Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254. Hélioparc Pau Pyrénées 2 avenue du Président Angot; 64053 PAU Cedex 09 France
| | - Claude Pouchan
- Equipe de Chimie Physique; IPREM Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254. Hélioparc Pau Pyrénées 2 avenue du Président Angot; 64053 PAU Cedex 09 France
| | - Juan José Torres
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; República 275 Santiago Chile
| | - William Tiznado
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; República 275 Santiago Chile
| | - Aggelos Avramopoulos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation; 48 Vasileos Constadinou Avenue 11635 Athens Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation; 48 Vasileos Constadinou Avenue 11635 Athens Greece
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23
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Coe BJ, Avramopoulos A, Papadopoulos MG, Pierloot K, Vancoillie S, Reis H. Theoretical modelling of photoswitching of hyperpolarisabilities in ruthenium complexes. Chemistry 2013; 19:15955-63. [PMID: 24123546 PMCID: PMC4068215 DOI: 10.1002/chem.201301380] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Indexed: 11/17/2022]
Abstract
Static excited-state polarisabilities and hyperpolarisabilities of three RuII ammine complexes are computed at the density functional theory (DFT) and several correlated ab initio levels. Most accurate modelling of the low energy electronic absorption spectrum is obtained with the hybrid functionals B3LYP, B3P86 or M06 for the complex [RuII(NH3)5(MeQ+)]3+ (MeQ+=N-methyl-4,4′-bipyridinium, 3) in acetonitrile. The match with experimental data is less good for [RuII(NH3)5L]3+ (L=N-methylpyrazinium, 2; N-methyl-4-{E,E-4-(4-pyridyl)buta-1,3-dienyl}pyridinium, 4). These calculations confirm that the first dipole- allowed excited state (FDAES) has metal-to-ligand charge-transfer (MLCT) character. Both the solution and gas-phase results obtained for 3 by using B3LYP, B3P86 or M06 are very similar to those from restricted active-space SCF second-order perturbation theory (RASPT2) with a very large basis set and large active space. However, the time-dependent DFT λmax predictions from the long-range corrected functionals CAM-B3LYP, LC-ωPBE and wB97XB and also the fully ab initio resolution of identity approximate coupled-cluster method (gas-phase only) are less accurate for all three complexes. The ground state (GS) two-state approximation first hyperpolarisability β2SA for 3 from RASPT2 is very close to that derived experimentally via hyper-Rayleigh scattering, whereas the corresponding DFT-based values are considerably larger. The β responses calculated by using B3LYP, B3P86 or M06 increase markedly as the π-conjugation extends on moving along the series 2→4, for both the GS and FDAES species. All three functionals predict substantial FDAES β enhancements for each complex, increasing with the π-conjugation, up to about sevenfold for 4. Also, the computed second hyperpolarisabilities γ generally increase in the FDAES, but the results vary between the different functionals.
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Affiliation(s)
- Benjamin J Coe
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL (UK).
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24
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Leonis G, Steinbrecher T, Papadopoulos MG. A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM–PBSA and Thermodynamic Integration Study. J Chem Inf Model 2013; 53:2141-53. [DOI: 10.1021/ci4002102] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Georgios Leonis
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635,
Greece
| | - Thomas Steinbrecher
- Institute of Physical
Chemistry, Department of Theoretical Chemical Biology, KIT, Kaiserstrasse 12, 76131 Karlsruhe,
Germany
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635,
Greece
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25
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 116 35, Greece, http://www.eie.gr/nhrf/institutes/iopc/researchgroups/ccg‐group/ccg‐en.html
| | - Heribert Reis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 116 35, Greece, http://www.eie.gr/nhrf/institutes/iopc/researchgroups/ccg‐group/ccg‐en.html
| | - George A. Mousdis
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., Athens 116 35, Greece, http://www.eie.gr/nhrf/institutes/iopc/researchgroups/ccg‐group/ccg‐en.html
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26
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Avramopoulos A, Reis H, Luis JM, Papadopoulos MG. On the vibrational linear and nonlinear optical properties of compounds involving noble gas atoms: HXeOXeH, HXeOXeF, and FXeOXeF. J Comput Chem 2013; 34:1446-55. [PMID: 23553331 DOI: 10.1002/jcc.23280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 11/11/2022]
Abstract
The vibrational (hyper)polarizabilities of some selected Xe derivatives are studied in the context of Bishop-Kirtman perturbation theory (BKPT) and numerical finite field methodology. It was found that for this set of rare gas compounds, the static vibrational properties are quite large, in comparison to the corresponding electronic ones, especially those of the second hyperpolarizability. This also holds for the dc-Pockels β(-ω;ω,0), Kerr γ(-ω;ω,0,0) and electric field second harmonic generation γ (-2ω;ω,ω,0) effects, although the computed nuclear relaxation (nr) vibrational contributions are smaller in magnitude than the static ones. HXeOXeH was used to study the effects of electron correlation, basis set, and geometry. Geometry effects were found to lead to noticeable changes of the vibrational and electronic second hyperpolarizability. A limited study of the effect of Xe insertion to the nr vibrational properties is also reported. Assessment of the results revealed that Xe insertion has a remarkable effect on the nr (hyper)polarizabilities. In terms of the BKPT, this is associated with a remarkable increase of the electrical and mechanical anharmonicity terms. The latter is consistent with the anharmonic character of several vibrational modes reported for rare gas compounds.
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens 116 35, Greece.
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27
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Bulik IW, Zaleśny R, Bartkowiak W, Luis JM, Kirtman B, Scuseria GE, Avramopoulos A, Reis H, Papadopoulos MG. Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities. J Comput Chem 2013; 34:1775-84. [PMID: 23677638 DOI: 10.1002/jcc.23316] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 12/14/2022]
Abstract
A set of exchange-correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM-B3LYP, LC-BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of all-trans polymethineimine (PMI) oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the Møller-Plesset second-order perturbation theory (MP2) and CCSD methods. For the smallest oligomer, CCSD(T) calculations confirm the choice of MP2 and CCSD as appropriate for assessing the density functionals. By and large, CAM-B3LYP is the most successful, because it is best for the nuclear relaxation contribution to the static linear polarizability, intensity-dependent refractive index second hyperpolarizability, static second hyperpolarizability, and is close to the best for the electro-optical Pockels effect first hyperpolarizability. However, none of the functionals perform satisfactorily for all the vibrational (hyper)polarizabilities studied. In fact, in the case of electric field-induced second harmonic generation all of them, as well as the Hartree-Fock approximation, yield the wrong sign. We have also found that the Pople 6-31+G(d) basis set is unreliable for computing nuclear relaxation (hyper)polarizabilities of PMI oligomers due to the spurious prediction of a nonplanar equilibrium geometry.
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Affiliation(s)
- Ireneusz W Bulik
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, USA
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28
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Tzoupis H, Leonis G, Mavromoustakos T, Papadopoulos MG. A Comparative Molecular Dynamics, MM–PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants. J Chem Theory Comput 2013; 9:1754-64. [DOI: 10.1021/ct301063k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haralambos Tzoupis
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
- Department of Chemistry, National
and Kapodistrian University of Athens, Panepistimioupolis Zographou
15771, Greece
| | - Georgios Leonis
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, National
and Kapodistrian University of Athens, Panepistimioupolis Zographou
15771, Greece
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal
Chemistry and Biotechnology, National Hellenic Research Foundation,
48 Vas. Constantinou Ave., Athens 11635, Greece
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29
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Agelis G, Resvani A, Koukoulitsa C, Tůmová T, Slaninová J, Kalavrizioti D, Spyridaki K, Afantitis A, Melagraki G, Siafaka A, Gkini E, Megariotis G, Grdadolnik SG, Papadopoulos MG, Vlahakos D, Maragoudakis M, Liapakis G, Mavromoustakos T, Matsoukas J. Rational design, efficient syntheses and biological evaluation of N,N'-symmetrically bis-substituted butylimidazole analogs as a new class of potent Angiotensin II receptor blockers. Eur J Med Chem 2013; 62:352-70. [PMID: 23376252 DOI: 10.1016/j.ejmech.2012.12.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/25/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022]
Abstract
A series of symmetrically bis-substituted imidazole analogs bearing at the N-1 and N-3 two biphenyl moieties ortho substituted either with tetrazole or carboxylate functional groups was designed based on docking studies and utilizing for the first time an extra hydrophobic binding cleft of AT1 receptor. The synthesized analogs were evaluated for their in vitro antagonistic activities (pA2 values) and binding affinities (-logIC50 values) to the Angiotensin II AT1 receptor. Among them, the potassium (-logIC50 = 9.04) and the sodium (-logIC50 = 8.54) salts of 4-butyl-N,N'-bis{[2'-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide (12a and 12b, respectively) as well as its free acid 11 (-logIC50 = 9.46) and the 4-butyl-2-hydroxymethyl-N,N'-bis{[2'-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide (14) (-logIC50 = 8.37, pA2 = 8.58) showed high binding affinity to the AT1 receptor and high antagonistic activity (potency). The potency was similar or even superior to that of Losartan (-logIC50 = 8.25, pA2 = 8.25). On the contrary, 2-butyl-N,N'-bis{[2'-[2H-tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide (27) (-logIC50 = 5.77) and 2-butyl-4-chloro-5-hydroxymethyl-N,N'-bis{[2'-[2H-tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide (30) (-logIC50 = 6.38) displayed very low binding affinity indicating that the orientation of the n-butyl group is of primary importance. Docking studies of the representative highly active 12b clearly showed that this molecule has an extra hydrophobic binding feature compared to prototype drug Losartan and it fits to the extra hydrophobic cavity. These results may contribute to the discovery and development of a new class of biologically active molecules through bis-alkylation of the imidazole ring by a convenient and cost effective synthetic strategy.
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Affiliation(s)
- George Agelis
- Department of Chemistry, University of Patras, 26500 Patras, Greece.
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30
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Lynch I, Ahluwalia A, Boraschi D, Byrne HJ, Fadeel B, Gehr P, Gutleb AC, Kendall M, Papadopoulos MG. The bio-nano-interface in predicting nanoparticle fate and behaviour in living organisms: towards grouping and categorising nanomaterials and ensuring nanosafety by design. ACTA ACUST UNITED AC 2013. [DOI: 10.1515/bnm-2013-0011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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31
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Fotakis C, Megariotis G, Christodouleas D, Kritsi E, Zoumpoulakis P, Ntountaniotis D, Zervou M, Potamitis C, Hodzic A, Pabst G, Rappolt M, Mali G, Baldus J, Glaubitz C, Papadopoulos MG, Afantitis A, Melagraki G, Mavromoustakos T. Comparative study of the AT1 receptor prodrug antagonist candesartan cilexetil with other sartans on the interactions with membrane bilayers. Biochimica et Biophysica Acta (BBA) - Biomembranes 2012; 1818:3107-20. [DOI: 10.1016/j.bbamem.2012.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/26/2012] [Accepted: 08/13/2012] [Indexed: 11/28/2022]
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32
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Varvarigou N, Megariotis G, Leonis G, Vrontaki E, Maniati AM, Vlachou M, Eikosipentaki A, Kompogennitaki R, Papadopoulos MG, Grdadolnik SG, Komiotis D, Mavromoustakos T, Tsotinis A. Conformational analysis of two novel cytotoxic C2-substituted pyrrolo[2,3-f]quinolines in aqueous media, organic solvents, membrane bilayers and at the putative active site. Bioorg Med Chem 2012; 20:6276-84. [PMID: 23040892 DOI: 10.1016/j.bmc.2012.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/01/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
Abstract
We have performed: (i) conformational analysis of two novel cytotoxic C2-substituted pyrrolo[2,3-f]quinolines 5e and 5g in deuterated dimethylsulfoxide (DMSO-d(6)) utilizing NOE results from NMR spectroscopy; (ii) molecular dynamics (MD) calculations in water, DMSO and dimyristoyl phosphatidylcholine bilayers and (iii) molecular docking and MD calculations on DNA nucleotide sequences. The obtained results for the two similar in structure molecules showed differences in: (i) their conformational properties in silico and in media that reasonably simulate the biological environment; (ii) the way they are incorporated into the lipid bilayers and therefore their diffusion ability and (iii) molecular docking capacity as it is depicted from their different binding scores.
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Affiliation(s)
- Nicole Varvarigou
- National and Kapodistrian University of Athens, Chemistry Department, Laboratory of Organic Chemistry, Panepistimioupoli-Zografou, 15771 Athens, Greece
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33
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Leonis G, Czyżnikowska Ż, Megariotis G, Reis H, Papadopoulos MG. Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps. J Chem Inf Model 2012; 52:1542-58. [PMID: 22587384 DOI: 10.1021/ci300014z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.
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Affiliation(s)
- Georgios Leonis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece.
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34
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Tzoupis H, Leonis G, Megariotis G, Supuran CT, Mavromoustakos T, Papadopoulos MG. Dual Inhibitors for Aspartic Proteases HIV-1 PR and Renin: Advancements in AIDS–Hypertension–Diabetes Linkage via Molecular Dynamics, Inhibition Assays, and Binding Free Energy Calculations. J Med Chem 2012; 55:5784-96. [DOI: 10.1021/jm300180r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haralambos Tzoupis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis
Zographou, Athens 15771, Greece
| | - Georgios Leonis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Grigorios Megariotis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou
Street, Athens 15780, Greece
| | - Claudiu T. Supuran
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Rm
18, 50019 Sesto Fiorentino (Florence), Italy
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis
Zographou, Athens 15771, Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
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35
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Koukaras EN, Zdetsis AD, Karamanis P, Pouchan C, Avramopoulos A, Papadopoulos MG. Structural and static electric response properties of highly symmetric lithiated silicon cages: Theoretical predictions. J Comput Chem 2012; 33:1068-79. [DOI: 10.1002/jcc.22938] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 12/14/2011] [Accepted: 01/02/2012] [Indexed: 02/04/2023]
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36
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Durdagi S, Papadopoulos MG, Mavromoustakos T. An effort to discover the preferred conformation of the potent AMG3 cannabinoid analog when reaching the active sites of the cannabinoid receptors. Eur J Med Chem 2012; 47:44-51. [DOI: 10.1016/j.ejmech.2011.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/29/2011] [Accepted: 10/06/2011] [Indexed: 11/26/2022]
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37
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Politi A, Leonis G, Tzoupis H, Ntountaniotis D, Papadopoulos MG, Grdadolnik SG, Mavromoustakos T. Conformational Properties and Energetic Analysis of Aliskiren in Solution and Receptor Site. Mol Inform 2011; 30:973-85. [DOI: 10.1002/minf.201100077] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 10/18/2011] [Indexed: 11/06/2022]
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38
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Avramopoulos A, Li J, Holzmann N, Frenking G, Papadopoulos MG. On the stability, electronic structure, and nonlinear optical properties of HXeOXeF and FXeOXeF. J Phys Chem A 2011; 115:10226-36. [PMID: 21793516 DOI: 10.1021/jp203961k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic ground state, stability, and linear and nonlinear optical properties of HXeOXeF and FXeOXeF have been studied theoretically by employing complete active space valence bond (CASVB), multistate complete active space perturbation theory (MS-CASPT2), and coupled cluster methods. It is shown that the oxygen inserted between the two Xe atoms significantly modifies the ground-state electronic configuration of the formed derivative by increasing the closed-shell contribution (σ(2)) and removing the diradicaloid character observed in HXe(2)F. The electronic charge distribution has been analyzed by employing the atoms-in-molecules (AIM) method. The dissociation channels of HXeOXeF and FXeOXeF have been studied in detail. It was found that these compounds are metastable, protected by substantial energy barriers and, thus, they can be prepared under appropriate conditions. Both two- and three-body dissociation reactions have been considered. The effects of inserting O in HXe(2)F and substituting H (HXeOXeF) by F, leading to FXeOXeF, on the energy barriers are discussed. The significant effects of the inserted oxygen on the polarizability and even more on the first hyperpolarizability have been computed and rationalized.
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 116 35, Greece.
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39
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Skwara B, Góra RW, Zaleśny R, Lipkowski P, Bartkowiak W, Reis H, Papadopoulos MG, Luis JM, Kirtman B. Electronic Structure, Bonding, Spectra, and Linear and Nonlinear Electric Properties of Ti@C28. J Phys Chem A 2011; 115:10370-81. [DOI: 10.1021/jp206331n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bartłomiej Skwara
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Robert Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Paweł Lipkowski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Wojciech Bartkowiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiánskiego 27, 50-370 Wrocław, Poland
| | - Heribert Reis
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | | | - Bernard Kirtman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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40
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Neophytou N, Leonis G, Stavrinoudakis N, Simčič M, Grdadolnik SG, Papavassilopoulou E, Michas G, Moutevelis-Minakakis P, Papadopoulos MG, Zing M, Mavromoustakos T. Docking and Molecular Dynamics Calculations of Pyrrolidinone Analog MMK16 Bound to COX and LOX Enzymes. Mol Inform 2011; 30:473-86. [PMID: 27467091 DOI: 10.1002/minf.201000131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 02/14/2011] [Indexed: 11/07/2022]
Abstract
The new molecule 4-[(2S)-2-(1H-imidazol-1-ylmethyl)-5-oxotetrahydro-1H-pyrrol-1-yl]methylbenzenecarboxylic acid (MMK16) was found to have promising anti-inflammatory activity. This biological behavior of MMK16 triggered our interest to study its binding affinity using NMR spectroscopy in LOX and its docking and molecular dynamics (MD) properties in LOX and COX enzymes. The present NMR and docking binding studies not only rationalize the obtained biological results since in all three receptors MMK16 shows high affinity and scoring but also make it a potential dual LOX-5/COX-2 inhibitor. Thus, this class of molecules must be further investigated for discovering compounds possessing better biological activity and more lasting biological effect.
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Affiliation(s)
- N Neophytou
- Kapodistrian University of Athens, Panepistimiopolis, Zographou 15784, Athens, Greece
- Authors contributed equally to this work
| | - G Leonis
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas. Constantinou 48, 11635 Athens, Greece.
- Authors contributed equally to this work.
| | - N Stavrinoudakis
- Kapodistrian University of Athens, Panepistimiopolis, Zographou 15784, Athens, Greece
| | - M Simčič
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - S Golič Grdadolnik
- Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - E Papavassilopoulou
- Kapodistrian University of Athens, Panepistimiopolis, Zographou 15784, Athens, Greece
| | - G Michas
- Kapodistrian University of Athens, Panepistimiopolis, Zographou 15784, Athens, Greece
| | | | - M G Papadopoulos
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas. Constantinou 48, 11635 Athens, Greece
| | - M Zing
- Drug Discovery and Design Center (DDDC), Box 1201, Shanghai Institute of Materia Medica No. 555 Rd. Zuchongzhi, Shanghai, P. R. China
| | - T Mavromoustakos
- Kapodistrian University of Athens, Panepistimiopolis, Zographou 15784, Athens, Greece.
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41
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Fotakis C, Christodouleas D, Zoumpoulakis P, Kritsi E, Benetis NP, Mavromoustakos T, Reis H, Gili A, Papadopoulos MG, Zervou M. Comparative Biophysical Studies of Sartan Class Drug Molecules Losartan and Candesartan (CV-11974) with Membrane Bilayers. J Phys Chem B 2011; 115:6180-92. [DOI: 10.1021/jp110371k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Charalambos Fotakis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
- Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zographou 15771, Greece
| | - Dionysios Christodouleas
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
- Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zographou 15771, Greece
| | - Panagiotis Zoumpoulakis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - Eftichia Kritsi
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
- Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zographou 15771, Greece
| | - Nikolas-Ploutarch Benetis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - Thomas Mavromoustakos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
- Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis Zographou 15771, Greece
| | - Heribert Reis
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - Argiro Gili
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
- School of Applied Mathematical and Physical Science, National Technical University of Athens, Zographou Campus, 15700 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - Maria Zervou
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
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Góra RW, Zaleśny R, Zawada A, Bartkowiak W, Skwara B, Papadopoulos MG, Silva DL. Large Changes of Static Electric Properties Induced by Hydrogen Bonding: An ab Initio Study of Linear HCN Oligomers. J Phys Chem A 2011; 115:4691-700. [DOI: 10.1021/jp110226h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Robert Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Agnieszka Zawada
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Wojciech Bartkowiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Bartłomiej Skwara
- The Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 116 35, Greece
| | - Manthos G. Papadopoulos
- The Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 116 35, Greece
| | - Daniel L. Silva
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, SP, Brazil
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Zaleśny R, Bulik IW, Bartkowiak W, Luis JM, Avramopoulos A, Papadopoulos MG, Krawczyk P. Electronic and vibrational contributions to first hyperpolarizability of donor–acceptor-substituted azobenzene. J Chem Phys 2010; 133:244308. [DOI: 10.1063/1.3516209] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Zaleśny R, Loboda O, Iliopoulos K, Chatzikyriakos G, Couris S, Rotas G, Tagmatarchis N, Avramopoulos A, Papadopoulos MG. Linear and nonlinear optical properties of triphenylamine-functionalized C60: insights from theory and experiment. Phys Chem Chem Phys 2010; 12:373-81. [DOI: 10.1039/b917825b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Bégué D, Labéguerie P, Zhang-Negrerie DY, Avramopoulos A, Serrano-Andrés L, Papadopoulos MG. Theoretical investigations of the IR spectroscopy of Ni(C2S2H2)2. A case study of the P_VMWCI2 algorithm including anharmonic effects. Phys Chem Chem Phys 2010; 12:13746-51. [DOI: 10.1039/c0cp00760a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Serrano-Andrés L, Avramopoulos A, Li J, Labéguerie P, Bégué D, Kellö V, Papadopoulos MG. Linear and nonlinear optical properties of a series of Ni-dithiolene derivatives. J Chem Phys 2009; 131:134312. [PMID: 19814558 DOI: 10.1063/1.3238234] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luis Serrano-Andrés
- Molecular Science Institute, Universitat de València, Apartado 22085, Valencia ES-46071, Spain.
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Durdagi S, Papadopoulos MG, Zoumpoulakis PG, Koukoulitsa C, Mavromoustakos T. A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling, docking, de novo drug design and molecular dynamics analysis. Mol Divers 2009; 14:257-76. [DOI: 10.1007/s11030-009-9166-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 05/17/2009] [Indexed: 11/28/2022]
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48
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Durdagi S, Supuran CT, Strom TA, Doostdar N, Kumar MK, Barron AR, Mavromoustakos T, Papadopoulos MG. In Silico Drug Screening Approach for the Design of Magic Bullets: A Successful Example with Anti-HIV Fullerene Derivatized Amino Acids. J Chem Inf Model 2009; 49:1139-43. [DOI: 10.1021/ci900047s] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Serdar Durdagi
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Claudiu T. Supuran
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - T. Amanda Strom
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Nadjmeh Doostdar
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Mananjali K. Kumar
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Andrew R. Barron
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Thomas Mavromoustakos
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, Vas. Constantinou Avenue 48, 11635 Athens, Greece; Department of Biology Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany; Laboratorio di Chimica Bioinorganica, Dipartimento di Chimica, University of Florence Via della Lastruccia, 3, Room 188 Polo Scientifico, 50019 - Sesto Fiorentino, Italy; Richard E. Smalley Institute for Nanoscale Science and Technology, Center for
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Potamitis C, Zervou M, Katsiaras V, Zoumpoulakis P, Durdagi S, Papadopoulos MG, Hayes JM, Grdadolnik SG, Kyrikou I, Argyropoulos D, Vatougia G, Mavromoustakos T. Antihypertensive Drug Valsartan in Solution and at the AT1 Receptor: Conformational Analysis, Dynamic NMR Spectroscopy, in Silico Docking, and Molecular Dynamics Simulations. J Chem Inf Model 2009; 49:726-39. [DOI: 10.1021/ci800427s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Constantinos Potamitis
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Maria Zervou
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Vassilis Katsiaras
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Panagiotis Zoumpoulakis
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Serdar Durdagi
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Manthos G. Papadopoulos
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Joseph M. Hayes
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Simona Golic Grdadolnik
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Ioanna Kyrikou
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Dimitris Argyropoulos
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Georgia Vatougia
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
| | - Thomas Mavromoustakos
- National Hellenic Research Foundation, Institute of Organic and Pharmaceutical Chemistry, Vas, Constantinou 48, 11635, Athens, Greece, Department of Biology Chemistry and Pharmacy, Free University of Berlin, Takustrasse, 3, 14195 Berlin, Germany, Laboratory of Biomolecular Structure, National Institute of Chemistry, Hajdrihova 19, POB 30 SI-1115 Ljubljana, Slovenia, Varian Ltd., 10 Mead Road, Oxford Industrial Park, Yarnton, Oxford OX5 1QU, United Kingdom, Chemistry Department, National & Kapodistrian
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Durdagi S, Mavromoustakos T, Chronakis N, Papadopoulos MG. Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations. Bioorg Med Chem 2008; 16:9957-74. [DOI: 10.1016/j.bmc.2008.10.039] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 10/08/2008] [Accepted: 10/12/2008] [Indexed: 11/15/2022]
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