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Tytuł:
Identification of anti-cyanobacterial leads targeting carbonic anhydrase from phytochemical database using in silico approach
Autorzy:
Padhiary, Archana
Mir, Showkat A.
Tete, Sheary S.
Baitharu, Iswar
Nayak, Binata
Powiązania:
https://bibliotekanauki.pl/articles/16704466.pdf
Data publikacji:
2023
Wydawca:
Polska Akademia Nauk. Czasopisma i Monografie PAN
Tematy:
phytochemical database
lead optimizations
ADMET analysis
molecular docking simulations
Opis:
In cyanobacteria, carbonic anhydrase (zinc metalloenzyme) is a major enzyme that converts CO2 to HCO3 maintaining the carbon concentration around the vicinity of RuBisCo, leading to cyanobacterial biomass generation. Anthropogenic activities, disposal of leached micro nutrients effluents from industries into the aquatic environment results in cyanobacterial blooms. The harmful cyanobacteria release cyanotoxins in open-water system which on ingression through oral route causes major health issues like hepatotoxicity and immunotoxicity. A database was prepared consisting of approximately 3k phytochemicals curated from previous literatures, earlier identified by GC-MS analysis. The phytochemicals were subjected to online servers to identify the novel lead molecules which followed ADMET and drug-like candidates. The identified leads were optimized by density functional theory method using B3YLP/G* level of theory. Carbonic anhydrase chosen as target to observe the binding interaction through molecular docking simulations. From the molecules included in the database the highest binding energy exhibited by alpha-tocopherol succinate and mycophenolic acid were found to be -9.23 kcal/mol and -14.41 kcal/mol and displayed interactions with GLY A102, GLN B30, ASP A41, LYS A105 including Zn2+ and their adjacent amino acids CYS 101, HIS 98, CYS 39 in both chain A and chain A-B of carbonic anhydrase. The identified molecular orbitals decipher computed global electrophilicity values (Energy gap, electrophilicity and Softness) of alpha tocopherol succinate and mycophenolic acid were found to be (5.262, 1.948, 0.380) eV and (4.710, 2.805, 0.424) eV demonstrates both molecules are effective and stable. The identified leads may serve as a better anti-carbonic anhydrase agent because they accommodate in the binding site and hampers the catalytic activity of Carbonic anhydrase thus inhibiting the generation of cyanobacterial biomass. This identified lead molecules may serve as a substructure to design novel phytochemicals against carbonic anhydrase present in cyanobacteria. Further in vitro study is necessary to evaluate the efficacy of these molecules.
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2023, 104, 2; 121-136
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Synergistic mechanism of dodecylamine/octanol mixtures enhancing lepidolite flotation from the self-aggregation behaviors at the air/liquid interface
Autorzy:
Bai, Yang
Xu, Mengxu
Wen, Weixiang
Zhu, Shifei
Mo, Weichen
Yan, Pingke
Powiązania:
https://bibliotekanauki.pl/articles/27323641.pdf
Data publikacji:
2023
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
DDA/OCT mixtures
self-aggregation behaviors
flotation foam
molecular dynamics simulations
surface tension
air interface
liquid interface
Opis:
Surface tension measurements and molecular dynamics (MD) simulations were used to explore the flotation foam properties and self-aggregation behaviors of dodecylamine (DDA)/octanol (OCT) mixtures formed with different mole ratios at the air/liquid interface. Based on the surface and thermodynamic parameters, the DDA/OCT mixtures exhibited greater interfacial activities and adsorption capacities than their individual components. The MD simulations showed that DDA and OCT were aggregated through hydrogen bonding, coulombic forces and hydrophobic association. OCT was inserted into the DDA adsorption layer, causing the alkyl chains of both DDA and OCT to extend from water to air at varying heights and angles. The addition of OCT improved the hydration of the amino groups and reduced the overall number of hydrogen bonds. The stability of the flotation foam decreased, and the high viscosity and difficult defoaming of the DDA flotation foam were significantly improved. When the DDA/OCT mole ratio was 2:1, the included angle formed between the alkyl chains and the interface was maximized, leading to enhanced compatibility among the alkyl chains, and the hydrogen bond energy was relatively large, which showed a strong synergistic effect. The MD simulation findings were consistent with the results obtained from the lepidolite flotation and surface tension experiments conducted in this study; our results could provide a theoretical foundation for the selection of superior mixed collectors and frothers.
Źródło:
Physicochemical Problems of Mineral Processing; 2023, 59, 6; art. no. 176510
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
Autorzy:
Rybicki, J.
Witkowska, A.
Bergmański, G.
Mancini, G.
Feliziani, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954650.pdf
Data publikacji:
2022-01-20
Wydawca:
Politechnika Gdańska
Tematy:
lead-silicate glasses
oxide glasses
medium-range order
ring analysis
molecular dynamics simulations
Opis:
The paper is dedicated to a molecular dynamics (MD) study of the structure of partially reduced lead-silicate glass of composition 1Pb 1PbO 1SiO2. The simulations have been performed in the constant volume regime, using a two-body potential (Born-Mayer repulsive forces, and Coulomb forces due to full ionic charges). The system was initially prepared as a well equilibrated hot melt, and then slowly cooled down to 300K. The information on short-range correlations were obtained in a conventional way (from pair and angular distribution functions), while the medium-range order was studied via cation-anion ring analysis. In the paper, the short- and medium-range order in the simulated system is discussed and compared with the structure of a glassy completely reduced system, i.e. 2Pb 1SiO2 and unreduced one, i.e. 2PbO 1SiO2 glass.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2003, 7, 2; 243-256
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Dopant ions size impact on structural properties of ordered poly(3,4-ethylenedioxythiophene) systems
Wpływ wielkości jonów domieszkujących na właściwości strukturalne uporządkowanych układów poli(3,4-etylenodioksytiofenu)
Autorzy:
Śniechowski, Maciej
Kozik, Tomasz A.
Łużny, Wojciech
Powiązania:
https://bibliotekanauki.pl/articles/947384.pdf
Data publikacji:
2020
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
Tematy:
self-organization
molecular dynamics simulations
conductive polymers
X-ray diffraction
crystal structure
samoorganizacja
symulacja dynamiki molekularnej
polimery przewodzące
dyfrakcja promieniowania rentgenowskiego
struktura krystaliczna
Opis:
The purpose of this work was to determine whether the structures of ordered part of novel poly(3,4-ethylenedioxythiophene) PEDOT : OTf (doped with trifluoromethanesulfonate anions) and PEDOT : HSulf (doped with hydrogensulfate anions) systems could really be simply the layered structure of PEDOT : Tos (doped with tosylate anions) with the counter ion changed to the appropriate one. Insight into this problem could be provided by molecular dynamics simulations but also by swarm intelligence optimization, developed earlier for the purpose of investigating the other structures.
Zbadano zdolność struktury uporządkowanej części nowych układów domieszkowanych poli(3,4-etylenodioksytiofenu) (PEDOT) [PEDOT : OTf (domieszkowane anionami trifluorometanosulfonianowymi) i PEDOT : HSulf (domieszkowane anionami wodorosiarczanowymi)] do powielania znanej z literatury warstwowej struktury PEDOT : Tos (domieszkowane anionami tosylanowymi) z jonem domieszki zmienionym na odpowiedni. Poszukiwania nowych struktur wspomagano symulacjami dynamiki molekularnej, a także z zastosowaniem optymalizacji opartej na algorytmach inteligencji stadnej.
Źródło:
Polimery; 2020, 65, 9; 639-643
0032-2725
Pojawia się w:
Polimery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces
Autorzy:
Jin, J.
Dang, L. X.
Miller, J. D.
Powiązania:
https://bibliotekanauki.pl/articles/109533.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
molecular dynamics simulations (MDS)
film stability
bubble attachment
interfacial water structure
Opis:
Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, the film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.
Źródło:
Physicochemical Problems of Mineral Processing; 2018, 54, 1; 89-101
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Wykorzystanie dynamiki molekularnej w badaniach szkieł
Application of molecular dynamics in examination of glasses
Autorzy:
Goj, P.
Powiązania:
https://bibliotekanauki.pl/articles/169158.pdf
Data publikacji:
2018
Wydawca:
Sieć Badawcza Łukasiewicz - Instytut Ceramiki i Materiałów Budowlanych
Tematy:
dynamika molekularna
badania więźby szkieł
symulacje komputerowe
szkła krzemowo-sodowe
molecular dynamics
glass network examination
computer simulations
sodium silicate glasses
Opis:
Klasyczna dynamika molekularna MD jest jedną z technik symulacji komputerowych wieloatomowych lub wielocząsteczkowych układów. Pozwala na badanie struktury oraz właściwości zarówno materiałów krystalicznych, jak i amorficznych. Opiera się na rozwiązywaniu numerycznym klasycznych równań ruchu. Nie tylko uzupełnia badania eksperymentalne, ale jest również narzędziem pozwalającym na badanie budowy materiałów na poziomie nieosiągalnym konwencjonalnymi technikami. W celu przedstawienia klasycznej dynamiki molekularnej wykonano symulacje dwóch szkieł 80SiO2-20Na2O i 85SiO2-15Na2O [%mol]. Otrzymane wyniki dobrze zgadzały się z obecnym stanem wiedzy. Wykonane symulacje świadczą o tym, że technika ta jest niezwykle użyteczna przy poznawaniu struktury szkieł. Wykorzystując tę technikę, można przewidywać wpływ modyfikatorów na więźbę szkła, a przez to możliwe jest wskazywanie kierunku dalszych badań oraz optymalizacja składów chemicznych.
Molecular dynamics MD is one of computer simulation methods of multiatomic or multimolecular systems. It allows to examination of structure and properties both crystalline and amorphous materials. This technique consists of the numerical solution of the classical equation of motion. It complements not only experimental methods but also it is tool make possible examination of material structure on the unavailable level for conventional methods. In order to introduce to molecular dynamics, the simulations of two glasses 80SiO2‑20Na2O and 85SiO2-15Na2O [%mol] were performed. Obtained results corresponds well to the actual state of knowledge. Performed simulation testify that this technique is a very useful to examine glass structure. Using this method, it is possible to predict influence of modifiers on glass network, it’s make possible indication research direction and optimization of chemical composition.
Źródło:
Szkło i Ceramika; 2018, R. 69, nr 1, 1; 12-15
0039-8144
Pojawia się w:
Szkło i Ceramika
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Probing of Cu2+ ions binding to A β (5−16) peptide using ITC measurements and MD simulations
Autorzy:
Makowska, J.
Żmudzińska, W.
Wyrzykowski, D.
Brzozowski, K.
Zblewska, H.
Chmurzyński, L.
Powiązania:
https://bibliotekanauki.pl/articles/1938620.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
A β (5 − 16) fragments
metal-peptide binding
isothermal titration calorimetry
molecular dynamics simulations
Opis:
It is shown that probably three residues: His6, His14 and His16 in the original sequence A β (1−42) serve as metal-binding sites for Cu2+ions. On the other hand, there is a possibility that only one of them plays a crucial role in the formation of the{A β (1-42)-Cu2+} complex. The isothermal titration calorimetry (ITC) measurements supported by molecular dynamic simulation (MD) with the NMR-derived restrains were used to investigate the interactions of Cu2+ with A β(5-16), a fragment of the A β(1-42) protein, with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, termed HZ1. The conditional thermodynamic parameters suggest that the formation of the Cu2+-HZ1 complex is both an enthalpy and entropy driven process under the experimental conditions. The studies presented here (after comparison with our previous results) show that the affinity of peptides to copper metal ions depends on two factors: the primary structure (amino acid composition) and the shape of the peptide conformation adopted.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 409-416
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mechanical properties of 2D flexyne and reflexyne polyphenylacetylene networks: a comparative computer studies with various force-fields
Autorzy:
Trapani, L.
Gatt, R.
Mizzi, L.
Grima, J. N.
Powiązania:
https://bibliotekanauki.pl/articles/1938614.pdf
Data publikacji:
2015
Wydawca:
Politechnika Gdańska
Tematy:
2D flexyne polyphenylacetylene networks
2D reflexyne polyphenylacetylene networks
auxetics
molecular simulations
Opis:
Auxetic materials exhibit the very unusual property of becoming wider when stretched and narrower when compressed, – they have a negative Poisson’s ratio. This unusual behaviour is the source of many desired effects in the materials’ properties and it is therefore, no wonder that auxetics are described as being superior to conventional materials in many practical applications. Here we make use of force-field based molecular modelling simulations in order to investigate the mechanical properties of polypehyleacetylene systems known as (n, m)-flexyne and (n, m)-reflexyne in an attempt to extend the existing knowledge there is regarding these systems. These systems have already attracted considerable consideration since negative on-axis Poisson’s ratios have been discovered for the reflexynes. We first developed a methodology for the modelling and property determination of flexyne and reflexyne network systems which we validated against existing published data. Then, extended the study to prove the simulated results were independent of the modelling methodology or the force-field used. In particular, we showed that on-axis auxeticity in the reflexynes is a force-field independent property, i.e. a property which is not an artefact of the simulations but a property which is likely to be present in the real materials if these were to be synthesised. We also studied and reported the shear behaviour of these systems were we show that the flexynes and reflexynes have very low shear moduli, a property which regrettably limits the prospects of these systems in many practical applications. Finally we examine the in-plane off-axis mechanical properties of the systems and we report that in general, these mechanical properties are highly dependent on the direction of loading. We also find that the auxeticity exhibited by the reflexynes on-axis is lost when these systems are loaded off axis since the Poisson’s ratios becomes positive very rapidly as the structure is stretched slightly off-axis (e.g. 15deg off-axis). This is once again of great practical significance as it highlights another major limitation of these systems in their use as auxetics.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2015, 19, 3; 237-296
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15
Autorzy:
Yaacob, Mohd
Hasan, Wan
Ali, Mohd
Rahman, Raja
Salleh, Abu
Basri, Mahiran
Leow, Thean
Powiązania:
https://bibliotekanauki.pl/articles/1039206.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
J15 asparaginase
Photobacterium sp.
expression
purification
Molecular Dynamic (MD) simulations
Opis:
Genome mining revealed a 1011 nucleotide-long fragment encoding a type I l-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni2+-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni2+ and Mg2+, but it was inhibited by Mn2+, Fe3+ and Zn2+ at the same concentration. J15 asparaginase actively hydrolysed its native substrate, l-asparagine, but had low activity towards l-glutamine. The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s-1, and 4.21 s-1 mM-1, respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr24, His22, Gly23, Val25 and Pro26 may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment.
Źródło:
Acta Biochimica Polonica; 2014, 61, 4; 745-752
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
2D simulations of liquid percolation through model porous media: preliminary MD and DPD results
Autorzy:
Rychcik, M.
Bośko, J.
Rybicki, J.
Alda, W.
Dzwinel, W.
Mancini, G.
Fioretti, L.
Powiązania:
https://bibliotekanauki.pl/articles/1964080.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
2D flow simulations
particle methods
molecular dynamics
dissipative particle dynamics method
Opis:
In the paper we make a short overview of computer models based on particle approach, which can be suitable for the simulation of fluid flow through porous media. We concentrate on Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) methods. We describe main features of our simulation programs, and present and discuss preliminary results of MD and DPD simulations of 2D fluid flow through a simple model rigid porous media. The paper aims at the evaluation of the applicability of MD and DPD methods for simulations of liquid flows in media of complicated geometry.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 85-97
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Flows in microchannels
Autorzy:
Kucaba-Piętal, A.
Walenta, Z.
Peradzyński, Z.
Powiązania:
https://bibliotekanauki.pl/articles/1955808.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
microchannel flow
microflows
micropolar fluid
molecular dynamics simulations
direct Monte Carlo simulation
direct Monte Carlo methods
Opis:
The aim of this paper is to present a survey of the results for the flows of simple gases and liquids with substructure through narrow channels, obtained with the Direct Monte-Carlo and Molecular Dynamics Simulation methods.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 2; 179-189
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data
Autorzy:
Zielkiewicz, J.
Powiązania:
https://bibliotekanauki.pl/articles/1965827.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
amides
alcohols
preferential solvation
Kirkwood-Buff integrals
molecular dynamics simulations
Opis:
Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 317-329
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulation studies of lipid bilayer systems.
Autorzy:
Pasenkiewicz-Gierula, Marta
Murzyn, Krzysztof
Róg, Tomasz
Czaplewski, Cezary
Powiązania:
https://bibliotekanauki.pl/articles/1044295.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
phosphatidylethanolamine
cholesterol
vasopressin receptor,molecular dynamics simulations
magainin-2
phosphatidylcholine
phosphatidylglycerol
Opis:
The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents, i.e. proteins, sterols and peptides, either intercalate into or loosely attach to the bilayer. We applied a molecular dynamics simulation method to study membrane systems at various levels of compositional complexity. The studies were started from simple lipid bilayers containing a single type phosphatidylcholine (PC) and water molecules (PC bilayers). As a next step, cholesterol (Chol) molecules were introduced to the PC bilayers (PC-Chol bilayers). These studies provided detailed information about the structure and dynamics of the membrane/water interface and the hydrocarbon chain region in bilayers built of various types of PCs and Chol. This enabled studies of membrane systems of higher complexity. They included the investigation of an integral membrane protein in its natural environment of a PC bilayer, and the antibacterial activity of magainin-2. The latter study required the construction of a model bacterial membrane which consisted of two types of phospholipids and counter ions. Whenever published experimental data were available, the results of the simulations were compared with them.
Źródło:
Acta Biochimica Polonica; 2000, 47, 3; 601-611
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.
Autorzy:
Mazerski, Jan
Muchewicz, Karolina
Powiązania:
https://bibliotekanauki.pl/articles/1044393.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
molecular dynamics simulations
conformational changes
structure of intercalation complex
C-1311
antitumor drugs
imidazoacridinones
Opis:
Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.
Źródło:
Acta Biochimica Polonica; 2000, 47, 1; 65-78
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: Molecular dynamics simulations.
Autorzy:
Mazerski, Jan
Antonini, Ippolito
Martelli, Sante
Powiązania:
https://bibliotekanauki.pl/articles/1044390.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
molecular dynamics simulations
structure of intercalation complex
pyrimidoacridinetrione antitumor agents
role of side chain(s)
Opis:
Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.
Źródło:
Acta Biochimica Polonica; 2000, 47, 1; 47-57
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 16

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