Search results for "molecular model"
showing 10 items of 274 documents
Synthesis, Anti-Inflammatory Activity, and in Vitro Antitumor Effect of a Novel Class of Cyclooxygenase Inhibitors: 4-(Aryloyl)phenyl Methyl Sulfones
2010
Following our previous research on anti-inflammatory drugs (NSAIDs), we report on the design and synthesis of 4-(aryloyl)phenyl methyl sulfones. These substances were characterized for their capacity to inhibit cyclooxygenase (COX-1 and COX-2) isoenzymes. Molecular modeling studies showed that the methylsulfone group of these compounds was inserted deep in the pocket of the human COX-2 binding site, in an orientation that precludes hydrogen bonding with Arg120, Ser353, and Tyr355 through their oxygen atoms. The N-arylindole 33 was the most potent inhibitor of COX-2 and also the most selective (COX-1/COX-2 IC(50) ratio was 262). The indole derivative 33 was further tested in vivo for its ant…
Identification of 2-(thiophen-2-yl)acetic Acid-Based Lead Compound for mPGES-1 Inhibition.
2021
We report the implementation of our in silico/synthesis pipeline by targeting the glutathione-dependent enzyme mPGES-1, a valuable macromolecular target in both cancer therapy and inflammation therapy. Specifically, by using a virtual fragment screening approach of aromatic bromides, straightforwardly modifiable by the Suzuki-Miyaura reaction, we identified 3-phenylpropanoic acid and 2-(thiophen-2-yl)acetic acid to be suitable chemical platforms to develop tighter mPGES-1 inhibitors. Among these, compounds 1c and 2c showed selective inhibitory activity against mPGES-1 in the low micromolar range in accordance with molecular modeling calculations. Moreover, 1c and 2c exhibited interesting IC…
Transition metal chlorides complexes with tetrahydrofuran [MtCl(4)(THF)(2)] used as precursors of ethylene polymerization
2002
Otrzymano trzy kompleksy chlorków metali przejściowych z THF - [TiCl4(THF)2] (I), [ZrCl4(THF)2] (II), oraz [HfCWTHF),] (III) i zastosowano je jako prekursory katalizatorów tytanowo-magnezowych w niskociśnieniowej polimeryzacji (0,5 MPa, 323 K) etylenu przy użyciu AlEt3 (najkorzystniej), AlEt2Cl lub Al(z'-Bu)3 jako kokatalizatora (rys. 1, tabela 1). Zmierzono gęstość, gęstość nasypową, stopień krystaliczno-ści, ciężary cząsteczkowe i ich rozkład oraz temperaturę topnienia uzyskanego PE-HD (tabela 1). Aktywność katalizatorów wzrastała w szeregu (III) < (II) < (I), tzn. ze wzrostem elektroujemności pierwiastka metalu i ze spadkiem wartości ładunku cząstkowego na atomie metalu grupy przejściowe…
PET/PEN Blends of Industrial Interest as Barrier Materials. Part I. Many-Scale Molecular Modeling of PET/PEN Blends
2006
Mesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities and …
Introduction to MIP synthesis, characteristics and analytical application
2019
One of the trends in analytical chemistry is associated with designing and developing new types of sample preparation techniques, which might significantly increase the efficiency and selectivity of the analytes isolation or/and preconcentration process. One of the most widely employed solutions is selective sorption materials, defined as molecularly imprinted polymers (MIPs), as well as the sorbents with the molecular fingerprint. Due to their simple preparation protocol, mechanical, thermal and chemical stability and selectivity, MIPs have found application as a stationary phase in separation techniques such as liquid chromatography or capillary electrophoresis, in electrochemical sensors…
Pentapeptides containing two dehydrophenylalanine residues - synthesis, structural studies and evaluation of their activity towards cathepsin C
2008
Synthesis, structural and biological studies of pentapeptides containing two Delta Phe residues (Z and E isomers) in position 2 and 4 in peptide chain were performed. All the investigated peptides adopted bent conformation and majority of them could exist as two different. conformers in solution. Only pentapeptides. containing free N-termini appeared to act as weak inhibitors of cathepsin C with the slow-binding, competitive mechanism of inhibition. free acids being bound slightly better than their methyl esters. Results of Molecular modeling suggested significant difference between peptides, depending of the type of amino acid residue in position 5 in peptide chain. Dehydropeptides contain…
On the relations between aromaticity and substituent effect
2019
Aromaticity/aromatic and substituent/substituent effects belong to the most commonly used terms in organic chemistry and related fields. The quantitative description of aromaticity is based on energetic, geometric (e.g., HOMA), magnetic (e.g., NICS) and reactivity criteria, as well as the properties of the electronic structure (e.g., FLU). The substituent effect can be described using either traditional Hammett-type substituent constants or characteristics based on quantum-chemistry. For this purpose, the energies of properly designed homodesmotic reactions and electron density distribution are used. In the first case, a descriptor named SESE (energy stabilizing the substituent effect) is o…
Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.
2007
Abstract Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein–ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein–inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg 2+ cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct rela…
Small hydrocarbon cyclophanes: Synthesis, X-ray analysis and molecular modelling
2002
Small hydrocarbon cyclophanes, such as [2.2.0]m,m,m-cyclophane (20) and [2.2.0]p,m,m-cyclophane (21), are strained analogues of the well-known π-prismand [2.2.2]p,p,p-cyclophane (1). The synthetic route to these molecules is based on well-established cyclophane methodology which offers a general access to a whole family of hydrocarbon cyclophanes. Single crystal X-ray analysis and molecular modelling showed that the reduction of the ring size from 18-membered (1) to 14-membered (21) or 13-membered (20) has a substantial effect on the size and the shape of the cyclophane’s cavity, thus blocking its ability to complex Ag+ ions. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
3He NMR: from free gas to its encapsulation in fullerene
2013
The 3He nuclear magnetic shieldings were calculated for single helium atom, its dimer, simple models of fullerene cages (He@Cn), and single wall carbon nanotubes. The performances of several levels of theory (HF, MP2, DFT-VSXC, CCSD, CCSD(T), and CCSDT) were tested. Two sets of polarization-consistent basis sets were used (pcS-n and aug-pcS-n), and an estimate of 3He nuclear magnetic shieldings in the complete basis set limit using a two-parameter fit was established. Theoretical 3He results reproduced accurately previously reported theoretical values for helium gas, dimer, and helium probe inside several fullerene cages. Excellent agreement with experimental values was achieved. 3He nuclea…