Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2)

Molecular models of the complex between the selective COX-2 inhibitor nimesulide and the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 have been built using a combination of homology modelling, conformational searching and automated docking techniques. The stability of the resulting complexes has been assessed by molecular dynamics simulations and interaction energy decomposition. It is found that nimesulide exploits the extra space made available by the replacement at position 523 of an isoleucine residue in COX-1 by a valine in COX-2 and establishes electrostatic interactions with both Arg-106 and Arg-499 (Arg-120 and Arg-513 in PGHS-1 numbering). Two alternate binding modes are proposed which are compatible with the pharmacological profile of this agent as a COX-2 selective inhibitor.     

Coarse‐grained molecular dynamics simulations of stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends

The stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends with a wide formulation range are extensively simulated using the coarse‐grained (CG) molecular dynamics (MD) method. To improve the representability, the bonded CG potentials are re‐parameterized against the atomistic simulated melt systems whereas the nonbonded CG potentials are adopted as developed in our previous work. Based on the CG potentials, the MD simulations reproduce all the local distributions of pure systems and the miscibility of mixed systems. Moreover, the global conformational properties are also closer to the target ones than those obtained using the previous CG potentials. The changes in density and volume upon mixing are computed together with the energies of mixing. They are all negative over the entire composition range and indicate stronger intermolecular interactions between distinct components than those between identical components. In particular, it is found that upon mixing the changes in density are insensible to chain tacticity but the changes in volume and the energies of mixing do, which quantitatively confirms that both inter‐molecular interactions and free‐volumes mainly contribute to the observed phase behaviors. Such models and methods reported herein can be used to quickly optimize formulations of polymer blends. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 203–212     

Temperature effects on spreading of water nano‐droplet on poly(methyl methacrylate): A molecular dynamics simulation study

In this article, the effect of temperature on the spreading behavior of a water nano‐droplet on poly(methyl methacrylate) substrate is investigated. The contact angle analysis illustrates that the spreading process occurs in a stage‐like manner and the increase in temperature causes a regime change from partial to total wetting. The interaction energy distributions show that there exist sites on the surface which could trap water molecules and provide a better path for other molecules to overcome the asperities. Estimations of the coefficients of self‐diffusivity suggest that temperature has a major effect in the reorientation stage, which results in the formation of the interfacial layer. In the second stage of spreading, temperature affects the process by providing sufficient energy for water molecules to overcome the interactions with the substrate. Therefore, this stage is controlled by the movement of water molecules on the surface and is highly influenced by their interaction with the surface asperities, strong interaction sites, and the carbonyl groups. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1532–1541     

Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions

Ab initio and molecular mechanics studies of LiPF₆ and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li⁺/PF₆^? complexes obtained from quantum chemistry revealed a preference for C_3V symmetry structures for Li⁺–P separations under 2.8 Å, C_2V symmetry for Li⁺–P in the range of 2.8–3.3 Å and C_4V symmetry for Li⁺–P separations larger than 3.3 Å. Electron correlation effects were found to make an insignificant contribution to binding in the Li⁺/PF₆^? complex. By contrast, analogous studies of PF₆^?/PF₆^? and PF₆^?/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF₆ melts was parameterized to reproduce the geometries and energies of Li⁺/PF₆^?, PF₆^?/PF₆^?, PF₆^?/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF₆ melts were performed to validate this quantum chemistry‐based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF₆ solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001     

Two MnII,CuII complexes derived from 3,5‐bis(1‐imidazoly) pyridine: Synthesis,DNA binding,Molecular docking and cytotoxicity studies

Two complexes [MnL₂ (H₂O)₂]·2ClO₄ (complex 1) and [CuL(H₂O)₃]·2NO₃ (complex 2) (where L = 3,5‐bis(1‐imidazoly) pyridine) were designed and synthesized. The structures of the complexes were characterized by X‐ray crystallography, elemental analyses, and infrared spectrum. The interaction capacity of the complexes with calf thymus DNA has been investigated by UV and fluorescence spectroscopy. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pBR322 plasmid DNA. Efficient binding properties of DNA were established by UV–vis, fluorescence, and gel electrophoresis. The intrinsic binding constants (K_b) were calculated to be 0.1524, 0.1041 for complexes 1–2, respectively. The cytotoxic activity of the two complexes exhibited a higher cytotoxicity against HeLa cell lines and lower cytotoxicity toward the normal cell lines. Flow cytometry demonstrated the cancer cell inhibitory rate of two complexes. Furthermore, computer‐aided molecular docking studies were performed to visualize the binding mode of the drug candidate at the molecular level. Interestingly, complex 1 exhibited a significant cancer cell inhibitory rate than cisplatin and other complexes.     

Synthesis,characterization, DNA binding,apoptosis and molecular docking of three Mn(II), Zn(II) and Cu(II) complexes with terpyridine‐based carboxylic acid

A series of novel cytotoxic compounds, [Mn(cpt)₂], [Zn(tpt)(H₂O)₂]?DMA?2(H₂O) and [Cu(tpt)]?DMA (cpt = 4′‐(4‐carboxyphenyl)‐2,2′:6′,2″‐terpyridine, tpt = 4‐(2,4,6‐tricarboxylphenyl)‐2,2′:6′,2″‐terpyridine, DMA = (CH₃)₂NH), were isolated and characterized. The structures of these complexes were characterized using single‐crystal X‐ray diffraction. The mode and extent of binding between fish sperm DNA and the complexes were investigated using fluorescence spectroscopy and molecular docking. These results indicate the ability of the complexes to bind to DNA with different binding affinities. The binding of the Zn(II) complex with DNA is stronger than that of the corresponding Cu(II) analogue, which is expected due to the z* effect and geometry. The ability of these complexes to cleave pBR322 plasmid DNA was demonstrated using gel electrophoresis assay, showing that the complexes have effective DNA cleavage activity. In addition, the cytotoxic effects of these complexes were examined on HeLa cells (human cervix epithelia carcinoma cells) in vitro. The three complexes exhibit different cytotoxic effects and decent cancer cell inhibitory rate. This means that the structures and type of metal have a great influence on the activity of these novel complexes.     

Molecular dynamics of cyclic and linear poly(dimethylsiloxanes)

Dielectric spectroscopy (10^–1 Hz to 10⁷ Hz) has been employed to study the molecular dynamics of a series of cyclic and linear polydimethylsiloxanes (PDMS) of various molecular weights ranging from 300 to 10 000 g/mol in the temperature range above the glass transition (from 130 K to 190 K). The observed -relaxation depends strongly on both molecular weight and structure of the samples. For linear PDMS oligomers, the -relaxation shifts towards lower temperatures with decreasing molecular weight in good accordance with the Fox-Flory-model. Cyclic PDMS reveals a qualitatively different molecular weight dependence: for a given temperature the -relaxation time increases with decreasing ring length, but has a maximum for small oligomers (degree of polymerizationn6). The shape of relaxation curves and, with it, the relaxation time distribution is independent from length and architecture of the chains The observed experimental findings are in qualitative agreement with dynamic Monte-Carlo simulations.Dedicated to Prof. E.W. Fischer on the occasion of his 65th birthday Fast macht' das WLF ihn krank, jetzt raucht er wieder, Gott sei Dank! (frei nach Wilhelm Busch)     

Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking,dynamics simulations,and MMGBSA

Antimicrobial resistance (AMR) threatens millions of people around the world and has been declared a global risk by the World Economic Forum. One of the important AMR mechanisms in Enterobacteriaceae is the production of extended-spectrum β-lactamases. The most common ESBL, CTX-M β-lactamases, is spread to the world by CTX-M-15 and CTX-M-14. Sulbactam, clavulanic acid, and tazobactam are first-generation β-lactamase inhibitors and avibactam is a new non-β-lactam β-lactamase inhibitor. We studied that avibactam, sulbactam, clavulanic acid, tazobactam, and quercetin natural flavonoids were docked to target protein CTXM-15. Subsequently, the complexes were simulated using the molecular dynamics simulations method during 100 ns for determining the final binding positions of ligands. Clavulanic acid left CTX-M-15 and other ligands remained in the binding site after the simulation. The estimated binding energies were calculated during 100 ns simulation by the MMGBSA-MMPBSA method. The estimated free binding energies of avibactam, sulbactam, quercetin, tazobactam, and clavulanic acid were sorted as –33.61 kcal/mol, –16.04 kcal/mol, –14 kcal/mol, –12.68 kcal/mol, and –2.95 kcal/mol. As a result of both final binding positions and free binding energy calculations, Quercetin may be evaluated an alternative candidate and a more potent β-lactamases inhibitor for new antimicrobial combinations to CTX-M-15. The results obtained in silico studies are predicted to be a preliminary study for in vitro studies for quercetin and similar bioactive natural compounds. These studies are notable for the discovery of natural compounds that can be used in the treatment of infections caused by β-lactamase-producing pathogens.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

Synthesis,structure elucidation,DNA binding and molecular docking studies of novel copper(II) complexes of two 1,3,4-thiadiazolethiosemicarbazone derivatives

Four novel Cu(II) chelates were synthesized by reacting hydrated CuCl₂ and Cu(CH₃COO)₂ with two derivatives of 1,3,4-thiadiazolethiosemicarbazone. The structures and geometries of the synthesized complexes were deduced applying the alternative analytical and spectral tools confirming the complexes to have the formulae [(LH)Cu(Cl)]•0.5H₂O, [(LH)Cu(OAc)(H₂O)₂]•0.5H₂O, [(LCl)Cu(Cl)(H₂O)₂]•H₂O and [(LCl)Cu(OAc)]; where LH and LCl are phenyl and p-chlorophenyl derivatives of 1,3,4-thiadiazolethiosemicarbazone ligands, respectively (deprotonated form). IR spectral data confirmed the coordination of the ligands to the copper center as monobasic tridentate in the thiol form. Thermal analysis, UV–Vis spectra and magnetic moment assured the geometry around the copper center to be square planar, trigonal bipyramid and octahedral which have been confirmed by the computational studies. The two ligand derivatives and their copper complexes were applied to evaluate their binding modes with SS-DNA via UV–Vis spectral titration and viscosity measurements. The DNA-binding constant (k_b) values of the investigated derivatives were calculated and compared with ethidium bromide in order to assess their mode of binding with DNA. Moreover, docking study of these complexes was carried out to recognize the drug–DNA interactions and to calculate their binding energies.     

Spectroscopic studies,structural characterization and electrochemical studies of two cobalt (III) complexes with tridentate hydrazone Schiff base ligands: Evaluation of antibacterial activities,DNA‐binding,BSA interaction and molecular docking

Co(III) complexes of tridentate Schiff base ligands derived from N‐(2‐hydroxybenzylideneamino)benzamide (H ₂ L ¹ ) and 2‐(2‐hydroxybenzylidene)hydrazine‐1‐carboxamide ( H ₂ L ² ) were synthesized and characterized using IR, Raman, ¹H–NMR and UV–Vis spectroscopies. X‐ray single crystal structures of complexes 1 and 2 have also been determined, and it was indicated that these Co(III) complexes are in a distorted octahedral geometry. The cyclic voltammetry (CV) of the complexes indicates an irreversible redox behavior for both complexes 1 and 2 . The antibacterial effects of the synthesized compounds have been tested by minimum inhibitory concentration and minimum bactericidal concentration methods, which suggested that the metal complexes exhibit better antibacterial effects than the ligands against Gram‐positive bacteria. The effects of the drug (drug  =  ligands and complexes) on bovine serum albumin (BSA) were examined using circular dichroism (CD) spectropolarimetry, and it was revealed that the BSA (BSA, as a carrier protein) secondary structure changed in the presence of the drug. Interaction of the drug with calf‐thymus DNA (CT‐DNA) was investigated by UV–Vis absorption, fluorescence emission, CV and CD spectroscopy. Binding constants were determined using UV–Vis absorption. The results indicated that the studied Schiff bases bind to DNA, with the hyperchromic effect and non‐intercalative mode in which the metal complexes are more effective than ligands. Furthermore, molecular docking simulation was used to obtain the energetic and binding sites for the interaction of the complexes with Mycobacterium tuberculosis enoyl‐acyl carrier protein reductase (InhA), and results showed that complex 1 has more binding energy.     

Biological contour,molecular docking and antiproliferative studies of DNA targeted histidine based transition metal(II) complexes: Invention and its depiction

A novel series of histidine derived transition metal complexes were synthesized and characterized by multispectral techniques such as UV‐Vis., FT IR, EPR, NMR, ESI‐mass analysis and other physico‐chemical methods like elemental analysis, molar conductivity, magnetic susceptibility. The synthesized compounds were attempted for their biological prospective. The biological studies involved are DNA interaction (binding and damage), antimicrobial, antioxidant, antiproliferative and molecular docking. DNA interaction studies were carried out with the help of UV‐Vis absorption titration, viscosity measurement and cyclic voltammetric techniques which revealed that the synthesized compounds could interact with CT‐DNA through intercalative binding mode. A gel electrophoresis assay demonstrated the ability of complexes to cleave the supercoiled pUC18 DNA. The antioxidant property shows that the metal complexes have preferable ability to scavenge hydroxyl radical than the ligand. Moreover, the antimicrobial assay indicates that these complexes are good antimicrobial agents against various pathogens. Furthermore, the in vitro antiproliferative activities of the complexes were examined on HeLa, Hep G2 and NIH 3 T3 cell lines using an MTT assay. The morphological changes were investigated using Hoechst 33258 staining apoptosis assay. In addition, molecular docking studies were executed to considerate the nature of binding of the synthesized complexes with protein and DNA.     

Antioxidant,DNA interaction,molecular docking and cytotoxicity studies of aminoethylpiperazine‐containing macrocyclic binuclear copper(II) complexes

A series of new macrocyclic binuclear copper(II) complexes of the type [Cu₂L^1–5(ClO₄)](ClO₄) ( 1 – 5 ) were synthesized by template condensation between precursor compounds 2,6‐bis(4‐aminoethylpiperazin‐1‐ylmethyl)‐4‐substituted phenols and 2,6‐diformyl‐4‐substituted phenols. The synthesized precursors and complexes were characterized using regular physicochemical techniques. The rate constant values obtained for the hydrolysis of 4‐nitrophenylphosphate were in the range 1.83 × 10⁻²–4.19 × 10⁻² min⁻¹. Antioxidant studies against 2,2′‐diphenyl‐1‐picrylhydrazyl revealed the antioxidant potency of the synthesized complexes. Binding studies of the complexes with calf thymus DNA were conducted using electronic, viscometric and voltammetric techniques, and the obtained results suggested a non‐covalent groove mode of binding. The oxidative cleavage of pBR322 DNA in the presence of co‐reactant H₂O₂ and radical scavengers showed single strand scission and involvement of H₂O₂ radical in the cleavage process. Molecular docking studies were performed to insert complexes into the crystal structures of 1BNA and VEGFR kinase at active sites to determine the possible binding mode and predominant binding interactions. In vitro cytotoxicity of the complexes was tested against human epidermoid carcinoma cells (A431) by MTT assay, which revealed the effective anticancer activity of the complexes. Live cell and fluorescent imaging of A431 cells showed that the complexes induce cell death through apoptosis.     

Energy migration in poly(N‐vinyl carbazole) and its copolymers with methyl methacrylate: Fluorescence polarization,quenching, and molecular dynamics

Fluorescence polarization and quenching measurements were used to examine intramolecular energy migration for poly(N‐vinyl carbazole) and copolymers of N‐vinyl carbazole with methyl methacrylate. Quenching measurements of the carbazole fluorescence by CCl₄ were performed in dilute solution in toluene, and fluorescence anisotropy, r, was measured for the chains dispersed in a solid matrix of poly(methyl methacrylate) (PMMA). The results suggested that the chains with a high carbazole content, that is, a high content of excimer trapping sites, do not show the highest values of the singlet energy‐migration rate. Isotropies, r^?1, of the samples in vitrified PMMA corroborated such conclusions. Molecular dynamics simulations on isotactic and syndiotactic trichromophoric copolymer fragments were used to obtain parameters related to the energy‐transfer process as a function of the methyl methacrylate content. The parameters from the simulations supported the interpretation of the experiments. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1615–1626, 2003     

Molecular docking,dynamics simulations and 3D-QSAR modeling of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT1AR agonists

Serotonin receptor, 5-HT_1AR, agonists and partial agonists have established drug candidates for psychiatric and neurologic disorders. Recently, we reported the synthesis and evaluation of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT_1AR ligands. Herein, we generated a homology model of the receptor and docked the ligands against it, predicted the stability of the receptor model and complexes by molecular dynamics and generated a 3D-QSAR model for the arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine. The model suggests the hydrophobic part that arises from the aromatic region and the electron withdrawing parts play a vital role in the agonist activity of the lead molecules.     

Structure elucidation,DNA binding,DFT, molecular docking and cytotoxic activity studies on novel single crystal (E)-1-(2-fluorobenzylidene)thiosemicarbazide

Compound 3 {(E)-1-(2-fluorobenzylidene)thiosemicarbazide} – a new Schiff base of thiosemicarbazide has been synthesized, characterized and reported for crystal structure. Planer side chain in the crystal structure was observed co-planer with aromatic ring plane and molecules were connected into centrosymmetric dimmers via intermolecular hydrogen bonding. DFT geometry optimization and the relevant quantum parameters indicated unstable and reactive nature of compound 3. Experimental and theoretical findings for DNA binding by UV–visible, cyclic voltammetry and molecular docking studies showed consistency in kinetic (K_b) and thermodynamic (ΔG) parameters and that compound 3 significantly interacted with DNA via intercalation. Viscometric analysis further comprehended intercalation as possible binding mode of the compound with DNA and non-denaturing of DNA in the presence of 10% aqueous DMSO. Docked parameters further assured the drug like characteristics of the investigated compound as fit in Lipinski’s criteria. Dose dependant cytotoxic activity of compound 3 against human Huh-7 cell line indicated its anti-cancer potential at 100?µg/ml concentration.     

The performance of ANI-ML potentials for ligand-n(H2O) interaction energies and estimation of hydration free energies from end-point MD simulations

Here, we investigate the performance of “Accurate NeurAl networK engINe for Molecular Energies” (ANI), trained on small organic compounds, on bulk systems including non-covalent interactions and applicability to estimate solvation (hydration) free energies using the interaction between the ligand and explicit solvent (water) from single-step MD simulations. The method is adopted from ANI using the Atomic Simulation Environment (ASE) and predicts the non-covalent interaction energies at the accuracy of wb97x/6-31G(d) level by a simple linear scaling for the conformations sampled by molecular dynamics (MD) simulations of ligand-n(H₂O) systems. For the first time, we test ANI potentials' abilities to reproduce solvation free energies using linear interaction energy (LIE) formulism by modifying the original LIE equation. Our results on ~250 different complexes show that the method can be accurate and have a correlation of R² = 0.88–0.89 (MAE <1.0 kcal/mol) to the experimental solvation free energies, outperforming current end-state methods. Moreover, it is competitive to other conventional free energy methods such as FEP and BAR with 15-20 × fold reduced computational cost.