Search results for "Molecular mechanics"
showing 10 items of 55 documents
Modeling ?-lactam interactions in aqueous solution through combined quantum mechanics-molecular mechanics methods
1999
Reliability of Virtual Screening Methods in Prediction of PDE4Binhibitor Activity
2015
Identification of active ligands using computational methods is a challenging task. For example, molecular docking, pharmacophore modeling, and three dimensional quantitative structure-activity relationship models (3D-QSAR) are widely used methods to identify novel small molecules. However, all these methods have, in addition to advantages, also significant pitfalls. The aim of this study was to compare some commonly used computational methods to estimate their ability to separate highly active PDE4B-inhibitors from less active and inactive ones. Here, 152 molecules with pIC 50 -range of 3.4-10.5, originating from six original studies were used. High correlation coefficients by using dockin…
Structural Studies on Polyaza[n]paracyclophanes. A Molecular Mechanics and Crystallographic Study
1997
Abstract Structural analysis of polyaza[n]paracyclophanes 1-5 has been carried out by the use of molecular mechanics and other techniques. NMR data and molecular mechanics calculations show that conformations in which the polyamine chain is arching above the aromatic ring are prevalent in solution. The crystal structure of triprotonated durene derivative 2b agrees with those studies. Crystals of 3H+.2b are triclinic, space group P1, with a = 11.758(4) A, b = 13.870(5) A, c = 17.181(3) A, α = 96.66(2)°, β = 106.02(2)°, γ = 104.87(3)°, Z = 4, R1 = 0.072, wR2 = 0.18. Three different conformations are present in the crystal. Good agreement between the crystal structures and calculated conformat…
On the interaction of doxorubicin with polynucleotides
2014
The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (poly-AT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV−vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.
Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials.…
1997
The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional transl…
Scalable Constant pH Molecular Dynamics in GROMACS
2022
Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to…
Construction of Spirooxindole Analogues Engrafted with Indole and Pyrazole Scaffolds as Acetylcholinesterase Inhibitors
2021
Twenty-five new hits of spirooxindole analogs 8a–y engrafted with indole and pyrazole scaffolds were designed and constructed via a [3+2]cycloaddition (32CA) reaction starting from three components: new chalcone-based indole and pyrazole scaffolds 5a–d, substituted isatins 6a–c, and secondary amines 7a–d. The potency of the compounds were assessed in modulating cholinesterase (AChE) activity using Ellman’s method. Compounds 8i and 8y showed the strongest acetylcholine esterase inhibition (AChEI) with IC50 values of 24.1 and 27.8 μM, respectively. Molecular docking was used to study their interaction with the active site of hAChE. peerReviewed
Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization
2016
International audience; We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar. The chemical process is studied using both high level multiconfigurational perturbation and density functional theory. Both methods show good agreement in predicting small kinetic barriers. Furthermore the behavior of benzophenone in DNA is simulated using molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. The accessibility of benzophenone to the labile hydrogens within B-DNA is demonstrated, as well as the driving force for this reaction. We evidence a strong dependence of the H-…
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
2016
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
Selective targeting of PARP-1 zinc finger recognition domains with Au(III) organometallics
2018
The binding of Au(iii) complexes to the zinc finger domain of the anticancer drug target PARP-1 was studied using a hyphenated mass spectrometry approach combined with quantum mechanics/molecular mechanics (QM/MM) studies. Competition experiments were carried out, whereby each Au complex was exposed to two types of zinc fingers. Notably, the cyclometallated Au-C^N complex was identified as the most selective candidate to disrupt the PARP-1 zinc finger domain, forming distinct adducts compared to the coordination compound Auphen.